Starting phenix.real_space_refine on Thu Mar 5 11:20:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kfu_22856/03_2026/7kfu_22856.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kfu_22856/03_2026/7kfu_22856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kfu_22856/03_2026/7kfu_22856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kfu_22856/03_2026/7kfu_22856.map" model { file = "/net/cci-nas-00/data/ceres_data/7kfu_22856/03_2026/7kfu_22856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kfu_22856/03_2026/7kfu_22856.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 46 5.16 5 C 13912 2.51 5 N 3988 2.21 5 O 3902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 157 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21848 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7401 Classifications: {'peptide': 909} Link IDs: {'PTRANS': 33, 'TRANS': 875} Chain breaks: 6 Chain: "D" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Chain: "E" Number of atoms: 7401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 909, 7401 Classifications: {'peptide': 909} Link IDs: {'PTRANS': 33, 'TRANS': 875} Chain breaks: 6 Chain: "F" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2727 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 8, 'TRANS': 323} Time building chain proxies: 4.92, per 1000 atoms: 0.23 Number of scatterers: 21848 At special positions: 0 Unit cell: (148.375, 142.44, 179.237, 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 46 16.00 O 3902 8.00 N 3988 7.00 C 13912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.0 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 20 sheets defined 49.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.832A pdb=" N LYS A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU A 19 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.953A pdb=" N LYS A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.699A pdb=" N GLU B 24 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 removed outlier: 3.661A pdb=" N LYS B 45 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.510A pdb=" N ILE B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 41 Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 150 removed outlier: 4.004A pdb=" N TRP C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR C 184 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.510A pdb=" N LEU C 227 " --> pdb=" O HIS C 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN C 230 " --> pdb=" O TRP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 3.542A pdb=" N CYS C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 344 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 370 removed outlier: 3.782A pdb=" N THR C 356 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 420 Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 430 through 445 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.646A pdb=" N ASP C 456 " --> pdb=" O ASP C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 474 removed outlier: 3.798A pdb=" N LEU C 466 " --> pdb=" O TYR C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN C 482 " --> pdb=" O PRO C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 518 removed outlier: 4.371A pdb=" N LEU C 515 " --> pdb=" O PRO C 511 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN C 518 " --> pdb=" O PRO C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 523 removed outlier: 3.546A pdb=" N ASP C 523 " --> pdb=" O ILE C 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 523' Processing helix chain 'C' and resid 524 through 530 Processing helix chain 'C' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 587 Processing helix chain 'C' and resid 620 through 628 removed outlier: 4.118A pdb=" N ALA C 624 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 625 " --> pdb=" O PRO C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 709 Processing helix chain 'C' and resid 736 through 746 Processing helix chain 'C' and resid 748 through 771 Processing helix chain 'C' and resid 772 through 773 No H-bonds generated for 'chain 'C' and resid 772 through 773' Processing helix chain 'C' and resid 774 through 780 removed outlier: 3.538A pdb=" N HIS C 777 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS C 779 " --> pdb=" O ALA C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 796 removed outlier: 3.636A pdb=" N LEU C 785 " --> pdb=" O LEU C 781 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR C 796 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 817 removed outlier: 4.508A pdb=" N ASN C 805 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY C 806 " --> pdb=" O SER C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 824 through 828 removed outlier: 3.737A pdb=" N HIS C 828 " --> pdb=" O GLU C 825 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 864 removed outlier: 3.700A pdb=" N VAL C 843 " --> pdb=" O ASP C 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU C 844 " --> pdb=" O PRO C 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 845 " --> pdb=" O PHE C 841 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR C 850 " --> pdb=" O SER C 846 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE C 851 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 887 Processing helix chain 'C' and resid 896 through 904 Processing helix chain 'C' and resid 927 through 944 Processing helix chain 'C' and resid 951 through 968 removed outlier: 4.033A pdb=" N GLN C 957 " --> pdb=" O GLN C 953 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 709 Processing helix chain 'D' and resid 728 through 733 Processing helix chain 'D' and resid 739 through 746 Processing helix chain 'D' and resid 748 through 773 removed outlier: 3.710A pdb=" N VAL D 760 " --> pdb=" O ALA D 756 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU D 771 " --> pdb=" O GLN D 767 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN D 783 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR D 784 " --> pdb=" O GLN D 780 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS D 794 " --> pdb=" O LYS D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 800 through 817 removed outlier: 3.525A pdb=" N LEU D 804 " --> pdb=" O LYS D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 822 Processing helix chain 'D' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL D 843 " --> pdb=" O ASP D 839 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 863 " --> pdb=" O ILE D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 887 Processing helix chain 'D' and resid 891 through 904 removed outlier: 3.816A pdb=" N GLU D 895 " --> pdb=" O ARG D 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 910 No H-bonds generated for 'chain 'D' and resid 908 through 910' Processing helix chain 'D' and resid 927 through 944 Processing helix chain 'D' and resid 950 through 969 Processing helix chain 'E' and resid 28 through 41 Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.263A pdb=" N HIS E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 150 removed outlier: 4.003A pdb=" N TRP E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 