Starting phenix.real_space_refine on Sun Oct 12 01:20:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbv_7851/10_2025/6dbv_7851_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbv_7851/10_2025/6dbv_7851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6dbv_7851/10_2025/6dbv_7851_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbv_7851/10_2025/6dbv_7851_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbv_7851/10_2025/6dbv_7851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbv_7851/10_2025/6dbv_7851.map" } resolution = 4.29 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= 0.009 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 222 5.49 5 S 112 5.16 5 C 11837 2.51 5 N 3567 2.21 5 O 4214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19958 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4974 Classifications: {'peptide': 616} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4999 Classifications: {'peptide': 621} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 596} Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1245 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2646 SG CYS A 749 63.182 58.280 104.600 1.00 45.82 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" P DA E 39 " occ=0.57 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.57 residue: pdb=" P DA E 40 " occ=0.81 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.81 residue: pdb=" P DA E 41 " occ=0.63 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.63 residue: pdb=" P DA E 42 " occ=0.59 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.59 residue: pdb=" P DC E 44 " occ=0.30 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.30 residue: pdb=" P DG F 7 " occ=0.51 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.51 residue: pdb=" P DG F 8 " occ=0.47 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.47 residue: pdb=" P DT F 9 " occ=0.49 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.49 residue: pdb=" P DT F 10 " occ=0.56 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.56 residue: pdb=" P DT F 11 " occ=0.63 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.63 residue: pdb=" P DT F 12 " occ=0.74 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.74 residue: pdb=" P DT F 13 " occ=0.78 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.78 ... (remaining 16 not shown) Time building chain proxies: 4.71, per 1000 atoms: 0.24 Number of scatterers: 19958 At special positions: 0 Unit cell: (158.464, 146.084, 123.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 112 16.00 P 222 15.00 O 4214 8.00 N 3567 7.00 C 11837 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 806.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3602 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 18 sheets defined 37.2% alpha, 20.7% beta 89 base pairs and 168 stacking pairs defined. Time for finding SS restraints: 2.92 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.614A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 460 Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.630A pdb=" N ALA A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 510 Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.085A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 518 through 523' Processing helix chain 'A' and resid 577 through 600 removed outlier: 5.218A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 Proline residue: A 696 - end of helix removed outlier: 3.611A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 4.084A pdb=" N GLN A 761 " --> pdb=" O ALA A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 815 through 835 removed outlier: 3.618A pdb=" N ASP A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 862 Processing helix chain 'A' and resid 872 through 879 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 894 through 912 Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.593A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.888A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 947 Processing helix chain 'A' and resid 955 through 964 Processing helix chain 'A' and resid 964 through 972 removed outlier: 3.601A pdb=" N ILE A 968 " --> pdb=" O HIS A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 987 removed outlier: 3.671A pdb=" N GLU A 984 " --> pdb=" O SER A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 997 removed outlier: 3.537A pdb=" N ARG A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS A 995 " --> pdb=" O ARG A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1018 removed outlier: 4.163A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1027 removed outlier: 3.736A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 419 through 441 removed outlier: 5.755A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 459 removed outlier: 3.935A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 473 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 511 Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.992A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 703 removed outlier: 3.921A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 737 Processing helix chain 'C' and resid 755 through 762 Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 819 through 835 removed outlier: 3.516A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 