Starting phenix.real_space_refine on Tue Nov 18 21:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbx_7853/11_2025/6dbx_7853.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbx_7853/11_2025/6dbx_7853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbx_7853/11_2025/6dbx_7853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbx_7853/11_2025/6dbx_7853.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbx_7853/11_2025/6dbx_7853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbx_7853/11_2025/6dbx_7853.cif" } resolution = 4.2 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= 0.007 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 100 5.49 5 S 112 5.16 5 C 10634 2.51 5 N 3107 2.21 5 O 3477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17436 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4966 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} 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: 4980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 615, 4964 Classifications: {'peptide': 615} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 590} Chain breaks: 1 bond proxies already assigned to first conformer: 5041 Chain: "D" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2720 Classifications: {'peptide': 352} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 318} 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: "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 2647 SG CYS A 749 32.932 54.101 52.515 1.00 92.47 S ATOM 10316 SG CYS C 749 105.234 99.787 56.404 1.00107.55 S Residues with excluded nonbonded symmetry interactions: 13 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=0.77 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.77 residue: pdb=" P DA E 41 " occ=0.80 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.80 residue: pdb=" P DA E 42 " occ=0.71 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.71 residue: pdb=" P DC E 44 " occ=0.64 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.64 residue: pdb=" P DG F 7 " occ=0.68 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.68 residue: pdb=" P DG F 8 " occ=0.66 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.66 residue: pdb=" P DT F 9 " occ=0.78 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.78 residue: pdb=" P DT F 10 " occ=0.72 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.72 residue: pdb=" P DT F 11 " occ=0.96 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.96 residue: pdb=" P DT F 12 " occ=0.79 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.79 residue: pdb=" P DT F 13 " occ=0.80 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.80 residue: pdb=" P DG F 14 " occ=0.51 ... (20 atoms not shown) pdb=" C4 DG F 14 " occ=0.51 Time building chain proxies: 5.17, per 1000 atoms: 0.30 Number of scatterers: 17436 At special positions: 0 Unit cell: (131.44, 156.88, 143.1, 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 100 15.00 O 3477 8.00 N 3107 7.00 C 10634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 976.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3598 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 19 sheets defined 37.2% alpha, 19.2% beta 40 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.493A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 474 removed outlier: 4.163A 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 511 removed outlier: 3.513A pdb=" N SER A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 589 Processing helix chain 'A' and resid 589 through 601 Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 707 removed outlier: 3.580A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 4.482A pdb=" N GLU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER A 707 " --> pdb=" O ALA A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 756 through 762 removed outlier: 3.968A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 819 through 835 Processing helix chain 'A' and resid 844 through 864 removed outlier: 3.883A pdb=" N ARG A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.557A pdb=" N ALA A 876 " --> pdb=" O ASN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 894 through 916 removed outlier: 3.773A pdb=" N ARG A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 924 through 946 removed outlier: 4.135A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 934 " --> pdb=" O GLN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.974A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 972 Processing helix chain 'A' and resid 975 through 983 removed outlier: 7.575A pdb=" N SER A 980 " --> pdb=" O ALA A 977 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU A 981 " --> pdb=" O TRP A 978 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 982 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 removed outlier: 4.021A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 3.856A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1023 removed outlier: 3.523A pdb=" N GLN A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.810A pdb=" N LEU B 14 " --> pdb=" O CYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.694A pdb=" N LEU C 418 " --> pdb=" O LEU C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 442 removed outlier: 5.708A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 460 removed outlier: 3.776A pdb=" N VAL C 449 " --> pdb=" O ASP C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.690A pdb=" N ALA C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 496 through 510 Processing helix chain 'C' and resid 518 through 527 removed outlier: 3.817A pdb=" N LEU C 522 " --> pdb=" O PRO C 518 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C 527 " --> pdb=" O ARG