180 through 184 removed outlier: 3.718A pdb=" N TYR E 184 " --> pdb=" O GLU E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 211 removed outlier: 3.883A pdb=" N PHE E 211 " --> pdb=" O VAL E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.509A pdb=" N LEU E 227 " --> pdb=" O HIS E 223 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 288 removed outlier: 3.949A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 331 removed outlier: 3.543A pdb=" N CYS E 329 " --> pdb=" O THR E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 344 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 370 removed outlier: 3.783A pdb=" N THR E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 420 Proline residue: E 412 - end of helix Processing helix chain 'E' and resid 430 through 445 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.647A pdb=" N ASP E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 474 removed outlier: 3.798A pdb=" N LEU E 466 " --> pdb=" O TYR E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 488 removed outlier: 4.218A pdb=" N GLN E 482 " --> pdb=" O PRO E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 518 removed outlier: 4.372A pdb=" N LEU E 515 " --> pdb=" O PRO E 511 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASN E 518 " --> pdb=" O PRO E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 523 removed outlier: 3.545A pdb=" N ASP E 523 " --> pdb=" O ILE E 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 520 through 523' Processing helix chain 'E' and resid 524 through 530 Processing helix chain 'E' and resid 549 through 572 removed outlier: 3.896A pdb=" N GLN E 553 " --> pdb=" O GLN E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 587 Processing helix chain 'E' and resid 620 through 628 removed outlier: 4.119A pdb=" N ALA E 624 " --> pdb=" O PRO E 620 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN E 625 " --> pdb=" O PRO E 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 709 Processing helix chain 'E' and resid 736 through 746 Processing helix chain 'E' and resid 748 through 771 Processing helix chain 'E' and resid 772 through 773 No H-bonds generated for 'chain 'E' and resid 772 through 773' Processing helix chain 'E' and resid 774 through 780 removed outlier: 3.539A pdb=" N HIS E 777 " --> pdb=" O ARG E 774 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LYS E 779 " --> pdb=" O ALA E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 796 removed outlier: 3.635A pdb=" N LEU E 785 " --> pdb=" O LEU E 781 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 796 " --> pdb=" O GLN E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 801 through 817 removed outlier: 4.509A pdb=" N ASN E 805 " --> pdb=" O ARG E 801 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY E 806 " --> pdb=" O SER E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 828 removed outlier: 3.737A pdb=" N HIS E 828 " --> pdb=" O GLU E 825 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 864 removed outlier: 3.699A pdb=" N VAL E 843 " --> pdb=" O ASP E 839 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU E 844 " --> pdb=" O PRO E 840 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 845 " --> pdb=" O PHE E 841 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR E 850 " --> pdb=" O SER E 846 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 851 " --> pdb=" O LEU E 847 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 887 Processing helix chain 'E' and resid 896 through 904 Processing helix chain 'E' and resid 927 through 944 Processing helix chain 'E' and resid 951 through 968 removed outlier: 4.032A pdb=" N GLN E 957 " --> pdb=" O GLN E 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 709 Processing helix chain 'F' and resid 728 through 733 Processing helix chain 'F' and resid 739 through 746 Processing helix chain 'F' and resid 748 through 773 removed outlier: 3.710A pdb=" N VAL F 760 " --> pdb=" O ALA F 756 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU F 771 " --> pdb=" O GLN F 767 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 794 removed outlier: 5.026A pdb=" N GLN F 783 " --> pdb=" O LYS F 779 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR F 784 " --> pdb=" O GLN F 780 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 800 through 817 removed outlier: 3.524A pdb=" N LEU F 804 " --> pdb=" O LYS F 800 " (cutoff:3.500A) Processing helix chain 'F' and resid 818 through 822 Processing helix chain 'F' and resid 839 through 863 removed outlier: 3.741A pdb=" N VAL F 843 " --> pdb=" O ASP F 839 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F 863 " --> pdb=" O ILE F 859 " (cutoff:3.500A) Processing helix chain 'F' and resid 880 through 887 Processing helix chain 'F' and resid 891 through 904 removed outlier: 3.814A pdb=" N GLU F 895 " --> pdb=" O ARG F 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 908 through 910 No H-bonds generated for 'chain 'F' and resid 908 through 910' Processing helix chain 'F' and resid 927 through 944 Processing helix chain 'F' and resid 950 through 969 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.486A pdb=" N ARG A 29 " --> pdb=" O GLU A 36 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLU A 36 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 31 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 34 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 68 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 80 " --> pdb=" O PHE A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.560A pdb=" N HIS A 80 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS B 3 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA4, first strand: chain 'C' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE C 236 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 268 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS C 238 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY C 263 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 161 " --> pdb=" O LYS C 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 391 through 394 removed outlier: 3.508A pdb=" N HIS C 492 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 580 " --> pdb=" O GLU C 499 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 533 through 538 removed outlier: 4.111A pdb=" N ILE C 544 " --> pdb=" O TYR C 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 652 through 656 removed outlier: 6.986A pdb=" N THR C 652 " --> pdb=" O HIS C 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL C 690 " --> pdb=" O THR C 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU C 654 " --> pdb=" O VAL C 690 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 692 " --> pdb=" O LEU C 654 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU C 656 " --> pdb=" O LEU C 692 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL C 713 " --> pdb=" O VAL C 726 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY C 724 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 724 " --> pdb=" O ILE F 715 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N HIS