863 removed outlier: 3.618A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 880 removed outlier: 3.710A pdb=" N ALA C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 889 Processing helix chain 'C' and resid 894 through 917 Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 924 through 930 removed outlier: 4.066A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 946 Processing helix chain 'C' and resid 955 through 972 removed outlier: 3.704A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS C 964 " --> pdb=" O LYS C 960 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Proline residue: C 966 - end of helix Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.599A pdb=" N ALA C 979 " --> pdb=" O GLY C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 998 removed outlier: 4.510A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1017 removed outlier: 4.158A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1024 Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.759A pdb=" N SER D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.784A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 728 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.784A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 728 " --> pdb=" O GLU A 617 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.132A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 7.543A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.614A pdb=" N GLU B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.325A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.325A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 620 " --> pdb=" O ARG C 641 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 23 removed outlier: 4.454A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU D 322 " --> pdb=" O THR D 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 80 removed outlier: 3.664A pdb=" N HIS D 93 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 89 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 707 hydrogen bonds defined for protein. 1953 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 222 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 89 basepair parallelities 168 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4525 1.33 - 1.46: 5954 1.46 - 1.58: 9749 1.58 - 1.71: 440 1.71 - 1.83: 168 Bond restraints: 20836 Sorted by residual: bond pdb=" CA PRO D 179 " pdb=" C PRO D 179 " ideal model delta sigma weight residual 1.514 1.496 0.019 5.50e-03 3.31e+04 1.17e+01 bond pdb=" CA ASN C 492 " pdb=" C ASN C 492 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 8.95e+00 bond pdb=" C3' DC G 55 " pdb=" O3' DC G 55 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.67e+00 bond pdb=" C THR D 97 " pdb=" N PRO D 98 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.08e-02 8.57e+03 2.36e+00 bond pdb=" CA GLN C 514 " pdb=" CB GLN C 514 " ideal model delta sigma weight residual 1.526 1.503 0.023 1.53e-02 4.27e+03 2.33e+00 ... (remaining 20831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 28908 3.28 - 6.56: 180 6.56 - 9.85: 8 9.85 - 13.13: 4 13.13 - 16.41: 4 Bond angle restraints: 29104 Sorted by residual: angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.55 -13.55 2.40e+00 1.74e-01 3.19e+01 angle pdb=" O4' DG F 34 " pdb=" C1' DG F 34 " pdb=" N9 DG F 34 " ideal model delta sigma weight residual 108.40 115.95 -7.55 1.50e+00 4.44e-01 2.53e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 109.58 11.02 2.20e+00 2.07e-01 2.51e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 138.18 -11.18 2.40e+00 1.74e-01 2.17e+01 angle pdb=" C GLY B 131 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " ideal model delta sigma weight residual 121.70 129.04 -7.34 1.80e+00 3.09e-01 1.66e+01 ... (remaining 29099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 10840 35.45 - 70.89: 1103 70.89 - 106.34: 28 106.34 - 141.78: 3 141.78 - 177.23: 5 Dihedral angle restraints: 11979 sinusoidal: 6381 harmonic: 5598 Sorted by residual: dihedral pdb=" CA GLY A 512 " pdb=" C GLY A 512 " pdb=" N ARG A 513 " pdb=" CA ARG A 513 " ideal model delta harmonic sigma weight residual 180.00 141.74 38.26 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA SER C 511 " pdb=" C SER C 511 " pdb=" N GLY C 512 " pdb=" CA GLY C 512 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE A 576 " pdb=" C PHE A 576 " pdb=" N ARG A 577 " pdb=" CA ARG A 577 " ideal model delta harmonic sigma weight residual 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2808 0.074 - 0.148: 365 0.148 - 0.222: 11 0.222 - 0.297: 1 0.297 - 0.371: 2 Chirality restraints: 3187 Sorted by residual: chirality pdb=" CA GLN C1000 " pdb=" N GLN C1000 " pdb=" C GLN C1000 " pdb=" CB GLN C1000 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1' DG F 34 " pdb=" O4' DG F 34 " pdb=" C2' DG F 34 " pdb=" N9 DG F 34 " both_signs ideal model delta sigma weight residual False 2.42 2.12 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE B 311 " pdb=" CA ILE B 311 " pdb=" CG1 ILE B 311 " pdb=" CG2 ILE B 311 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 3184 not shown) Planarity restraints: 2985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG F 34 " -0.047 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" N9 DG F 34 " 0.052 2.00e-02 2.50e+03 pdb=" C8 DG F 34 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG F 34 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG F 34 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG F 34 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG F 34 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG F 34 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N2 DG F 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG F 34 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG F 34 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 338 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO D 339 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 339 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 339 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC F 28 " 0.030 2.00e-02 2.50e+03 1.63e-02 5.98e+00 pdb=" N1 DC F 28 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DC F 28 " -0.022 2.00e-02 2.50e+03 pdb=" O2 DC F 28 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC F 28 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DC F 28 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC F 28 " 0.017 2.00e-02 2.50e+03 pdb=" C5 DC F 28 " -0.006 2.00e-02 2.50e+03 pdb=" C6 DC F 28 " -0.002 2.00e-02 2.50e+03 ... (remaining 2982 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 106 2.35 - 2.99: 10558 2.99 - 3.62: 32345 3.62 - 4.26: 47227 4.26 - 4.90: 70905 Nonbonded interactions: 161141 Sorted by model distance: nonbonded pdb=" NH2 ARG C 505 " pdb=" OP2 DT F 25 " model vdw 1.709 3.120 nonbonded pdb=" NH1 ARG A 523 " pdb=" OP2 DG G 24 " model vdw 1.808 3.120 nonbonded pdb=" OE2 GLU C 789 " pdb=" NH1 ARG C 797 " model vdw 1.894 3.120 nonbonded pdb=" OD2 ASP A 814 " pdb=" ND1 HIS A 817 " model vdw 1.924 3.120 nonbonded pdb=" OE2 GLU C 738 " pdb=" ND2 ASN C 775 " model vdw 1.934 3.120 ... (remaining 161136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 408 through 464 or resid 466 through 1028 or resid 1101 th \ rough 1103)) selection = (chain 'C' and (resid 408 through 464 or resid 466 through 628 or resid 635 thro \ ugh 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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=0.00 max=1.00 mean=0.98 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: 0.660 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.740 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 0.137 20840 Z= 0.290 Angle : 0.851 16.412 29104 Z= 0.473 Chirality : 0.048 0.371 3187 Planarity : 0.005 0.066 2985 Dihedral : 22.585 177.231 8377 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.78 % Favored : 89.06 % Rotamer: Outliers : 0.06 % Allowed : 24.73 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -4.29 (0.15), residues: 1929 helix: -2.87 (0.15), residues: 645 sheet: -1.48 (0.26), residues: 335 loop : -3.38 (0.16), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 513 TYR 0.028 0.003 TYR B 343 PHE 0.022 0.003 PHE A 724 TRP 0.018 0.002 TRP C1014 HIS 0.011 0.002 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00582 (20836) covalent geometry : angle 0.85086 (29104) hydrogen bonds : bond 0.12226 ( 891) hydrogen bonds : angle 6.69017 ( 2389) metal coordination : bond 0.11273 ( 3) Misc. bond : bond 0.13703 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 475 GLN cc_start: 0.8131 (mt0) cc_final: 0.7805 (tp40) REVERT: A 517 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8640 (mp10) REVERT: A 670 SER cc_start: 0.8365 (m) cc_final: 0.7398 (m) REVERT: A 704 MET cc_start: 0.6820 (tpp) cc_final: 0.6616 (tpp) REVERT: A 740 LEU cc_start: 0.8376 (mt) cc_final: 0.8066 (mt) REVERT: A 806 PHE cc_start: 0.8551 (p90) cc_final: 0.8297 (p90) REVERT: C 429 ASP cc_start: 0.7901 (m-30) cc_final: 0.7342 (p0) REVERT: C 479 PHE cc_start: 0.7864 (t80) cc_final: 0.7022 (m-80) REVERT: C 604 ASP cc_start: 0.6865 (m-30) cc_final: 0.6538 (p0) REVERT: C 680 MET cc_start: 0.7856 (mtm) cc_final: 0.7588 (mtm) REVERT: C 731 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8393 (tm-30) REVERT: C 869 MET cc_start: 0.8080 (pp-130) cc_final: 0.7745 (ppp) REVERT: C 951 ASP cc_start: 0.7999 (p0) cc_final: 0.7253 (p0) REVERT: D 129 LEU cc_start: 0.7924 (mt) cc_final: 0.7705 (pt) outliers start: 1 outliers final: 1 residues processed: 381 average time/residue: 0.1785 time to fit residues: 98.7749 Evaluate side-chains 199 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 198 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 HIS A 874 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 HIS ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 936 GLN ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.083353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.059944 restraints weight = 95661.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.061518 restraints weight = 54891.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062496 restraints weight = 38498.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.063111 restraints weight = 30814.