C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 600 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.789A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR C 691 " --> pdb=" O HIS C 687 " (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 757 through 762 removed outlier: 3.751A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 799 Processing helix chain 'C' and resid 815 through 834 Processing helix chain 'C' and resid 844 through 862 Processing helix chain 'C' and resid 872 through 878 removed outlier: 3.879A pdb=" N ALA C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 890 Processing helix chain 'C' and resid 895 through 910 removed outlier: 3.879A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.769A pdb=" N TRP C 915 " --> pdb=" O MET C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 Processing helix chain 'C' and resid 924 through 930 removed outlier: 3.614A pdb=" N GLN C 930 " --> pdb=" O ASP C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 945 Processing helix chain 'C' and resid 955 through 964 Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 980 through 998 removed outlier: 4.615A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER C 985 " --> pdb=" O GLU C 981 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1016 removed outlier: 4.309A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS C1011 " --> pdb=" O GLU C1007 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1027 removed outlier: 4.950A pdb=" N PHE C1024 " --> pdb=" O TYR C1020 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.862A pdb=" N GLU A 537 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 710 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 716 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N PHE A 644 " --> pdb=" O PRO A 676 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 539 removed outlier: 3.862A pdb=" N GLU A 537 " --> pdb=" O ILE A 710 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE A 710 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 716 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 611 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE A 722 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL A 613 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE A 724 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 615 " --> pdb=" O PHE A 724 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N GLY A 726 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU A 617 " --> pdb=" O GLY A 726 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N MET A 647 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLN A 664 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE A 649 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 660 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.507A pdb=" N SER B 2 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 346 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 329 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 330 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 318 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.507A pdb=" N SER B 2 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR B 346 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 329 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS B 344 " --> pdb=" O ILE B 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 20 through 23 removed outlier: 4.981A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 48 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 80 removed outlier: 3.930A pdb=" N CYS B 89 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 141 through 147 removed outlier: 3.861A pdb=" N LYS B 150 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 160 removed outlier: 3.565A pdb=" N VAL B 176 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 210 Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 265 removed outlier: 3.656A pdb=" N SER B 264 " --> pdb=" O ILE B 272 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 272 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 3.766A pdb=" N GLU C 537 " --> pdb=" O ILE C 710 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 711 " --> pdb=" O ARG C 718 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 554 through 555 removed outlier: 5.939A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N MET C 647 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLN C 664 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 649 " --> pdb=" O ILE C 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 554 through 555 removed outlier: 5.939A pdb=" N PHE C 644 " --> pdb=" O PRO C 676 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG C 725 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 615 " --> pdb=" O ARG C 725 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 5.997A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 48 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE D 46 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N LEU D 55 " --> pdb=" O PRO D 5 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 2 " --> pdb=" O SER D 349 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE D 345 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA D 8 " --> pdb=" O TYR D 343 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N TYR D 343 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS D 344 " --> pdb=" O ILE D 331 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR D 346 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL D 348 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.025A pdb=" N SER D 61 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N CYS D 124 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER D 110 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 106 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 78 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 removed outlier: 3.518A pdb=" N THR D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 155 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR D 183 " --> pdb=" O LEU D 155 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AC1, first strand: chain 'D' and resid 263 through 265 654 hydrogen bonds defined for protein. 