F 714 " --> pdb=" O HIS F 688 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 690 " --> pdb=" O HIS F 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA F 716 " --> pdb=" O VAL F 690 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU F 692 " --> pdb=" O ALA F 716 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N THR F 652 " --> pdb=" O LEU F 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA F 689 " --> pdb=" O THR F 652 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL C 672 " --> pdb=" O THR C 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS C 681 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU C 670 " --> pdb=" O LYS C 681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 912 through 916 Processing sheet with id=AB1, first strand: chain 'D' and resid 652 through 656 removed outlier: 5.724A pdb=" N THR D 652 " --> pdb=" O LEU D 687 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 689 " --> pdb=" O THR D 652 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N HIS D 714 " --> pdb=" O HIS D 688 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 690 " --> pdb=" O HIS D 714 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ALA D 716 " --> pdb=" O VAL D 690 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU D 692 " --> pdb=" O ALA D 716 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY D 724 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 724 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL E 713 " --> pdb=" O VAL E 726 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR E 652 " --> pdb=" O HIS E 688 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL E 690 " --> pdb=" O THR E 652 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU E 654 " --> pdb=" O VAL E 690 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU E 692 " --> pdb=" O LEU E 654 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU E 656 " --> pdb=" O LEU E 692 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE D 678 " --> pdb=" O LYS D 674 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS D 674 " --> pdb=" O ILE D 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 912 through 916 Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 53 Processing sheet with id=AB5, first strand: chain 'E' and resid 235 through 244 removed outlier: 5.682A pdb=" N ILE E 236 " --> pdb=" O SER E 268 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER E 268 " --> pdb=" O ILE E 236 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS E 238 " --> pdb=" O THR E 266 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY E 263 " --> pdb=" O TRP E 164 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN E 161 " --> pdb=" O LYS E 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 391 through 394 removed outlier: 3.508A pdb=" N HIS E 492 " --> pdb=" O LEU E 377 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU E 580 " --> pdb=" O GLU E 499 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 533 through 538 removed outlier: 4.111A pdb=" N ILE E 544 " --> pdb=" O TYR E 450 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 677 through 683 removed outlier: 6.419A pdb=" N VAL E 672 " --> pdb=" O THR E 679 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS E 681 " --> pdb=" O LEU E 670 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU E 670 " --> pdb=" O LYS E 681 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 912 through 916 Processing sheet with id=AC1, first strand: chain 'F' and resid 677 through 683 removed outlier: 5.397A pdb=" N ILE F 678 " --> pdb=" O LYS F 674 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS F 674 " --> pdb=" O ILE F 678 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 912 through 916 1021 hydrogen bonds defined for protein. 2913 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: 4.30 Time building geometry restraints manager: 2.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6774 1.34 - 1.45: 3211 1.45 - 1.57: 12265 1.57 - 1.69: 2 1.69 - 1.81: 80 Bond restraints: 22332 Sorted by residual: bond pdb=" N GLN A 89 " pdb=" CA GLN A 89 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.07e+00 bond pdb=" CB VAL C 713 " pdb=" CG1 VAL C 713 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.36e+00 bond pdb=" CB VAL E 713 " pdb=" CG1 VAL E 713 " ideal model delta sigma weight residual 1.521 1.446 0.075 3.30e-02 9.18e+02 5.12e+00 bond pdb=" CB VAL E 690 " pdb=" CG1 VAL E 690 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 bond pdb=" CB LYS C 346 " pdb=" CG LYS C 346 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.35e+00 ... (remaining 22327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 28954 1.79 - 3.58: 993 3.58 - 5.38: 157 5.38 - 7.17: 58 7.17 - 8.96: 12 Bond angle restraints: 30174 Sorted by residual: angle pdb=" C GLU C 979 " pdb=" N LEU C 980 " pdb=" CA LEU C 980 " ideal model delta sigma weight residual 120.82 126.61 -5.79 1.47e+00 4.63e-01 1.55e+01 angle pdb=" C GLU E 979 " pdb=" N LEU E 980 " pdb=" CA LEU E 980 " ideal model delta sigma weight residual 120.82 126.57 -5.75 1.47e+00 4.63e-01 1.53e+01 angle pdb=" C ASP D 666 " pdb=" N ASN D 667 " pdb=" CA ASN D 667 " ideal model delta sigma weight residual 121.54 129.00 -7.46 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C ASP F 666 " pdb=" N ASN F 667 " pdb=" CA ASN F 667 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N LEU C 919 " pdb=" CA LEU C 919 " pdb=" C LEU C 919 " ideal model delta sigma weight residual 114.75 109.96 4.79 1.26e+00 6.30e-01 1.45e+01 ... (remaining 30169 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 12009 17.86 - 35.72: 1199 35.72 - 53.59: 195 53.59 - 71.45: 41 71.45 - 89.31: 10 Dihedral angle restraints: 13454 sinusoidal: 5606 harmonic: 7848 Sorted by residual: dihedral pdb=" CA ARG C 891 " pdb=" C ARG C 891 " pdb=" N HIS C 892 " pdb=" CA HIS C 892 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG E 891 " pdb=" C ARG E 891 " pdb=" N HIS E 892 " pdb=" CA HIS E 892 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA ARG D 835 " pdb=" C ARG D 835 " pdb=" N PRO D 836 " pdb=" CA PRO D 836 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 13451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2734 0.064 - 0.129: 517 0.129 - 0.193: 58 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 3312 Sorted by residual: chirality pdb=" CB ILE A 66 " pdb=" CA ILE A 66 " pdb=" CG1 ILE A 66 " pdb=" CG2 ILE A 66 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CG LEU C 36 " pdb=" CB LEU C 36 " pdb=" CD1 LEU C 36 " pdb=" CD2 LEU C 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU E 36 " pdb=" CB LEU E 36 " pdb=" CD1 LEU E 36 " pdb=" CD2 LEU E 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3309 not shown) Planarity restraints: 3870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 41 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO A 42 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 42 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 42 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 477 " -0.043 5.00e-02 4.00e+02 6.45e-02 6.67e+00 pdb=" N PRO