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063490 restraints weight = 26872.931| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20840 Z= 0.193 Angle : 0.754 10.907 29104 Z= 0.410 Chirality : 0.045 0.209 3187 Planarity : 0.006 0.061 2985 Dihedral : 25.836 176.795 4567 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 0.12 % Allowed : 3.53 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.90 (0.17), residues: 1929 helix: -1.21 (0.18), residues: 650 sheet: -1.22 (0.27), residues: 344 loop : -2.76 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 675 TYR 0.017 0.002 TYR C1016 PHE 0.018 0.002 PHE B 46 TRP 0.023 0.002 TRP A 782 HIS 0.016 0.002 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00422 (20836) covalent geometry : angle 0.75434 (29104) hydrogen bonds : bond 0.05295 ( 891) hydrogen bonds : angle 5.10464 ( 2389) metal coordination : bond 0.00439 ( 3) Misc. bond : bond 0.00203 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8363 (mm-40) REVERT: A 594 MET cc_start: 0.8651 (mmt) cc_final: 0.8303 (mmt) REVERT: A 617 GLU cc_start: 0.7967 (pm20) cc_final: 0.7644 (pm20) REVERT: A 806 PHE cc_start: 0.9236 (p90) cc_final: 0.8310 (p90) REVERT: A 863 MET cc_start: 0.7686 (mmm) cc_final: 0.6724 (mmp) REVERT: A 883 GLU cc_start: 0.8805 (pm20) cc_final: 0.8508 (pp20) REVERT: C 429 ASP cc_start: 0.7954 (m-30) cc_final: 0.7555 (p0) REVERT: C 473 MET cc_start: 0.8806 (ttp) cc_final: 0.7877 (ttt) REVERT: C 474 MET cc_start: 0.6813 (mmt) cc_final: 0.6507 (mpp) REVERT: C 479 PHE cc_start: 0.7481 (t80) cc_final: 0.6689 (m-80) REVERT: C 594 MET cc_start: 0.8907 (mmm) cc_final: 0.8519 (mmm) REVERT: C 737 MET cc_start: 0.6930 (ttm) cc_final: 0.5838 (ttm) REVERT: C 911 MET cc_start: 0.8682 (ptm) cc_final: 0.8424 (ptt) REVERT: C 951 ASP cc_start: 0.7655 (p0) cc_final: 0.7246 (p0) REVERT: D 129 LEU cc_start: 0.8167 (mt) cc_final: 0.7838 (pt) REVERT: D 155 LEU cc_start: 0.8876 (tt) cc_final: 0.7993 (mm) REVERT: D 227 ASP cc_start: 0.8502 (m-30) cc_final: 0.8251 (m-30) REVERT: D 241 LEU cc_start: 0.7957 (mm) cc_final: 0.7465 (tt) outliers start: 2 outliers final: 0 residues processed: 297 average time/residue: 0.1668 time to fit residues: 73.2912 Evaluate side-chains 171 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 145 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 96 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN C1012 HIS ** C1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3597 r_free = 0.3597 target = 0.077969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054387 restraints weight = 95370.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055779 restraints weight = 55240.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056645 restraints weight = 39175.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057190 restraints weight = 31669.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057520 restraints weight = 27772.342| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 75 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.139 20840 Z= 0.320 Angle : 0.829 18.528 29104 Z= 0.444 Chirality : 0.045 0.210 3187 Planarity : 0.006 0.057 2985 Dihedral : 25.791 173.772 4567 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.86 % Favored : 91.08 % Rotamer: Outliers : 0.24 % Allowed : 6.18 % Favored : 93.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -2.57 (0.17), residues: 1929 helix: -1.03 (0.18), residues: 659 sheet: -1.17 (0.27), residues: 344 loop : -2.43 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 778 TYR 0.027 0.003 TYR A 578 PHE 0.019 0.003 PHE A 494 TRP 0.028 0.003 TRP C1014 HIS 0.015 0.002 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00692 (20836) covalent geometry : angle 0.82882 (29104) hydrogen bonds : bond 0.06001 ( 891) hydrogen bonds : angle 5.09019 ( 2389) metal coordination : bond 0.01101 ( 3) Misc. bond : bond 0.00540 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 208 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 517 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8635 (mm-40) REVERT: A 590 GLU cc_start: 0.8776 (tt0) cc_final: 0.8415 (tt0) REVERT: A 594 MET cc_start: 0.8927 (mmt) cc_final: 0.8546 (mmt) REVERT: A 617 GLU cc_start: 0.8377 (pm20) cc_final: 0.7969 (pm20) REVERT: A 675 ARG cc_start: 0.9207 (mmm-85) cc_final: 0.8178 (mmm-85) REVERT: A 945 MET cc_start: 0.8496 (mmp) cc_final: 0.8281 (mmm) REVERT: B 341 GLU cc_start: 0.8233 (mp0) cc_final: 0.7955 (mp0) REVERT: C 429 ASP cc_start: 0.7955 (m-30) cc_final: 0.7594 (p0) REVERT: C 473 MET cc_start: 0.8809 (ttp) cc_final: 0.8109 (ttt) REVERT: C 474 MET cc_start: 0.7208 (mmt) cc_final: 0.6994 (mpp) REVERT: C 479 PHE cc_start: 0.7337 (t80) cc_final: 0.6356 (m-80) REVERT: C 680 MET cc_start: 0.8510 (mtm) cc_final: 0.8282 (mtm) REVERT: C 733 MET cc_start: 0.8974 (tpp) cc_final: 0.8614 (tpp) REVERT: C 737 MET cc_start: 0.7821 (ttm) cc_final: 0.7253 (ttm) REVERT: C 869 MET cc_start: 0.7961 (ppp) cc_final: 0.7532 (ppp) REVERT: C 911 MET cc_start: 0.8789 (ptm) cc_final: 0.8472 (ptt) REVERT: C 951 ASP cc_start: 0.7863 (p0) cc_final: 0.7526 (p0) REVERT: D 129 LEU cc_start: 0.8327 (mt) cc_final: 0.7883 (pt) outliers start: 4 outliers final: 2 residues processed: 212 average time/residue: 0.1521 time to fit residues: 49.8534 Evaluate side-chains 151 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 44 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 175 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 213 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN ** A 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 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 = 0.3635 r_free = 0.3635 target = 0.079828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056138 restraints weight = 93095.