1832 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5216 1.34 - 1.47: 4918 1.47 - 1.60: 7520 1.60 - 1.72: 189 1.72 - 1.85: 168 Bond restraints: 18011 Sorted by residual: bond pdb=" CA PRO D 163 " pdb=" C PRO D 163 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.59e+01 bond pdb=" C PHE C 516 " pdb=" N GLN C 517 " ideal model delta sigma weight residual 1.327 1.289 0.037 1.71e-02 3.42e+03 4.80e+00 bond pdb=" CA VAL C 965 " pdb=" CB VAL C 965 " ideal model delta sigma weight residual 1.537 1.529 0.008 5.00e-03 4.00e+04 2.40e+00 bond pdb=" N ASP D 214 " pdb=" CA ASP D 214 " ideal model delta sigma weight residual 1.460 1.489 -0.030 1.95e-02 2.63e+03 2.30e+00 bond pdb=" C LEU C 481 " pdb=" N HIS C 482 " ideal model delta sigma weight residual 1.331 1.362 -0.031 2.07e-02 2.33e+03 2.18e+00 ... (remaining 18006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 24406 2.78 - 5.56: 308 5.56 - 8.33: 28 8.33 - 11.11: 4 11.11 - 13.89: 4 Bond angle restraints: 24750 Sorted by residual: angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CA PRO B 340 " ideal model delta sigma weight residual 127.00 140.89 -13.89 2.40e+00 1.74e-01 3.35e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 139.60 -12.60 2.40e+00 1.74e-01 2.76e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.31 11.29 2.20e+00 2.07e-01 2.63e+01 angle pdb=" N ILE C 975 " pdb=" CA ILE C 975 " pdb=" C ILE C 975 " ideal model delta sigma weight residual 112.12 107.98 4.14 8.40e-01 1.42e+00 2.43e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 110.54 10.06 2.20e+00 2.07e-01 2.09e+01 ... (remaining 24745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 9932 35.97 - 71.94: 686 71.94 - 107.92: 17 107.92 - 143.89: 1 143.89 - 179.86: 4 Dihedral angle restraints: 10640 sinusoidal: 5049 harmonic: 5591 Sorted by residual: dihedral pdb=" CD BARG C 850 " pdb=" NE BARG C 850 " pdb=" CZ BARG C 850 " pdb=" NH1BARG C 850 " ideal model delta sinusoidal sigma weight residual 0.00 -179.86 179.86 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CA SER A 511 " pdb=" C SER A 511 " pdb=" N GLY A 512 " pdb=" CA GLY A 512 " ideal model delta harmonic sigma weight residual 180.00 150.03 29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLY A 623 " pdb=" C GLY A 623 " pdb=" N ASP A 624 " pdb=" CA ASP A 624 " ideal model delta harmonic sigma weight residual 180.00 152.33 27.67 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 10637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1642 0.035 - 0.071: 735 0.071 - 0.106: 220 0.106 - 0.142: 87 0.142 - 0.177: 11 Chirality restraints: 2695 Sorted by residual: chirality pdb=" CA VAL C 682 " pdb=" N VAL C 682 " pdb=" C VAL C 682 " pdb=" CB VAL C 682 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" CA ILE B 262 " pdb=" N ILE B 262 " pdb=" C ILE B 262 " pdb=" CB ILE B 262 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA MET A 863 " pdb=" N MET A 863 " pdb=" C MET A 863 " pdb=" CB MET A 863 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 2692 not shown) Planarity restraints: 2857 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO B 339 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 804 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO A 805 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 805 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 805 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 866 " 0.032 5.00e-02 4.00e+02 4.90e-02 3.83e+00 pdb=" N PRO C 867 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO C 867 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 867 " 0.027 5.00e-02 4.00e+02 ... (remaining 2854 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 424 2.64 - 3.21: 16377 3.21 - 3.77: 28005 3.77 - 4.34: 35142 4.34 - 4.90: 54122 Nonbonded interactions: 134070 Sorted by model distance: nonbonded pdb=" OG SER B 314 " pdb=" O THR B 316 " model vdw 2.076 3.040 nonbonded pdb=" O2 DC E 31 " pdb=" N2 DG F 20 " model vdw 2.095 2.496 nonbonded pdb=" O PRO A 913 " pdb=" OG SER A 917 " model vdw 2.125 3.040 nonbonded pdb=" OD2 ASP A 566 " pdb=" OH TYR B 138 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR B 97 " pdb=" O ASN B 99 " model vdw 2.156 3.040 ... (remaining 134065 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 512 or resid 514 through 627 or resid 636 thro \ ugh 849 or resid 851 through 1103)) selection = (chain 'C' and (resid 408 through 512 or resid 514 through 849 or resid 851 thro \ ugh 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 1 through 351) } 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=0.99 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.310 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 0.327 18016 Z= 0.278 Angle : 0.851 13.889 24750 Z= 0.475 Chirality : 0.046 0.177 2695 Planarity : 0.005 0.061 2857 Dihedral : 20.444 179.859 7042 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 20.