C 478 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 478 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 477 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO E 478 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 478 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 478 " -0.036 5.00e-02 4.00e+02 ... (remaining 3867 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 6 2.22 - 2.89: 7834 2.89 - 3.56: 28885 3.56 - 4.23: 45548 4.23 - 4.90: 82294 Nonbonded interactions: 164567 Sorted by model distance: nonbonded pdb=" CE1 TYR A 50 " pdb=" CG GLN E 554 " model vdw 1.548 3.740 nonbonded pdb=" CD1 TYR A 50 " pdb=" CG GLN E 554 " model vdw 1.892 3.740 nonbonded pdb=" NZ LYS A 25 " pdb=" OE1 GLN C 668 " model vdw 1.909 3.120 nonbonded pdb=" O LEU D 723 " pdb=" OG SER E 728 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASN A 65 " pdb=" NE2 GLN B 31 " model vdw 2.185 3.120 ... (remaining 164562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.080 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.550 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 : 0.006 0.076 22332 Z= 0.241 Angle : 0.829 8.962 30174 Z= 0.471 Chirality : 0.050 0.322 3312 Planarity : 0.006 0.068 3870 Dihedral : 14.440 89.310 8362 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.15), residues: 2638 helix: 0.28 (0.15), residues: 1192 sheet: -0.22 (0.31), residues: 280 loop : -1.86 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 834 TYR 0.021 0.002 TYR F 815 PHE 0.020 0.002 PHE D 819 TRP 0.028 0.002 TRP E 162 HIS 0.009 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00553 (22332) covalent geometry : angle 0.82884 (30174) hydrogen bonds : bond 0.13886 ( 1021) hydrogen bonds : angle 5.85104 ( 2913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 505 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7625 (ttpt) REVERT: A 53 HIS cc_start: 0.7879 (m-70) cc_final: 0.7557 (m-70) REVERT: A 87 ILE cc_start: 0.8549 (pt) cc_final: 0.8286 (tp) REVERT: A 96 LEU cc_start: 0.8566 (tp) cc_final: 0.8292 (tp) REVERT: B 90 LEU cc_start: 0.8775 (mt) cc_final: 0.8156 (mt) REVERT: C 40 LEU cc_start: 0.7401 (tp) cc_final: 0.6205 (tt) REVERT: C 327 LEU cc_start: 0.8108 (tp) cc_final: 0.7891 (pp) REVERT: C 389 GLU cc_start: 0.2834 (mt-10) cc_final: 0.1994 (tp30) REVERT: C 411 THR cc_start: 0.8080 (m) cc_final: 0.7840 (m) REVERT: C 417 ILE cc_start: 0.8463 (tp) cc_final: 0.8107 (tp) REVERT: C 444 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6947 (mp10) REVERT: C 564 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7861 (tmmt) REVERT: C 722 TYR cc_start: 0.4874 (t80) cc_final: 0.4622 (t80) REVERT: C 731 PRO cc_start: 0.7860 (Cg_exo) cc_final: 0.7616 (Cg_endo) REVERT: C 748 ARG cc_start: 0.6962 (mtt-85) cc_final: 0.6727 (ttt180) REVERT: C 759 ILE cc_start: 0.7769 (mt) cc_final: 0.7078 (tp) REVERT: C 784 THR cc_start: 0.6058 (m) cc_final: 0.5662 (p) REVERT: C 794 LYS cc_start: 0.7218 (mtpt) cc_final: 0.6905 (tptp) REVERT: C 819 PHE cc_start: 0.6796 (m-10) cc_final: 0.6520 (m-80) REVERT: C 874 GLN cc_start: 0.7813 (mt0) cc_final: 0.7574 (mt0) REVERT: C 924 ILE cc_start: 0.5345 (mp) cc_final: 0.4407 (tt) REVERT: C 966 MET cc_start: 0.7446 (mtp) cc_final: 0.7242 (mtt) REVERT: D 745 MET cc_start: 0.8544 (mmt) cc_final: 0.8139 (mmt) REVERT: D 979 GLU cc_start: 0.8726 (tt0) cc_final: 0.8513 (tt0) REVERT: E 261 MET cc_start: 0.6345 (ptm) cc_final: 0.5748 (mmm) REVERT: E 280 MET cc_start: -0.7255 (mtp) cc_final: -0.7593 (mmt) REVERT: E 853 TYR cc_start: 0.8494 (t80) cc_final: 0.8228 (t80) REVERT: F 676 ASP cc_start: 0.6563 (m-30) cc_final: 0.6109 (t70) REVERT: F 719 THR cc_start: 0.8605 (p) cc_final: 0.8260 (t) REVERT: F 792 GLN cc_start: 0.8470 (tt0) cc_final: 0.8256 (tt0) REVERT: F 813 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8223 (tpt90) REVERT: F 956 TYR cc_start: 0.7253 (t80) cc_final: 0.6766 (t80) REVERT: F 967 HIS cc_start: 0.8697 (t-90) cc_final: 0.8429 (t70) REVERT: F 973 GLN cc_start: 0.8217 (mt0) cc_final: 0.7907 (mt0) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.1950 time to fit residues: 142.5511 Evaluate side-chains 218 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.3980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 89 GLN B 54 GLN C 348 ASN C 447 HIS C 653 HIS C 767 GLN C 817 GLN ** C 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 HIS ** D 738 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 ASN E 554 GLN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 918 HIS E 921 GLN E 973 GLN F 767 GLN F 909 GLN F 952 HIS F 969 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.162621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.128966 restraints weight = 52424.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.127196 restraints weight = 53750.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126783 restraints weight = 46377.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127562 restraints weight = 36776.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.129363 restraints weight = 29431.065| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22332 Z= 0.155 Angle : 0.644 8.786 30174 Z= 0.340 Chirality : 0.044 0.213 3312 Planarity : 0.005 0.071 3870 Dihedral : 4.898 20.182 2910 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.08 % Allowed : 9.38 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.16), residues: 2638 helix: 1.06 (0.15), residues: 1192 sheet: 0.07 (0.31), residues: 294 loop : -1.51 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.017 0.002 TYR F 815 PHE 0.014 0.002 PHE E 70 TRP 0.026 0.002 TRP F 977 HIS 0.011 0.001 HIS F 828 Details of bonding type rmsd covalent geometry : bond 0.00347 (22332) covalent geometry : angle 0.64369 (30174) hydrogen bonds : bond 0.04502 ( 1021) hydrogen bonds : angle 4.67746 ( 2913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 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 9 ASP cc_start: 0.7001 (p0) cc_final: 0.6798 (p0) REVERT: A 13 ASP cc_start: 0.7080 (p0) cc_final: 0.6743 (p0) REVERT: A 29 ARG cc_start: 0.6754 (ttt180) cc_final: 0.6478 (ttt-90) REVERT: A 79 SER cc_start: 0.9372 (m) cc_final: 0.9074 (p) REVERT: C 389 GLU cc_start: 0.3287 (mt-10) cc_final: 0.1672 (tp30) REVERT: C 411 THR cc_start: 0.8351 (m) cc_final: 0.8113 (m) REVERT: C 417 ILE cc_start: 0.8913 (tp) cc_final: 0.8547 (tp) REVERT: C 520 ILE cc_start: 0.9162 (tt) cc_final: 0.8917 (tt) REVERT: C 711 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7973 (mt) REVERT: C 731 PRO cc_start: 0.7976 (Cg_exo) cc_final: 0.7737 (Cg_endo) REVERT: C 887 MET cc_start: 0.8571 (ttp) cc_final: 0.8245 (ttp) REVERT: D 815 TYR cc_start: 0.7238 (t80) cc_final: 0.6899 (t80) REVERT: E 853 TYR cc_start: 0.8315 (t80) cc_final: 0.8058 (t80) REVERT: E 970 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: F 845 LEU cc_start: 0.8619 (mt) cc_final: 0.8147 (pp) REVERT: F 909 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: F 956 TYR cc_start: 0.7071 (t80) cc_final: 0.6710 (t80) REVERT: F 970 GLN cc_start: 0.6313 (tm-30) cc_final: 0.5982 (tm-30) REVERT: F 973 GLN cc_start: 0.8463 (mt0) cc_final: 0.7858 (pt0) REVERT: F 980 LEU cc_start: 0.5909 (mt) cc_final: 0.5562 (tp) outliers start: 49 outliers final: 27 residues processed: 275 average time/residue: 0.1727 time to fit residues: 72.7951 Evaluate side-chains 213 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain C residue 85 TRP Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 570 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 711 ILE Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 817 GLN Chi-restraints excluded: chain C residue 946 SER Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 970 GLN Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 760 VAL Chi-restraints excluded: chain F residue 826 TRP Chi-restraints excluded: chain F residue 909 GLN Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 4 optimal weight: 0.7980 chunk 262 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 158 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 89 GLN B 12 HIS B 54 GLN B 85 ASN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 HIS C 632 GLN C 686 GLN C 855 HIS C 953 GLN D 668 GLN E 334 HIS ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 909 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.162147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.128242 restraints weight = 52620.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.125609 restraints weight = 47733.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.126208 restraints weight = 36056.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126875 restraints weight = 29058.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.127022 restraints weight = 25177.741| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22332 Z= 0.131 Angle : 0.579 9.421 30174 Z= 0.305 Chirality : 0.043 0.168 3312 Planarity : 0.004 0.062 3870 Dihedral : 4.610 20.269 2910 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 12.48 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.16), residues: 2638 helix: 1.45 (0.15), residues: 1194 sheet: 0.17 (0.31), residues: 312 loop : -1.39 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 813 TYR 0.022 0.001 TYR C 722 PHE 0.018 0.001 PHE C 816 TRP 0.018 0.001 TRP C 162 HIS 0.008 0.001 HIS F 828 Details of bonding type rmsd covalent geometry : bond 0.00293 (22332) covalent geometry : angle 0.57880 (30174) hydrogen bonds : bond 0.03992 ( 1021) hydrogen bonds : angle 4.38884 ( 2913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7319 (p0) cc_final: 0.7081 (p0) REVERT: A 49 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6531 (mt-10) REVERT: A 50 TYR cc_start: 0.7089 (t80) cc_final: 0.6821 (t80) REVERT: A 79 SER cc_start: 0.9350 (m) cc_final: 0.9062 (p) REVERT: B 9 ASP cc_start: 0.6624 (t0) cc_final: 0.6275 (t0) REVERT: B 26 TYR cc_start: 0.9121 (m-80) cc_final: 0.8758 (m-80) REVERT: B 61 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7232 (m) REVERT: C 389 GLU cc_start: 0.3148 (mt-10) cc_final: 0.1292 (tp30) REVERT: C 417 ILE cc_start: 0.8985 (tp) cc_final: 0.8624 (tp) REVERT: C 731 PRO cc_start: 0.7996 (Cg_exo) cc_final: 0.7759 (Cg_endo) REVERT: C 819 PHE cc_start: 0.6792 (m-10) cc_final: 0.6276 (m-80) REVERT: D 745 MET cc_start: 0.8444 (mmt) cc_final: 0.8176 (mmt) REVERT: D 779 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8321 (ptmt) REVERT: E 853 TYR cc_start: 0.8073 (t80) cc_final: 0.7822 (t80) REVERT: F 845 LEU cc_start: 0.8595 (mt) cc_final: 0.8134 (pp) REVERT: F 909 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: F 970 GLN cc_start: 0.6435 (tm-30) cc_final: 0.6124 (tm-30) outliers start: 53 outliers final: 30 residues processed: 246 average time/residue: 0.1474 time to fit residues: 58.0538 Evaluate side-chains 212 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 826 TRP Chi-restraints excluded: chain F residue 909 GLN Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 967 HIS Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 93 optimal weight: 0.0870 chunk 74 optimal weight: 0.5980 chunk 181 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 212 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 HIS C 667 ASN C 953 GLN D 767 GLN D 842 ASN ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 967 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.126149 restraints weight = 52439.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.123667 restraints weight = 44623.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123701 restraints weight = 35263.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.124310 restraints weight = 29699.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124621 restraints weight = 25955.575| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22332 Z= 0.122 Angle : 0.559 7.667 30174 Z= 0.294 Chirality : 0.042 0.163 3312 Planarity : 0.004 0.063 3870 Dihedral : 4.441 21.154 2910 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.21 % Allowed : 14.22 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.17), residues: 2638 helix: 1.63 (0.15), residues: 1194 sheet: 0.11 (0.30), residues: 312 loop : -1.33 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 186 TYR 0.014 0.001 TYR C 722 PHE 0.014 0.001 PHE E 70 TRP 0.017 0.001 TRP E 162 HIS 0.011 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00271 (22332) covalent geometry : angle 0.55912 (30174) hydrogen bonds : bond 0.03701 ( 1021) hydrogen bonds : angle 4.27809 ( 2913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.6958 (p0) cc_final: 0.6746 (p0) REVERT: A 13 ASP cc_start: 0.7324 (p0) cc_final: 0.7008 (p0) REVERT: A 18 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8151 (mmtp) REVERT: A 21 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7304 (mpp80) REVERT: A 50 TYR cc_start: 0.7235 (t80) cc_final: 0.6890 (t80) REVERT: A 79 SER cc_start: 0.9376 (m) cc_final: 0.9100 (p) REVERT: B 26 TYR cc_start: 0.9053 (m-80) cc_final: 0.8647 (m-80) REVERT: C 35 PHE cc_start: 0.7826 (t80) cc_final: 0.7518 (m-80) REVERT: C 389 GLU cc_start: 0.3204 (mt-10) cc_final: 0.1248 (tp30) REVERT: C 417 ILE cc_start: 0.8906 (tp) cc_final: 0.8559 (tp) REVERT: C 520 ILE cc_start: 0.8948 (tt) cc_final: 0.8661 (tt) REVERT: C 731 PRO cc_start: 0.8158 (Cg_exo) cc_final: 0.7926 (Cg_endo) REVERT: C 887 MET cc_start: 0.8566 (ttt) cc_final: 0.8314 (tmm) REVERT: C 966 MET cc_start: 0.7874 (mpp) cc_final: 0.6963 (mpp) REVERT: D 745 MET cc_start: 0.8479 (mmt) cc_final: 0.8203 (mmt) REVERT: E 553 GLN cc_start: 0.4317 (OUTLIER) cc_final: 0.3931 (mp10) REVERT: E 853 TYR cc_start: 0.8181 (t80) cc_final: 0.7867 (t80) REVERT: F 745 MET cc_start: 0.7983 (tpp) cc_final: 0.7661 (tpp) REVERT: F 845 LEU cc_start: 0.8632 (mt) cc_final: 0.8103 (pp) REVERT: F 909 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7601 (mp10) REVERT: F 956 TYR cc_start: 0.7579 (t80) cc_final: 0.7070 (t80) REVERT: F 970 GLN cc_start: 0.6328 (tm-30) cc_final: 0.5857 (tm-30) REVERT: F 973 GLN cc_start: 0.8626 (mt0) cc_final: 0.7884 (mt0) outliers start: 52 outliers final: 36 residues processed: 239 average time/residue: 0.1479 time to fit residues: 56.2629 Evaluate side-chains 211 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 553 GLN Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 826 TRP Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 967 HIS Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 93 optimal weight: 0.7980 chunk 217 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 576 HIS C 632 GLN C 653 HIS C 667 ASN C 973 GLN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.157546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.124175 restraints weight = 53010.