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.057618 restraints weight = 53360.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.058542 restraints weight = 37533.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.059109 restraints weight = 30047.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.059448 restraints weight = 26244.425| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 77 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 20840 Z= 0.197 Angle : 0.699 11.569 29104 Z= 0.381 Chirality : 0.042 0.201 3187 Planarity : 0.005 0.073 2985 Dihedral : 25.704 174.469 4567 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.99 (0.18), residues: 1929 helix: -0.37 (0.19), residues: 658 sheet: -0.99 (0.27), residues: 334 loop : -2.17 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 49 TYR 0.021 0.002 TYR C1020 PHE 0.014 0.002 PHE A 494 TRP 0.015 0.002 TRP A1014 HIS 0.009 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00430 (20836) covalent geometry : angle 0.69932 (29104) hydrogen bonds : bond 0.04829 ( 891) hydrogen bonds : angle 4.66364 ( 2389) metal coordination : bond 0.00355 ( 3) Misc. bond : bond 0.00175 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.7941 (ppp) cc_final: 0.7730 (ppp) REVERT: A 517 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8428 (mm-40) REVERT: A 617 GLU cc_start: 0.8448 (pm20) cc_final: 0.7976 (pm20) REVERT: A 675 ARG cc_start: 0.9151 (mmm-85) cc_final: 0.8602 (mmm-85) REVERT: B 341 GLU cc_start: 0.8276 (mp0) cc_final: 0.8066 (mp0) REVERT: C 429 ASP cc_start: 0.8089 (m-30) cc_final: 0.7747 (p0) REVERT: C 473 MET cc_start: 0.8811 (ttp) cc_final: 0.7022 (ttt) REVERT: C 474 MET cc_start: 0.6829 (mmt) cc_final: 0.5928 (mmm) REVERT: C 479 PHE cc_start: 0.7410 (t80) cc_final: 0.6751 (m-80) REVERT: C 733 MET cc_start: 0.9039 (tpp) cc_final: 0.8679 (tpp) REVERT: C 945 MET cc_start: 0.8796 (mmm) cc_final: 0.8495 (mmm) REVERT: C 951 ASP cc_start: 0.7753 (p0) cc_final: 0.7318 (p0) REVERT: D 129 LEU cc_start: 0.8315 (mt) cc_final: 0.7914 (pt) REVERT: D 155 LEU cc_start: 0.9050 (tt) cc_final: 0.8196 (mm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1484 time to fit residues: 50.3345 Evaluate side-chains 160 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 167 optimal weight: 7.9990 chunk 3 optimal weight: 50.0000 chunk 155 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 110 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 126 optimal weight: 0.0670 chunk 135 optimal weight: 2.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 987 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 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 = 0.3668 r_free = 0.3668 target = 0.081742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057586 restraints weight = 93609.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059113 restraints weight = 52757.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060079 restraints weight = 36696.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.060665 restraints weight = 29273.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.060971 restraints weight = 25571.631| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20840 Z= 0.156 Angle : 0.669 8.713 29104 Z= 0.364 Chirality : 0.041 0.176 3187 Planarity : 0.005 0.051 2985 Dihedral : 25.546 176.558 4567 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.63 (0.18), residues: 1929 helix: 0.01 (0.20), residues: 657 sheet: -0.83 (0.28), residues: 336 loop : -2.00 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 797 TYR 0.021 0.002 TYR A 504 PHE 0.025 0.001 PHE B 274 TRP 0.013 0.001 TRP C 915 HIS 0.005 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00344 (20836) covalent geometry : angle 0.66931 (29104) hydrogen bonds : bond 0.04507 ( 891) hydrogen bonds : angle 4.43923 ( 2389) metal coordination : bond 0.00234 ( 3) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 222 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8087 (ppp) cc_final: 0.7883 (ppp) REVERT: A 486 CYS cc_start: 0.7856 (t) cc_final: 0.7139 (t) REVERT: A 517 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8107 (mp10) REVERT: A 617 GLU cc_start: 0.8351 (pm20) cc_final: 0.8082 (pm20) REVERT: A 1025 MET cc_start: 0.8288 (tpp) cc_final: 0.7946 (tmm) REVERT: C 429 ASP cc_start: 0.7955 (m-30) cc_final: 0.7668 (p0) REVERT: C 473 MET cc_start: 0.8797 (ttp) cc_final: 0.8263 (ttt) REVERT: C 474 MET cc_start: 0.6810 (mmt) cc_final: 0.6262 (mmm) REVERT: C 945 MET cc_start: 0.8764 (mmm) cc_final: 0.8509 (mmm) REVERT: C 951 ASP cc_start: 0.7764 (p0) cc_final: 0.7281 (p0) REVERT: D 129 LEU cc_start: 0.8241 (mt) cc_final: 0.7869 (pt) REVERT: D 155 LEU cc_start: 0.9022 (tt) cc_final: 0.8189 (mm) REVERT: D 241 LEU cc_start: 0.8305 (mm) cc_final: 0.7870 (tp) outliers start: 1 outliers final: 0 residues processed: 223 average time/residue: 0.1403 time to fit residues: 50.1268 Evaluate side-chains 162 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 126 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 115 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 198 optimal weight: 30.0000 chunk 156 optimal weight: 4.