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.87 % Favored : 87.98 % Rotamer: Outliers : 0.00 % Allowed : 30.94 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.68 (0.15), residues: 1923 helix: -2.79 (0.15), residues: 613 sheet: -2.66 (0.25), residues: 314 loop : -3.53 (0.15), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 675 TYR 0.023 0.003 TYR A 948 PHE 0.024 0.002 PHE A 993 TRP 0.024 0.003 TRP A 978 HIS 0.010 0.002 HIS B 222 Details of bonding type rmsd covalent geometry : bond 0.00485 (18011) covalent geometry : angle 0.85142 (24750) hydrogen bonds : bond 0.19982 ( 721) hydrogen bonds : angle 8.08323 ( 2020) metal coordination : bond 0.24554 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 MET cc_start: 0.9047 (tpt) cc_final: 0.8054 (tpp) REVERT: A 735 ARG cc_start: 0.9117 (mmt90) cc_final: 0.8879 (mmm-85) REVERT: A 768 ILE cc_start: 0.7178 (mt) cc_final: 0.6908 (mp) REVERT: A 891 LEU cc_start: 0.8933 (mt) cc_final: 0.8662 (mt) REVERT: A 1007 GLU cc_start: 0.9492 (tt0) cc_final: 0.9155 (mt-10) REVERT: B 64 ASN cc_start: 0.9022 (m-40) cc_final: 0.8373 (m-40) REVERT: B 86 LYS cc_start: 0.8551 (tppt) cc_final: 0.8310 (mmtt) REVERT: C 503 MET cc_start: 0.8660 (ttm) cc_final: 0.8298 (ttp) REVERT: C 528 GLU cc_start: 0.9553 (tt0) cc_final: 0.9253 (tm-30) REVERT: C 598 ARG cc_start: 0.8839 (mmt-90) cc_final: 0.8438 (mmp80) REVERT: C 702 LYS cc_start: 0.9311 (mmmt) cc_final: 0.9024 (ttpp) REVERT: C 907 LEU cc_start: 0.8604 (mt) cc_final: 0.7999 (mm) REVERT: D 306 GLN cc_start: 0.8592 (mp10) cc_final: 0.8088 (pp30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1547 time to fit residues: 81.3688 Evaluate side-chains 176 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 100 ASN B 170 GLN ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN C 934 ASN C 959 HIS C 983 ASN D 83 GLN D 170 GLN D 195 HIS ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061133 restraints weight = 148188.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.063395 restraints weight = 64462.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064810 restraints weight = 37853.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.065717 restraints weight = 26643.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066272 restraints weight = 21153.367| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.725 18016 Z= 0.274 Angle : 0.757 8.111 24750 Z= 0.410 Chirality : 0.046 0.194 2695 Planarity : 0.005 0.050 2857 Dihedral : 21.389 179.901 3231 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.17), residues: 1923 helix: -1.24 (0.18), residues: 633 sheet: -1.94 (0.25), residues: 342 loop : -2.75 (0.17), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 922 TYR 0.028 0.002 TYR C 500 PHE 0.030 0.002 PHE C 993 TRP 0.019 0.002 TRP C 915 HIS 0.017 0.002 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00439 (18011) covalent geometry : angle 0.75690 (24750) hydrogen bonds : bond 0.05478 ( 721) hydrogen bonds : angle 5.96761 ( 2020) metal coordination : bond 0.32420 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.534 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: A 486 CYS cc_start: 0.8988 (m) cc_final: 0.8539 (m) REVERT: A 497 CYS cc_start: 0.7871 (m) cc_final: 0.7572 (m) REVERT: A 570 ASP cc_start: 0.7445 (p0) cc_final: 0.7050 (p0) REVERT: A 647 MET cc_start: 0.8997 (mmm) cc_final: 0.8461 (mmm) REVERT: A 777 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8205 (tm-30) REVERT: A 867 PRO cc_start: 0.8334 (Cg_exo) cc_final: 0.7821 (Cg_endo) REVERT: A 903 LYS cc_start: 0.9607 (ptpt) cc_final: 0.9207 (pttm) REVERT: A 1007 GLU cc_start: 0.8724 (tt0) cc_final: 0.8260 (mt-10) REVERT: B 64 ASN cc_start: 0.8846 (m-40) cc_final: 0.8393 (m-40) REVERT: B 86 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8416 (mmtt) REVERT: C 517 GLN cc_start: 0.8711 (mm110) cc_final: 0.8511 (mp10) REVERT: C 592 ASP cc_start: 0.8835 (m-30) cc_final: 0.8291 (t0) REVERT: C 598 ARG cc_start: 0.8743 (mmt-90) cc_final: 0.8321 (mmp80) REVERT: C 677 LEU cc_start: 0.9237 (tt) cc_final: 0.8995 (tp) REVERT: C 807 MET cc_start: 0.8438 (tmm) cc_final: 0.8068 (tmm) REVERT: C 906 ASP cc_start: 0.9201 (t70) cc_final: 0.8686 (m-30) REVERT: C 911 MET cc_start: 0.8936 (ttp) cc_final: 0.8692 (ttp) REVERT: D 306 GLN cc_start: 0.8798 (mp10) cc_final: 0.8290 (pp30) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1585 time to fit residues: 69.2323 Evaluate side-chains 181 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 199 optimal weight: 8.9990 chunk 118 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 185 optimal weight: 0.0670 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN A 937 GLN A 964 HIS A1013 HIS B 79 HIS B 100 ASN C 687 HIS ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 839 GLN C 930 GLN C1013 HIS ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.085745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060400 restraints weight = 174686.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062812 restraints weight = 69656.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.064353 restraints weight = 39723.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065345 restraints weight = 27189.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065935 restraints weight = 21192.232| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18016 Z= 0.146 Angle : 0.684 11.228 24750 Z= 0.366 Chirality : 0.042 0.166 2695 Planarity : 0.005 0.050 2857 Dihedral : 21.203 179.224 3231 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.18), residues: 1923 helix: -0.35 (0.20), residues: 637 sheet: -1.57 (0.25), residues: 366 loop : -2.32 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 949 TYR 0.020 0.002 TYR B 90 PHE 0.029 0.002 PHE C 938 TRP 0.021 0.002 TRP C 915 HIS 0.010 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00315 (18011) covalent geometry : angle 0.68372 (24750) hydrogen bonds : bond 0.04707 ( 721) hydrogen bonds : angle 5.40642 ( 2020) metal coordination : bond 0.01350 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.7910 (m) cc_final: 0.7598 (p) REVERT: A 570 ASP cc_start: 0.7564 (p0) cc_final: 0.7195 (p0) REVERT: A 647 MET cc_start: 0.9074 (mmm) cc_final: 0.8432 (mmm) REVERT: A 777 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 905 MET cc_start: 0.8683 (tpp) cc_final: 0.8434 (tpt) REVERT: A 906 ASP cc_start: 0.8874 (t70) cc_final: 0.8260 (t70) REVERT: A 960 LYS cc_start: 0.9188 (mttp) cc_final: 0.8908 (mtmm) REVERT: A 1007 GLU cc_start: 0.8821 (tt0) cc_final: 0.8556 (mt-10) REVERT: B 64 ASN cc_start: 0.8646 (m-40) cc_final: 0.8005 (t0) REVERT: B 69 LEU cc_start: 0.9201 (tp) cc_final: 0.8989 (tp) REVERT: B 86 LYS cc_start: 0.8818 (ttmm) cc_final: 0.8418 (mmtt) REVERT: C 473 MET cc_start: 0.3529 (tpp) cc_final: 0.2921 (tpt) REVERT: C 517 GLN cc_start: 0.8808 (mm110) cc_final: 0.8327 (mp10) REVERT: C 598 ARG cc_start: 0.8815 (mmt-90) cc_final: 0.8366 (mmp80) REVERT: C 622 MET cc_start: 0.8099 (pmm) cc_final: 0.6142 (tpt) REVERT: C 906 ASP cc_start: 0.9178 (t70) cc_final: 0.8655 (m-30) REVERT: D 93 HIS cc_start: 0.8307 (t70) cc_final: 0.7588 (t70) REVERT: D 145 ILE cc_start: 0.9376 (pt) cc_final: 0.9164 (mm) REVERT: D 218 PHE cc_start: 0.8587 (m-80) cc_final: 0.8377 (m-80) REVERT: D 306 GLN cc_start: 0.8885 (mp10) cc_final: 0.8314 (pp30) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.1455 time to fit residues: 55.4945 Evaluate side-chains 175 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 144 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 137 optimal weight: 0.0370 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 170 optimal weight: 7.9990 overall best weight: 3.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 GLN A 822 ASN A 997 ASN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 775 ASN ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.082104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057245 restraints weight = 152914.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.059392 restraints weight = 64958.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060755 restraints weight = 37966.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061620 restraints weight = 26810.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062145 restraints weight = 21430.895| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18016 Z= 0.234 Angle : 0.727 8.180 24750 Z= 0.390 Chirality : 0.044 0.377 2695 Planarity : 0.005 0.047 2857 Dihedral : 21.210 179.370 3231 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.56 % Favored : 93.39 % Rotamer: Outliers : 0.06 % Allowed : 4.01 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1923 helix: -0.23 (0.20), residues: 639 sheet: -1.43 (0.26), residues: 361 loop : -2.17 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 999 TYR 0.028 0.002 TYR C 500 PHE 0.026 0.002 PHE C 938 TRP 0.019 0.002 TRP B 307 HIS 0.013 0.002 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00495 (18011) covalent geometry : angle 0.72666 (24750) hydrogen bonds : bond 0.04984 ( 721) hydrogen bonds : angle 5.42296 ( 2020) metal coordination : bond 0.00683 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.8001 (m) cc_final: 0.7630 (p) REVERT: A 570 ASP cc_start: 0.7578 (p0) cc_final: 0.7199 (p0) REVERT: A 647 MET cc_start: 0.9139 (mmm) cc_final: 0.8861 (mmm) REVERT: A 909 LEU cc_start: 0.8655 (pp) cc_final: 0.8216 (pp) REVERT: A 922 ARG cc_start: 0.8732 (pmt-80) cc_final: 0.8421 (pmt-80) REVERT: A 960 LYS cc_start: 0.9265 (mttp) cc_final: 0.8992 (mtmm) REVERT: B 64 ASN cc_start: 0.8762 (m-40) cc_final: 0.8111 (m-40) REVERT: B 69 LEU cc_start: 0.9359 (tp) cc_final: 0.9132 (tp) REVERT: B 86 LYS cc_start: 0.8854 (ttmm) cc_final: 0.8575 (mmtt) REVERT: C 473 MET cc_start: 0.3114 (tpp) cc_final: 0.2344 (tpt) REVERT: C 589 LEU cc_start: 0.9692 (mt) cc_final: 0.9405 (mt) REVERT: C 598 ARG cc_start: 0.8818 (mmt-90) cc_final: 0.8366 (mmp80) REVERT: C 733 MET cc_start: 0.9400 (tpp) cc_final: 0.9134 (mmm) REVERT: C 947 LYS cc_start: 0.9507 (tttt) cc_final: 0.9171 (tptt) REVERT: C 983 ASN cc_start: 0.8005 (m-40) cc_final: 0.7700 (m-40) REVERT: D 218 PHE cc_start: 0.8643 (m-80) cc_final: 0.8425 (m-80) REVERT: D 306 GLN cc_start: 0.8724 (mp10) cc_final: 0.8245 (pp30) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1432 time to fit residues: 48.8797 Evaluate side-chains 157 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 26 optimal weight: 0.5980 chunk 110 optimal weight: 0.0870 chunk 197 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 193 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN C 664 GLN ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 810 GLN C 839 GLN C 930 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.084646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.059659 restraints weight = 140450.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.061894 restraints weight = 59952.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063293 restraints weight = 35144.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064195 restraints weight = 24779.