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121900 restraints weight = 42782.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122511 restraints weight = 33434.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.122916 restraints weight = 26245.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123047 restraints weight = 23418.388| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22332 Z= 0.174 Angle : 0.590 12.754 30174 Z= 0.312 Chirality : 0.043 0.169 3312 Planarity : 0.004 0.063 3870 Dihedral : 4.531 19.182 2910 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.67 % Allowed : 15.58 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2638 helix: 1.64 (0.16), residues: 1186 sheet: 0.04 (0.31), residues: 312 loop : -1.31 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 63 TYR 0.028 0.002 TYR D 815 PHE 0.014 0.001 PHE E 70 TRP 0.015 0.001 TRP C 162 HIS 0.016 0.001 HIS F 967 Details of bonding type rmsd covalent geometry : bond 0.00391 (22332) covalent geometry : angle 0.58969 (30174) hydrogen bonds : bond 0.03950 ( 1021) hydrogen bonds : angle 4.41868 ( 2913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 184 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.9402 (m) cc_final: 0.9114 (p) REVERT: B 12 HIS cc_start: 0.7657 (t-90) cc_final: 0.7383 (t-90) REVERT: B 26 TYR cc_start: 0.9096 (m-80) cc_final: 0.8739 (m-80) REVERT: B 44 ARG cc_start: 0.7621 (mmm-85) cc_final: 0.7363 (mmm-85) REVERT: C 417 ILE cc_start: 0.9032 (tp) cc_final: 0.8673 (tp) REVERT: C 731 PRO cc_start: 0.8243 (Cg_exo) cc_final: 0.8037 (Cg_endo) REVERT: C 887 MET cc_start: 0.8528 (ttt) cc_final: 0.8194 (tmm) REVERT: C 897 TYR cc_start: 0.7732 (t80) cc_final: 0.7436 (t80) REVERT: C 966 MET cc_start: 0.8082 (mpp) cc_final: 0.7418 (mpp) REVERT: D 745 MET cc_start: 0.8345 (mmt) cc_final: 0.8056 (mmt) REVERT: E 553 GLN cc_start: 0.4472 (OUTLIER) cc_final: 0.4126 (mp10) REVERT: E 853 TYR cc_start: 0.8302 (t80) cc_final: 0.8038 (t80) REVERT: F 852 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8294 (mm) outliers start: 63 outliers final: 42 residues processed: 232 average time/residue: 0.1444 time to fit residues: 54.6466 Evaluate side-chains 213 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 903 ASN Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 553 GLN Chi-restraints excluded: chain E residue 690 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 784 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 852 LEU Chi-restraints excluded: chain F residue 976 VAL Chi-restraints excluded: chain F residue 980 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 105 optimal weight: 0.1980 chunk 232 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 162 optimal weight: 0.0050 chunk 98 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 148 optimal weight: 0.2980 chunk 90 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 667 ASN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 967 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.159018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.125454 restraints weight = 52988.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122756 restraints weight = 44311.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.123614 restraints weight = 32762.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.123918 restraints weight = 26163.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.124163 restraints weight = 23742.389| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22332 Z= 0.112 Angle : 0.549 8.735 30174 Z= 0.287 Chirality : 0.042 0.208 3312 Planarity : 0.004 0.065 3870 Dihedral : 4.340 22.355 2910 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.33 % Allowed : 16.85 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.17), residues: 2638 helix: 1.81 (0.16), residues: 1186 sheet: 0.01 (0.31), residues: 310 loop : -1.25 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.028 0.001 TYR A 50 PHE 0.022 0.001 PHE C 35 TRP 0.017 0.001 TRP E 162 HIS 0.014 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00247 (22332) covalent geometry : angle 0.54866 (30174) hydrogen bonds : bond 0.03526 ( 1021) hydrogen bonds : angle 4.19777 ( 2913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ASP cc_start: 0.7538 (p0) cc_final: 0.7178 (p0) REVERT: A 79 SER cc_start: 0.9373 (m) cc_final: 0.9072 (p) REVERT: B 26 TYR cc_start: 0.9071 (m-80) cc_final: 0.8703 (m-80) REVERT: B 44 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7348 (mmm-85) REVERT: B 63 GLU cc_start: 0.7142 (mp0) cc_final: 0.6903 (pm20) REVERT: B 96 LEU cc_start: 0.8313 (tp) cc_final: 0.8101 (mt) REVERT: C 389 GLU cc_start: 0.4284 (mt-10) cc_final: 0.1797 (tp30) REVERT: C 417 ILE cc_start: 0.8966 (tp) cc_final: 0.8623 (tp) REVERT: C 731 PRO cc_start: 0.8045 (Cg_exo) cc_final: 0.7785 (Cg_endo) REVERT: C 897 TYR cc_start: 0.7700 (t80) cc_final: 0.7446 (t80) REVERT: C 966 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7495 (mpp) REVERT: D 745 MET cc_start: 0.8401 (mmt) cc_final: 0.8065 (mmt) REVERT: E 261 MET cc_start: 0.5660 (tmm) cc_final: 0.5199 (tmm) REVERT: E 853 TYR cc_start: 0.8204 (t80) cc_final: 0.7912 (t80) REVERT: F 970 GLN cc_start: 0.6916 (tm-30) cc_final: 0.6401 (tm-30) REVERT: F 973 GLN cc_start: 0.8613 (mt0) cc_final: 0.7997 (pt0) outliers start: 55 outliers final: 37 residues processed: 223 average time/residue: 0.1397 time to fit residues: 49.9822 Evaluate side-chains 205 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 938 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 553 GLN Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 784 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 202 optimal weight: 0.0000 chunk 78 optimal weight: 0.4980 chunk 238 optimal weight: 2.9990 chunk 117 optimal weight: 0.0370 chunk 234 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 46 optimal weight: 0.0570 chunk 256 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 148 HIS C 667 ASN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 571 ASN F 769 GLN F 879 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.159931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.126754 restraints weight = 52496.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.124683 restraints weight = 43181.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.125409 restraints weight = 32258.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125915 restraints weight = 26067.