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 987 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.080884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057110 restraints weight = 91895.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.058689 restraints weight = 51109.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059678 restraints weight = 35034.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060296 restraints weight = 27630.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.060661 restraints weight = 23803.091| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 20840 Z= 0.179 Angle : 0.683 13.701 29104 Z= 0.371 Chirality : 0.041 0.186 3187 Planarity : 0.005 0.054 2985 Dihedral : 25.455 175.350 4567 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.00 % Favored : 92.95 % Rotamer: Outliers : 0.06 % Allowed : 1.88 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.48 (0.18), residues: 1929 helix: 0.09 (0.20), residues: 658 sheet: -0.75 (0.28), residues: 336 loop : -1.87 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 992 TYR 0.023 0.002 TYR A 578 PHE 0.025 0.002 PHE C 494 TRP 0.009 0.001 TRP A1014 HIS 0.007 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00399 (20836) covalent geometry : angle 0.68348 (29104) hydrogen bonds : bond 0.04663 ( 891) hydrogen bonds : angle 4.43011 ( 2389) metal coordination : bond 0.00390 ( 3) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8160 (ppp) cc_final: 0.7934 (ppp) REVERT: A 486 CYS cc_start: 0.7856 (t) cc_final: 0.7381 (t) REVERT: A 517 GLN cc_start: 0.8817 (mm-40) cc_final: 0.8236 (mp10) REVERT: A 617 GLU cc_start: 0.8393 (pm20) cc_final: 0.8152 (pm20) REVERT: A 675 ARG cc_start: 0.9092 (mmm-85) cc_final: 0.8831 (mmm-85) REVERT: A 691 THR cc_start: 0.9351 (p) cc_final: 0.8867 (t) REVERT: A 1025 MET cc_start: 0.8306 (tpp) cc_final: 0.7895 (tmm) REVERT: C 429 ASP cc_start: 0.7959 (m-30) cc_final: 0.7670 (p0) REVERT: C 473 MET cc_start: 0.8677 (ttp) cc_final: 0.8343 (ttt) REVERT: C 474 MET cc_start: 0.6697 (mmt) cc_final: 0.6142 (mmm) REVERT: C 945 MET cc_start: 0.8738 (mmm) cc_final: 0.8501 (mmm) REVERT: C 951 ASP cc_start: 0.7824 (p0) cc_final: 0.7354 (p0) REVERT: D 34 LYS cc_start: 0.9342 (ttmm) cc_final: 0.9128 (ttmm) REVERT: D 129 LEU cc_start: 0.8289 (mt) cc_final: 0.7845 (pt) REVERT: D 155 LEU cc_start: 0.9058 (tt) cc_final: 0.8217 (mm) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1456 time to fit residues: 49.8823 Evaluate side-chains 155 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 198 optimal weight: 30.0000 chunk 150 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 53 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.079462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.055360 restraints weight = 95093.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056743 restraints weight = 55484.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.057579 restraints weight = 39586.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.058131 restraints weight = 32277.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.058470 restraints weight = 28415.637| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 78 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 20840 Z= 0.240 Angle : 0.728 12.530 29104 Z= 0.393 Chirality : 0.042 0.171 3187 Planarity : 0.005 0.055 2985 Dihedral : 25.486 175.911 4567 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.72 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.47 (0.19), residues: 1929 helix: 0.04 (0.20), residues: 658 sheet: -0.76 (0.28), residues: 336 loop : -1.81 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 574 TYR 0.020 0.002 TYR A 504 PHE 0.028 0.002 PHE C 494 TRP 0.013 0.002 TRP C 560 HIS 0.009 0.002 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00529 (20836) covalent geometry : angle 0.72819 (29104) hydrogen bonds : bond 0.05129 ( 891) hydrogen bonds : angle 4.58172 ( 2389) metal coordination : bond 0.00672 ( 3) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8181 (ppp) cc_final: 0.7950 (ppp) REVERT: A 486 CYS cc_start: 0.8176 (t) cc_final: 0.7828 (t) REVERT: A 517 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8330 (mp10) REVERT: A 617 GLU cc_start: 0.8451 (pm20) cc_final: 0.8222 (pm20) REVERT: A 675 ARG cc_start: 0.9146 (mmm-85) cc_final: 0.8525 (mmm-85) REVERT: A 691 THR cc_start: 0.9423 (p) cc_final: 0.8977 (t) REVERT: A 738 GLU cc_start: 0.8188 (tt0) cc_final: 0.7824 (tm-30) REVERT: B 173 ASN cc_start: 0.8782 (m110) cc_final: 0.8563 (m110) REVERT: B 268 TYR cc_start: 0.8420 (t80) cc_final: 0.8156 (t80) REVERT: B 285 MET cc_start: 0.8393 (tpp) cc_final: 0.8158 (tpp) REVERT: B 343 TYR cc_start: 0.8941 (m-80) cc_final: 0.8729 (m-80) REVERT: C 473 MET cc_start: 0.8689 (ttp) cc_final: 0.8318 (ttt) REVERT: C 474 MET cc_start: 0.6769 (mmt) cc_final: 0.6181 (mmm) REVERT: C 647 MET cc_start: 0.7648 (mpp) cc_final: 0.7220 (mpp) REVERT: C 705 MET cc_start: 0.8892 (mmm) cc_final: 0.8631 (mpp) REVERT: C 945 MET cc_start: 0.8732 (mmm) cc_final: 0.8488 (mmm) REVERT: C 951 ASP cc_start: 0.7834 (p0) cc_final: 0.7277 (p0) REVERT: D 129 LEU cc_start: 0.8256 (mt) cc_final: 0.7867 (pt) REVERT: D 155 LEU cc_start: 0.9068 (tt) cc_final: 0.8255 (mm) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1392 time to fit residues: 44.4247 Evaluate side-chains 146 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 140 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN A 987 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** 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 = 0.3654 r_free = 0.3654 target = 0.081183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056874 restraints weight = 93555.