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064682 restraints weight = 19735.919| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18016 Z= 0.136 Angle : 0.651 8.584 24750 Z= 0.348 Chirality : 0.041 0.179 2695 Planarity : 0.004 0.045 2857 Dihedral : 21.006 179.771 3231 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.18), residues: 1923 helix: 0.13 (0.20), residues: 642 sheet: -1.23 (0.26), residues: 373 loop : -2.01 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 229 TYR 0.018 0.001 TYR C 500 PHE 0.022 0.001 PHE D 206 TRP 0.017 0.002 TRP C 915 HIS 0.006 0.001 HIS C 964 Details of bonding type rmsd covalent geometry : bond 0.00289 (18011) covalent geometry : angle 0.65106 (24750) hydrogen bonds : bond 0.04286 ( 721) hydrogen bonds : angle 5.08844 ( 2020) metal coordination : bond 0.00355 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.666 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: A 497 CYS cc_start: 0.7951 (m) cc_final: 0.7519 (p) REVERT: A 570 ASP cc_start: 0.7546 (p0) cc_final: 0.7169 (p0) REVERT: A 647 MET cc_start: 0.9018 (mmm) cc_final: 0.8776 (mmm) REVERT: A 698 VAL cc_start: 0.9402 (t) cc_final: 0.9173 (p) REVERT: A 704 MET cc_start: 0.8841 (tpt) cc_final: 0.8600 (tpp) REVERT: A 705 MET cc_start: 0.8991 (mtm) cc_final: 0.8546 (mtp) REVERT: A 891 LEU cc_start: 0.8712 (mt) cc_final: 0.8512 (mt) REVERT: A 922 ARG cc_start: 0.8690 (pmt-80) cc_final: 0.8386 (pmt-80) REVERT: A 960 LYS cc_start: 0.9256 (mttp) cc_final: 0.8946 (mtmm) REVERT: B 64 ASN cc_start: 0.8771 (m-40) cc_final: 0.8234 (m-40) REVERT: B 86 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8528 (mmtt) REVERT: B 128 GLU cc_start: 0.9134 (mp0) cc_final: 0.8837 (mp0) REVERT: B 174 SER cc_start: 0.9036 (t) cc_final: 0.8749 (p) REVERT: C 473 MET cc_start: 0.3430 (tpp) cc_final: 0.2844 (tpt) REVERT: C 589 LEU cc_start: 0.9689 (mt) cc_final: 0.9397 (mt) REVERT: C 598 ARG cc_start: 0.8830 (mmt-90) cc_final: 0.8335 (mmp80) REVERT: C 733 MET cc_start: 0.9393 (tpp) cc_final: 0.9081 (mmm) REVERT: C 906 ASP cc_start: 0.9267 (t70) cc_final: 0.8768 (m-30) REVERT: C 947 LYS cc_start: 0.9506 (tttt) cc_final: 0.9167 (tptp) REVERT: C 1010 LEU cc_start: 0.9574 (tp) cc_final: 0.9358 (tp) REVERT: D 218 PHE cc_start: 0.8605 (m-80) cc_final: 0.8389 (m-80) REVERT: D 272 ILE cc_start: 0.8239 (tp) cc_final: 0.7997 (tp) REVERT: D 306 GLN cc_start: 0.8712 (mp10) cc_final: 0.8186 (pp30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1449 time to fit residues: 49.4027 Evaluate side-chains 167 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 6 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 121 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 997 ASN B 79 HIS ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 983 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 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 = 0.3673 r_free = 0.3673 target = 0.083671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058321 restraints weight = 168412.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060676 restraints weight = 67992.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.062154 restraints weight = 38853.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.063096 restraints weight = 26863.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.063694 restraints weight = 21143.287| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18016 Z= 0.156 Angle : 0.638 8.056 24750 Z= 0.343 Chirality : 0.041 0.174 2695 Planarity : 0.004 0.047 2857 Dihedral : 20.910 179.817 3231 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.19), residues: 1923 helix: 0.31 (0.21), residues: 643 sheet: -1.03 (0.27), residues: 372 loop : -1.96 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 756 TYR 0.027 0.002 TYR B 90 PHE 0.023 0.001 PHE C 946 TRP 0.039 0.002 TRP A 915 HIS 0.006 0.001 HIS C 964 Details of bonding type rmsd covalent geometry : bond 0.00339 (18011) covalent geometry : angle 0.63798 (24750) hydrogen bonds : bond 0.04320 ( 721) hydrogen bonds : angle 5.02513 ( 2020) metal coordination : bond 0.00319 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8957 (m) cc_final: 0.8746 (m) REVERT: A 497 CYS cc_start: 0.8186 (m) cc_final: 0.7638 (p) REVERT: A 570 ASP cc_start: 0.7503 (p0) cc_final: 0.7125 (p0) REVERT: A 647 MET cc_start: 0.9056 (mmm) cc_final: 0.8796 (mmm) REVERT: A 705 MET cc_start: 0.9028 (mtm) cc_final: 0.8466 (mtp) REVERT: A 922 ARG cc_start: 0.8737 (pmt-80) cc_final: 0.8341 (pmt-80) REVERT: A 960 LYS cc_start: 0.9270 (mttp) cc_final: 0.8985 (mtmm) REVERT: B 64 ASN cc_start: 0.8766 (m-40) cc_final: 0.8225 (m-40) REVERT: B 86 LYS cc_start: 0.8838 (ttmm) cc_final: 0.8531 (mmtt) REVERT: B 174 SER cc_start: 0.9053 (t) cc_final: 0.8772 (p) REVERT: C 473 MET cc_start: 0.2984 (tpp) cc_final: 0.2353 (tpt) REVERT: C 582 LEU cc_start: 0.9490 (mm) cc_final: 0.9220 (mt) REVERT: C 598 ARG cc_start: 0.8818 (mmt-90) cc_final: 0.8341 (mmp80) REVERT: C 698 VAL cc_start: 0.9145 (t) cc_final: 0.8937 (t) REVERT: C 733 MET cc_start: 0.9394 (tpp) cc_final: 0.9083 (mmm) REVERT: C 737 MET cc_start: 0.8304 (tpt) cc_final: 0.7557 (tmm) REVERT: C 807 MET cc_start: 0.8645 (tmm) cc_final: 0.8231 (tmm) REVERT: C 906 ASP cc_start: 0.9262 (t70) cc_final: 0.8670 (m-30) REVERT: C 947 LYS cc_start: 0.9522 (tttt) cc_final: 0.9175 (tptp) REVERT: D 306 GLN cc_start: 0.8693 (mp10) cc_final: 0.8204 (pp30) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1535 time to fit residues: 52.7265 Evaluate side-chains 163 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 195 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 ASN ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 930 GLN C 983 ASN D 100 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056826 restraints weight = 158654.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059273 restraints weight = 69503.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060390 restraints weight = 37210.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061204 restraints weight = 24152.