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126046 restraints weight = 22668.673| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22332 Z= 0.101 Angle : 0.533 7.942 30174 Z= 0.279 Chirality : 0.041 0.166 3312 Planarity : 0.004 0.065 3870 Dihedral : 4.173 23.049 2910 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.16 % Allowed : 16.72 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.17), residues: 2638 helix: 1.95 (0.16), residues: 1184 sheet: 0.14 (0.31), residues: 310 loop : -1.17 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 46 TYR 0.036 0.001 TYR D 815 PHE 0.019 0.001 PHE C 35 TRP 0.017 0.001 TRP E 162 HIS 0.017 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00215 (22332) covalent geometry : angle 0.53337 (30174) hydrogen bonds : bond 0.03252 ( 1021) hydrogen bonds : angle 4.10646 ( 2913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8432 (mmtp) REVERT: A 21 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7311 (mpp80) REVERT: A 46 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8142 (ttm170) REVERT: A 79 SER cc_start: 0.9355 (m) cc_final: 0.9031 (p) REVERT: B 26 TYR cc_start: 0.9098 (m-80) cc_final: 0.8753 (m-80) REVERT: B 44 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.7344 (mmm-85) REVERT: B 96 LEU cc_start: 0.8063 (tp) cc_final: 0.7858 (mt) REVERT: C 280 MET cc_start: 0.7930 (mmm) cc_final: 0.7728 (tpp) REVERT: C 297 LEU cc_start: 0.8038 (mm) cc_final: 0.7606 (mt) REVERT: C 389 GLU cc_start: 0.3820 (mt-10) cc_final: 0.1300 (tp30) REVERT: C 417 ILE cc_start: 0.8880 (tp) cc_final: 0.8549 (tp) REVERT: C 667 ASN cc_start: 0.8327 (t0) cc_final: 0.7923 (t0) REVERT: C 731 PRO cc_start: 0.8010 (Cg_exo) cc_final: 0.7751 (Cg_endo) REVERT: C 897 TYR cc_start: 0.7726 (t80) cc_final: 0.7502 (t80) REVERT: C 966 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7380 (mpp) REVERT: D 745 MET cc_start: 0.8417 (mmt) cc_final: 0.8100 (mmt) REVERT: D 814 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6705 (mp0) REVERT: E 141 MET cc_start: 0.0948 (mpp) cc_final: 0.0225 (ttm) REVERT: E 261 MET cc_start: 0.5370 (tmm) cc_final: 0.4968 (tmm) REVERT: E 853 TYR cc_start: 0.8272 (t80) cc_final: 0.7905 (t80) REVERT: F 970 GLN cc_start: 0.6765 (tm-30) cc_final: 0.6331 (tm-30) REVERT: F 973 GLN cc_start: 0.8599 (mt0) cc_final: 0.8021 (pt0) outliers start: 51 outliers final: 32 residues processed: 224 average time/residue: 0.1489 time to fit residues: 53.8175 Evaluate side-chains 206 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 217 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 0.0470 chunk 28 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 324 GLN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.157401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.124390 restraints weight = 53100.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.121870 restraints weight = 46705.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.122728 restraints weight = 35527.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123284 restraints weight = 26805.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123391 restraints weight = 23977.877| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22332 Z= 0.137 Angle : 0.562 8.838 30174 Z= 0.296 Chirality : 0.043 0.287 3312 Planarity : 0.004 0.065 3870 Dihedral : 4.271 22.031 2910 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.38 % Allowed : 17.32 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.17), residues: 2638 helix: 1.84 (0.16), residues: 1190 sheet: 0.09 (0.31), residues: 310 loop : -1.16 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.046 0.002 TYR D 815 PHE 0.016 0.001 PHE C 35 TRP 0.022 0.001 TRP F 739 HIS 0.011 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00314 (22332) covalent geometry : angle 0.56161 (30174) hydrogen bonds : bond 0.03641 ( 1021) hydrogen bonds : angle 4.25447 ( 2913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8406 (mmtp) REVERT: A 50 TYR cc_start: 0.7320 (t80) cc_final: 0.6957 (t80) REVERT: A 54 GLN cc_start: 0.8283 (mm-40) cc_final: 0.8008 (mm-40) REVERT: A 79 SER cc_start: 0.9383 (m) cc_final: 0.9100 (p) REVERT: B 26 TYR cc_start: 0.9093 (m-80) cc_final: 0.8747 (m-80) REVERT: B 44 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7238 (mmm-85) REVERT: C 280 MET cc_start: 0.7995 (mmm) cc_final: 0.7394 (tpp) REVERT: C 297 LEU cc_start: 0.7957 (mm) cc_final: 0.7474 (mt) REVERT: C 417 ILE cc_start: 0.9012 (tp) cc_final: 0.8680 (tp) REVERT: C 966 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7592 (mpp) REVERT: D 745 MET cc_start: 0.8445 (mmt) cc_final: 0.8166 (mmt) REVERT: D 966 MET cc_start: 0.8217 (mtt) cc_final: 0.7964 (mtt) REVERT: E 853 TYR cc_start: 0.8360 (t80) cc_final: 0.8064 (t80) REVERT: F 966 MET cc_start: 0.7906 (mmm) cc_final: 0.7262 (mpp) REVERT: F 970 GLN cc_start: 0.6798 (tm-30) cc_final: 0.6378 (tm-30) REVERT: F 973 GLN cc_start: 0.8628 (mt0) cc_final: 0.8043 (pt0) outliers start: 56 outliers final: 46 residues processed: 221 average time/residue: 0.1437 time to fit residues: 51.6577 Evaluate side-chains 215 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 38 SER Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 948 ASP Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 784 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 839 ASP Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 110 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 254 optimal weight: 0.4980 chunk 74 optimal weight: 0.0060 chunk 60 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN C 447 HIS C 667 ASN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.159050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.126579 restraints weight = 52746.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.124753 restraints weight = 49257.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.125892 restraints weight = 35953.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126186 restraints weight = 26752.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126284 restraints weight = 24921.646| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22332 Z= 0.103 Angle : 0.548 13.410 30174 Z= 0.285 Chirality : 0.042 0.188 3312 Planarity : 0.004 0.066 3870 Dihedral : 4.131 21.350 2910 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.08 % Allowed : 17.78 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.17), residues: 2638 helix: 1.99 (0.16), residues: 1188 sheet: -0.03 (0.30), residues: 334 loop : -1.13 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 46 TYR 0.035 0.001 TYR D 815 PHE 0.018 0.001 PHE C 35 TRP 0.015 0.001 TRP E 162 HIS 0.010 0.001 HIS C 765 Details of bonding type rmsd covalent geometry : bond 0.00223 (22332) covalent geometry : angle 0.54843 (30174) hydrogen bonds : bond 0.03308 ( 1021) hydrogen bonds : angle 4.13746 ( 2913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 182 time to evaluate : 0.781 Fit side-chains REVERT: A 18 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8415 (mmmt) REVERT: A 21 ARG cc_start: 0.8085 (mtt-85) cc_final: 0.7721 (mpt-90) REVERT: A 46 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8076 (ttm170) REVERT: A 54 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7844 (mm110) REVERT: A 63 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7151 (mp0) REVERT: A 79 SER cc_start: 0.9354 (m) cc_final: 0.9081 (p) REVERT: B 26 TYR cc_start: 0.9075 (m-80) cc_final: 0.8716 (m-80) REVERT: B 44 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7306 (mmm-85) REVERT: C 141 MET cc_start: 0.6718 (mmp) cc_final: 0.6428 (mmt) REVERT: C 280 MET cc_start: 0.8053 (mmm) cc_final: 0.7669 (tpp) REVERT: C 297 LEU cc_start: 0.7871 (mm) cc_final: 0.7399 (mt) REVERT: C 417 ILE cc_start: 0.8912 (tp) cc_final: 0.8565 (tp) REVERT: C 773 LYS cc_start: 0.6430 (mptt) cc_final: 0.6016 (mtpt) REVERT: C 897 TYR cc_start: 0.7722 (t80) cc_final: 0.7503 (t80) REVERT: C 966 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7606 (mpp) REVERT: D 745 MET cc_start: 0.8409 (mmt) cc_final: 0.8125 (mmt) REVERT: D 966 MET cc_start: 0.8167 (mtt) cc_final: 0.7932 (mtt) REVERT: E 853 TYR cc_start: 0.8207 (t80) cc_final: 0.7836 (t80) REVERT: F 966 MET cc_start: 0.7905 (mmm) cc_final: 0.7275 (mpp) REVERT: F 970 GLN cc_start: 0.6852 (tm-30) cc_final: 0.6300 (tm-30) REVERT: F 973 GLN cc_start: 0.8525 (mt0) cc_final: 0.8015 (pt0) outliers start: 49 outliers final: 37 residues processed: 218 average time/residue: 0.1468 time to fit residues: 52.0421 Evaluate side-chains 208 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 784 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 167 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 202 optimal weight: 0.5980 chunk 211 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.158966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.125084 restraints weight = 52792.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.122483 restraints weight = 46470.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.122644 restraints weight = 35893.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123225 restraints weight = 30302.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123369 restraints weight = 26307.758| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22332 Z= 0.111 Angle : 0.559 11.605 30174 Z= 0.291 Chirality : 0.042 0.176 3312 Planarity : 0.004 0.067 3870 Dihedral : 4.136 21.437 2910 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.95 % Allowed : 17.95 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.17), residues: 2638 helix: 1.99 (0.16), residues: 1188 sheet: -0.02 (0.30), residues: 334 loop : -1.11 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 46 TYR 0.042 0.001 TYR A 50 PHE 0.016 0.001 PHE C 35 TRP 0.015 0.001 TRP C 162 HIS 0.029 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00245 (22332) covalent geometry : angle 0.55922 (30174) hydrogen bonds : bond 0.03326 ( 1021) hydrogen bonds : angle 4.16009 ( 2913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.820 Fit side-chains REVERT: A 18 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8359 (mmmt) REVERT: A 21 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7767 (mpt-90) REVERT: A 46 ARG cc_start: 0.8381 (ttp-110) cc_final: 0.8087 (ttm170) REVERT: A 63 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7169 (mp0) REVERT: A 79 SER cc_start: 0.9361 (m) cc_final: 0.9084 (p) REVERT: B 26 TYR cc_start: 0.9080 (m-80) cc_final: 0.8733 (m-80) REVERT: B 44 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7256 (mmm-85) REVERT: C 141 MET cc_start: 0.6732 (mmp) cc_final: 0.6501 (mmt) REVERT: C 417 ILE cc_start: 0.8912 (tp) cc_final: 0.8567 (tp) REVERT: C 773 LYS cc_start: 0.6702 (mptt) cc_final: 0.6299 (mtpt) REVERT: C 887 MET cc_start: 0.8103 (tmm) cc_final: 0.7770 (tmm) REVERT: C 897 TYR cc_start: 0.7799 (t80) cc_final: 0.7539 (t80) REVERT: C 966 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7486 (mpp) REVERT: D 745 MET cc_start: 0.8387 (mmt) cc_final: 0.8114 (mmt) REVERT: D 966 MET cc_start: 0.8179 (mtt) cc_final: 0.7939 (mtt) REVERT: E 261 MET cc_start: 0.5798 (tpt) cc_final: 0.4224 (mtp) REVERT: E 418 MET cc_start: 0.5866 (tpp) cc_final: 0.4096 (ptp) REVERT: E 853 TYR cc_start: 0.8280 (t80) cc_final: 0.7978 (t80) REVERT: F 966 MET cc_start: 0.7936 (mmm) cc_final: 0.7226 (mpp) REVERT: F 970 GLN cc_start: 0.6832 (tm-30) cc_final: 0.6194 (tm-30) REVERT: F 973 GLN cc_start: 0.8626 (mt0) cc_final: 0.7921 (pt0) outliers start: 46 outliers final: 41 residues processed: 215 average time/residue: 0.1456 time to fit residues: 50.7218 Evaluate side-chains 215 residues out of total 2356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 64 ASN Chi-restraints excluded: chain B residue 85 ASN Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 680 HIS Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 758 GLN Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 803 SER Chi-restraints excluded: chain C residue 805 ASN Chi-restraints excluded: chain C residue 953 GLN Chi-restraints excluded: chain C residue 961 GLN Chi-restraints excluded: chain C residue 966 MET Chi-restraints excluded: chain C residue 967 HIS Chi-restraints excluded: chain D residue 743 LEU Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 652 THR Chi-restraints excluded: chain E residue 793 TYR Chi-restraints excluded: chain E residue 799 THR Chi-restraints excluded: chain E residue 839 ASP Chi-restraints excluded: chain E residue 879 HIS Chi-restraints excluded: chain E residue 894 VAL Chi-restraints excluded: chain E residue 955 LEU Chi-restraints excluded: chain F residue 679 THR Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 793 TYR Chi-restraints excluded: chain F residue 940 ASN Chi-restraints excluded: chain F residue 976 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 27 optimal weight: 0.0270 chunk 47 optimal weight: 0.8980 chunk 190 optimal weight: 0.0670 chunk 244 optimal weight: 4.9990 chunk 236 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN B 58 GLN C 667 ASN ** C 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 GLN ** D 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.158958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125613 restraints weight = 52649.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.122331 restraints weight = 44232.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122312 restraints weight = 37111.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.122938 restraints weight = 30784.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123071 restraints weight = 26689.814| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22332 Z= 0.106 Angle : 0.563 11.460 30174 Z= 0.291 Chirality : 0.042 0.180 3312 Planarity : 0.004 0.071 3870 Dihedral : 4.083 21.032 2910 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.04 % Allowed : 18.00 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.17), residues: 2638 helix: 2.01 (0.16), residues: 1188 sheet: 0.03 (0.30), residues: 334 loop : -1.09 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 46 TYR 0.066 0.001 TYR A 50 PHE 0.016 0.001 PHE C 35 TRP 0.015 0.001 TRP C 162 HIS 0.033 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00231 (22332) covalent geometry : angle 0.56289 (30174) hydrogen bonds : bond 0.03236 ( 1021) hydrogen bonds : angle 4.13528 ( 2913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.44 seconds wall clock time: 61 minutes 4.47 seconds (3664.47 seconds total)