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.058374 restraints weight = 52898.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059296 restraints weight = 36957.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.059867 restraints weight = 29609.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060176 restraints weight = 25831.328| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20840 Z= 0.171 Angle : 0.683 10.667 29104 Z= 0.372 Chirality : 0.041 0.158 3187 Planarity : 0.005 0.075 2985 Dihedral : 25.441 176.083 4567 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.35 (0.19), residues: 1929 helix: 0.12 (0.20), residues: 659 sheet: -0.55 (0.29), residues: 328 loop : -1.78 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 992 TYR 0.028 0.002 TYR C 908 PHE 0.026 0.002 PHE B 218 TRP 0.010 0.001 TRP B 317 HIS 0.006 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00377 (20836) covalent geometry : angle 0.68303 (29104) hydrogen bonds : bond 0.04581 ( 891) hydrogen bonds : angle 4.44935 ( 2389) metal coordination : bond 0.00360 ( 3) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8182 (ppp) cc_final: 0.7946 (ppp) REVERT: A 517 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8432 (mp10) REVERT: A 617 GLU cc_start: 0.8490 (pm20) cc_final: 0.8219 (pm20) REVERT: A 675 ARG cc_start: 0.9095 (mmm-85) cc_final: 0.8841 (mmm-85) REVERT: A 691 THR cc_start: 0.9367 (p) cc_final: 0.8901 (t) REVERT: A 738 GLU cc_start: 0.8192 (tt0) cc_final: 0.7633 (tm-30) REVERT: B 200 LEU cc_start: 0.9082 (mm) cc_final: 0.8693 (mm) REVERT: B 268 TYR cc_start: 0.8407 (t80) cc_final: 0.8144 (t80) REVERT: B 285 MET cc_start: 0.8343 (tpp) cc_final: 0.8051 (tpp) REVERT: B 343 TYR cc_start: 0.8928 (m-80) cc_final: 0.7884 (m-10) REVERT: C 473 MET cc_start: 0.8573 (ttp) cc_final: 0.8239 (ttt) REVERT: C 474 MET cc_start: 0.6672 (mmt) cc_final: 0.6086 (mmm) REVERT: C 588 ASP cc_start: 0.8219 (t70) cc_final: 0.7835 (t0) REVERT: C 647 MET cc_start: 0.7526 (mpp) cc_final: 0.7103 (mpp) REVERT: C 945 MET cc_start: 0.8651 (mmm) cc_final: 0.8436 (mmm) REVERT: C 951 ASP cc_start: 0.7715 (p0) cc_final: 0.7218 (p0) REVERT: D 129 LEU cc_start: 0.8435 (mt) cc_final: 0.7947 (pt) REVERT: D 155 LEU cc_start: 0.9030 (tt) cc_final: 0.8146 (mm) REVERT: D 241 LEU cc_start: 0.8299 (mm) cc_final: 0.7848 (tp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1395 time to fit residues: 47.8894 Evaluate side-chains 156 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 197 optimal weight: 40.0000 chunk 174 optimal weight: 0.3980 chunk 69 optimal weight: 0.0040 chunk 99 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 208 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 4.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.079662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055228 restraints weight = 94169.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.056619 restraints weight = 54637.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.057467 restraints weight = 38868.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057996 restraints weight = 31563.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058292 restraints weight = 27882.365| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 20840 Z= 0.228 Angle : 0.738 14.214 29104 Z= 0.395 Chirality : 0.042 0.167 3187 Planarity : 0.005 0.062 2985 Dihedral : 25.503 177.503 4567 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.41 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.43 (0.19), residues: 1929 helix: 0.05 (0.20), residues: 657 sheet: -0.69 (0.28), residues: 344 loop : -1.79 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 992 TYR 0.017 0.002 TYR C 950 PHE 0.024 0.002 PHE B 218 TRP 0.014 0.002 TRP C 560 HIS 0.009 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00503 (20836) covalent geometry : angle 0.73808 (29104) hydrogen bonds : bond 0.05039 ( 891) hydrogen bonds : angle 4.67248 ( 2389) metal coordination : bond 0.00568 ( 3) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8204 (ppp) cc_final: 0.7941 (ppp) REVERT: A 517 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8410 (mm-40) REVERT: A 617 GLU cc_start: 0.8524 (pm20) cc_final: 0.8279 (pm20) REVERT: A 675 ARG cc_start: 0.9158 (mmm-85) cc_final: 0.8597 (mmm-85) REVERT: A 691 THR cc_start: 0.9407 (p) cc_final: 0.9004 (t) REVERT: A 741 GLU cc_start: 0.8434 (mp0) cc_final: 0.8215 (mp0) REVERT: B 173 ASN cc_start: 0.8747 (m-40) cc_final: 0.8455 (m110) REVERT: B 200 LEU cc_start: 0.9122 (mm) cc_final: 0.8730 (mm) REVERT: B 268 TYR cc_start: 0.8455 (t80) cc_final: 0.8190 (t80) REVERT: B 285 MET cc_start: 0.8378 (tpp) cc_final: 0.8079 (tpp) REVERT: B 341 GLU cc_start: 0.8350 (mp0) cc_final: 0.8140 (mp0) REVERT: B 343 TYR cc_start: 0.9013 (m-80) cc_final: 0.8794 (m-80) REVERT: C 647 MET cc_start: 0.7610 (mpp) cc_final: 0.7130 (mpp) REVERT: C 945 MET cc_start: 0.8691 (mmm) cc_final: 0.8475 (mmm) REVERT: D 129 LEU cc_start: 0.8262 (mt) cc_final: 0.7872 (pt) REVERT: D 155 LEU cc_start: 0.9020 (tt) cc_final: 0.8161 (mm) REVERT: D 241 LEU cc_start: 0.8127 (mm) cc_final: 0.7658 (tp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1388 time to fit residues: 43.6724 Evaluate side-chains 145 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 130 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 139 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.080940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.057264 restraints weight = 90922.