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061138 restraints weight = 22869.636| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18016 Z= 0.230 Angle : 0.704 7.882 24750 Z= 0.378 Chirality : 0.043 0.199 2695 Planarity : 0.005 0.049 2857 Dihedral : 20.926 179.368 3231 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.19), residues: 1923 helix: 0.15 (0.20), residues: 645 sheet: -1.03 (0.27), residues: 371 loop : -1.99 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 870 TYR 0.026 0.002 TYR C 500 PHE 0.021 0.002 PHE C 938 TRP 0.061 0.003 TRP A 915 HIS 0.009 0.002 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00493 (18011) covalent geometry : angle 0.70417 (24750) hydrogen bonds : bond 0.04646 ( 721) hydrogen bonds : angle 5.17459 ( 2020) metal coordination : bond 0.00603 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8984 (m) cc_final: 0.8778 (m) REVERT: A 497 CYS cc_start: 0.8003 (m) cc_final: 0.7603 (p) REVERT: A 570 ASP cc_start: 0.7591 (p0) cc_final: 0.7201 (p0) REVERT: A 705 MET cc_start: 0.8980 (mtm) cc_final: 0.8519 (mtp) REVERT: A 922 ARG cc_start: 0.8887 (pmt-80) cc_final: 0.8414 (pmt-80) REVERT: A 960 LYS cc_start: 0.9285 (mttp) cc_final: 0.9004 (mtmm) REVERT: A 1007 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7734 (mt-10) REVERT: B 64 ASN cc_start: 0.8700 (m-40) cc_final: 0.8089 (m-40) REVERT: B 86 LYS cc_start: 0.8957 (ttmm) cc_final: 0.8592 (mmtt) REVERT: C 473 MET cc_start: 0.2949 (tpp) cc_final: 0.2274 (tpt) REVERT: C 528 GLU cc_start: 0.8867 (tt0) cc_final: 0.8616 (tm-30) REVERT: C 598 ARG cc_start: 0.8885 (mmt-90) cc_final: 0.8343 (mmp80) REVERT: C 733 MET cc_start: 0.9474 (tpp) cc_final: 0.9178 (mmm) REVERT: C 737 MET cc_start: 0.8496 (tpt) cc_final: 0.7937 (tmm) REVERT: C 807 MET cc_start: 0.8578 (tmm) cc_final: 0.7916 (tmm) REVERT: C 947 LYS cc_start: 0.9569 (tttt) cc_final: 0.9188 (tptp) REVERT: D 218 PHE cc_start: 0.8684 (m-80) cc_final: 0.8430 (m-80) REVERT: D 306 GLN cc_start: 0.8799 (mp10) cc_final: 0.8282 (pp30) REVERT: D 324 LYS cc_start: 0.7978 (mmmt) cc_final: 0.7730 (mmmt) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1446 time to fit residues: 47.4570 Evaluate side-chains 150 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 24 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 79 optimal weight: 0.3980 chunk 74 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN C 930 GLN C 983 ASN D 195 HIS ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 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 = 0.3664 r_free = 0.3664 target = 0.083409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058246 restraints weight = 165614.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060611 restraints weight = 66291.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.062113 restraints weight = 37698.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.063076 restraints weight = 25981.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063688 restraints weight = 20322.016| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18016 Z= 0.142 Angle : 0.655 8.940 24750 Z= 0.348 Chirality : 0.042 0.195 2695 Planarity : 0.004 0.046 2857 Dihedral : 20.828 179.766 3231 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1923 helix: 0.32 (0.20), residues: 644 sheet: -0.91 (0.28), residues: 359 loop : -1.88 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 756 TYR 0.022 0.002 TYR C 500 PHE 0.021 0.001 PHE A 993 TRP 0.049 0.002 TRP A 915 HIS 0.006 0.001 HIS C 959 Details of bonding type rmsd covalent geometry : bond 0.00309 (18011) covalent geometry : angle 0.65521 (24750) hydrogen bonds : bond 0.04218 ( 721) hydrogen bonds : angle 5.02637 ( 2020) metal coordination : bond 0.00576 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.8013 (m) cc_final: 0.7569 (p) REVERT: A 570 ASP cc_start: 0.7555 (p0) cc_final: 0.7211 (p0) REVERT: A 705 MET cc_start: 0.9000 (mtm) cc_final: 0.8581 (mtp) REVERT: A 861 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8807 (ptpp) REVERT: A 891 LEU cc_start: 0.8735 (mt) cc_final: 0.8530 (mt) REVERT: A 922 ARG cc_start: 0.8780 (pmt-80) cc_final: 0.8216 (pmt-80) REVERT: A 960 LYS cc_start: 0.9373 (mttp) cc_final: 0.9085 (mtmm) REVERT: B 64 ASN cc_start: 0.8762 (m-40) cc_final: 0.8153 (t0) REVERT: B 86 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8561 (mmtt) REVERT: B 162 MET cc_start: 0.8731 (mpp) cc_final: 0.8418 (mtm) REVERT: C 473 MET cc_start: 0.2883 (tpp) cc_final: 0.2340 (tpt) REVERT: C 528 GLU cc_start: 0.8928 (tt0) cc_final: 0.8620 (tm-30) REVERT: C 582 LEU cc_start: 0.9532 (mm) cc_final: 0.9183 (mt) REVERT: C 598 ARG cc_start: 0.8816 (mmt-90) cc_final: 0.8365 (mmp80) REVERT: C 733 MET cc_start: 0.9431 (tpp) cc_final: 0.9118 (mmm) REVERT: C 737 MET cc_start: 0.8563 (tpt) cc_final: 0.8225 (tpp) REVERT: C 875 TYR cc_start: 0.7606 (t80) cc_final: 0.7266 (t80) REVERT: C 947 LYS cc_start: 0.9576 (tttt) cc_final: 0.9176 (tptp) REVERT: C 1008 ASP cc_start: 0.8041 (m-30) cc_final: 0.7727 (m-30) REVERT: C 1010 LEU cc_start: 0.9648 (tp) cc_final: 0.9425 (tp) REVERT: D 218 PHE cc_start: 0.8602 (m-80) cc_final: 0.8395 (m-80) REVERT: D 306 GLN cc_start: 0.8732 (mp10) cc_final: 0.8198 (pp30) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1496 time to fit residues: 50.4455 Evaluate side-chains 158 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 97 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 HIS C 930 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.084452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059355 restraints weight = 179101.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062290 restraints weight = 71559.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.063641 restraints weight = 35221.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.063896 restraints weight = 22530.