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.058759 restraints weight = 51484.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.059696 restraints weight = 35793.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.060261 restraints weight = 28428.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.060645 restraints weight = 24687.372| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20840 Z= 0.165 Angle : 0.701 11.158 29104 Z= 0.377 Chirality : 0.041 0.168 3187 Planarity : 0.005 0.051 2985 Dihedral : 25.470 178.779 4567 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.06 % Allowed : 0.24 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.31 (0.19), residues: 1929 helix: 0.19 (0.20), residues: 656 sheet: -0.48 (0.28), residues: 336 loop : -1.82 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 992 TYR 0.021 0.002 TYR C1020 PHE 0.020 0.002 PHE B 218 TRP 0.014 0.001 TRP A 978 HIS 0.006 0.001 HIS B 237 Details of bonding type rmsd covalent geometry : bond 0.00366 (20836) covalent geometry : angle 0.70079 (29104) hydrogen bonds : bond 0.04574 ( 891) hydrogen bonds : angle 4.50472 ( 2389) metal coordination : bond 0.00271 ( 3) Misc. bond : bond 0.00010 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3858 Ramachandran restraints generated. 1929 Oldfield, 0 Emsley, 1929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 474 MET cc_start: 0.8155 (ppp) cc_final: 0.7872 (ppp) REVERT: A 517 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8448 (mp10) REVERT: A 617 GLU cc_start: 0.8510 (pm20) cc_final: 0.8270 (pm20) REVERT: A 691 THR cc_start: 0.9372 (p) cc_final: 0.9138 (t) REVERT: B 173 ASN cc_start: 0.8580 (m-40) cc_final: 0.8312 (m110) REVERT: B 268 TYR cc_start: 0.8303 (t80) cc_final: 0.8066 (t80) REVERT: B 285 MET cc_start: 0.8269 (tpp) cc_final: 0.7985 (tpp) REVERT: C 429 ASP cc_start: 0.7923 (m-30) cc_final: 0.7625 (p0) REVERT: C 503 MET cc_start: 0.9180 (ppp) cc_final: 0.8979 (tmm) REVERT: C 588 ASP cc_start: 0.8209 (t70) cc_final: 0.7806 (t0) REVERT: C 647 MET cc_start: 0.7571 (mpp) cc_final: 0.7077 (mpp) REVERT: C 704 MET cc_start: 0.9095 (mmp) cc_final: 0.8728 (mmm) REVERT: C 871 MET cc_start: 0.8461 (mmp) cc_final: 0.8175 (mmm) REVERT: C 1007 GLU cc_start: 0.8411 (mt-10) cc_final: 0.7784 (mp0) REVERT: D 129 LEU cc_start: 0.8282 (mt) cc_final: 0.7891 (pt) REVERT: D 155 LEU cc_start: 0.8996 (tt) cc_final: 0.8177 (mm) REVERT: D 185 ILE cc_start: 0.9610 (pt) cc_final: 0.9187 (mm) REVERT: D 238 VAL cc_start: 0.8966 (m) cc_final: 0.8726 (p) REVERT: D 241 LEU cc_start: 0.8277 (mm) cc_final: 0.7797 (tp) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.1397 time to fit residues: 45.1509 Evaluate side-chains 149 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 215 random chunks: chunk 183 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 209 optimal weight: 40.0000 chunk 113 optimal weight: 0.0570 chunk 87 optimal weight: 0.5980 chunk 208 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 overall best weight: 3.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN ** B 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN ** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 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 = 0.3637 r_free = 0.3637 target = 0.080315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.055651 restraints weight = 94296.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.057144 restraints weight = 53074.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.058064 restraints weight = 36949.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058652 restraints weight = 29628.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.058952 restraints weight = 25893.861| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.6155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 20840 Z= 0.199 Angle : 0.713 11.858 29104 Z= 0.383 Chirality : 0.041 0.169 3187 Planarity : 0.005 0.067 2985 Dihedral : 25.469 178.910 4567 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.59 % Cis-general : 1.25 % 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 aren not related in a simple way. whole: -1.31 (0.19), residues: 1929 helix: 0.21 (0.20), residues: 656 sheet: -0.51 (0.29), residues: 336 loop : -1.81 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 465 TYR 0.016 0.002 TYR A 500 PHE 0.020 0.002 PHE B 218 TRP 0.012 0.002 TRP C 560 HIS 0.007 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00443 (20836) covalent geometry : angle 0.71315 (29104) hydrogen bonds : bond 0.04805 ( 891) hydrogen bonds : angle 4.55047 ( 2389) metal coordination : bond 0.00390 ( 3) Misc. bond : bond 0.00074 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3564.97 seconds wall clock time: 62 minutes 38.48 seconds (3758.48 seconds total)