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.064117 restraints weight = 22321.650| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18016 Z= 0.132 Angle : 0.647 9.077 24750 Z= 0.342 Chirality : 0.041 0.194 2695 Planarity : 0.004 0.049 2857 Dihedral : 20.723 179.762 3231 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1923 helix: 0.50 (0.21), residues: 644 sheet: -0.73 (0.28), residues: 356 loop : -1.80 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 878 TYR 0.021 0.001 TYR C 500 PHE 0.014 0.001 PHE A 479 TRP 0.047 0.002 TRP A 915 HIS 0.006 0.001 HIS C 964 Details of bonding type rmsd covalent geometry : bond 0.00292 (18011) covalent geometry : angle 0.64689 (24750) hydrogen bonds : bond 0.04065 ( 721) hydrogen bonds : angle 4.87004 ( 2020) metal coordination : bond 0.00239 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.8044 (m) cc_final: 0.7594 (p) REVERT: A 570 ASP cc_start: 0.7474 (p0) cc_final: 0.7108 (p0) REVERT: A 705 MET cc_start: 0.8902 (mtm) cc_final: 0.8413 (mtp) REVERT: A 861 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8822 (ptpp) REVERT: A 867 PRO cc_start: 0.8249 (Cg_exo) cc_final: 0.8045 (Cg_endo) REVERT: A 908 TYR cc_start: 0.8323 (t80) cc_final: 0.8029 (t80) REVERT: A 909 LEU cc_start: 0.8603 (pp) cc_final: 0.8390 (pp) REVERT: A 960 LYS cc_start: 0.9313 (mttp) cc_final: 0.9050 (mtmm) REVERT: B 64 ASN cc_start: 0.8781 (m-40) cc_final: 0.8150 (t0) REVERT: B 86 LYS cc_start: 0.8965 (ttmm) cc_final: 0.8598 (mmtt) REVERT: B 142 LEU cc_start: 0.9229 (pt) cc_final: 0.8626 (tt) REVERT: C 473 MET cc_start: 0.3443 (tpp) cc_final: 0.3070 (tpt) REVERT: C 598 ARG cc_start: 0.8889 (mmt-90) cc_final: 0.8414 (mmp80) REVERT: C 733 MET cc_start: 0.9386 (tpp) cc_final: 0.9058 (mmm) REVERT: C 737 MET cc_start: 0.8498 (tpt) cc_final: 0.8286 (tpp) REVERT: C 875 TYR cc_start: 0.7910 (t80) cc_final: 0.7467 (t80) REVERT: C 947 LYS cc_start: 0.9570 (tttt) cc_final: 0.9155 (tptp) REVERT: C 1010 LEU cc_start: 0.9659 (tp) cc_final: 0.9433 (tp) REVERT: D 218 PHE cc_start: 0.8650 (m-80) cc_final: 0.8407 (m-80) REVERT: D 306 GLN cc_start: 0.8792 (mp10) cc_final: 0.8205 (pp30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1399 time to fit residues: 47.5459 Evaluate side-chains 158 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 200 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 47 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 539 GLN C 930 GLN C 983 ASN D 173 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.084319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058838 restraints weight = 168892.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.061323 restraints weight = 66279.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.062841 restraints weight = 37222.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063820 restraints weight = 25601.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064358 restraints weight = 20084.564| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.6005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18016 Z= 0.130 Angle : 0.637 8.768 24750 Z= 0.337 Chirality : 0.041 0.191 2695 Planarity : 0.004 0.050 2857 Dihedral : 20.656 179.924 3231 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1923 helix: 0.63 (0.21), residues: 641 sheet: -0.74 (0.29), residues: 349 loop : -1.71 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.023 0.001 TYR B 90 PHE 0.013 0.001 PHE D 206 TRP 0.046 0.002 TRP A 915 HIS 0.006 0.001 HIS C 964 Details of bonding type rmsd covalent geometry : bond 0.00284 (18011) covalent geometry : angle 0.63667 (24750) hydrogen bonds : bond 0.03984 ( 721) hydrogen bonds : angle 4.80972 ( 2020) metal coordination : bond 0.00264 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3846 Ramachandran restraints generated. 1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.7998 (m) cc_final: 0.7528 (p) REVERT: A 570 ASP cc_start: 0.7487 (p0) cc_final: 0.7116 (p0) REVERT: A 647 MET cc_start: 0.8515 (mmm) cc_final: 0.7922 (mtt) REVERT: A 698 VAL cc_start: 0.9314 (t) cc_final: 0.8996 (p) REVERT: A 705 MET cc_start: 0.8754 (mtm) cc_final: 0.8404 (mtp) REVERT: A 861 LYS cc_start: 0.9050 (ttpp) cc_final: 0.8814 (ptpp) REVERT: A 867 PRO cc_start: 0.8241 (Cg_exo) cc_final: 0.8023 (Cg_endo) REVERT: A 908 TYR cc_start: 0.8237 (t80) cc_final: 0.7984 (t80) REVERT: A 960 LYS cc_start: 0.9325 (mttp) cc_final: 0.9054 (mtmm) REVERT: B 64 ASN cc_start: 0.8808 (m-40) cc_final: 0.8330 (m-40) REVERT: B 86 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8530 (mmtt) REVERT: B 142 LEU cc_start: 0.9190 (pt) cc_final: 0.8612 (tt) REVERT: C 473 MET cc_start: 0.3484 (tpp) cc_final: 0.3164 (tpt) REVERT: C 598 ARG cc_start: 0.8809 (mmt-90) cc_final: 0.8355 (mmp80) REVERT: C 733 MET cc_start: 0.9385 (tpp) cc_final: 0.9040 (mmm) REVERT: C 737 MET cc_start: 0.8392 (tpt) cc_final: 0.8085 (tmm) REVERT: C 807 MET cc_start: 0.8587 (tmm) cc_final: 0.8186 (tmm) REVERT: C 869 MET cc_start: 0.0335 (ttm) cc_final: -0.0054 (ttp) REVERT: C 875 TYR cc_start: 0.7779 (t80) cc_final: 0.7352 (t80) REVERT: C 947 LYS cc_start: 0.9576 (tttt) cc_final: 0.9161 (tptp) REVERT: C 1010 LEU cc_start: 0.9658 (tp) cc_final: 0.9405 (tp) REVERT: D 65 ASN cc_start: 0.8725 (p0) cc_final: 0.8521 (p0) REVERT: D 306 GLN cc_start: 0.8676 (mp10) cc_final: 0.8147 (pp30) outliers start: 1 outliers final: 0 residues processed: 215 average time/residue: 0.1409 time to fit residues: 46.6051 Evaluate side-chains 166 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 135 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.0170 chunk 11 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 ASN A 539 GLN C 930 GLN C 983 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 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 = 0.3678 r_free = 0.3678 target = 0.084076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059367 restraints weight = 136160.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.061601 restraints weight = 58970.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063007 restraints weight = 34676.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063890 restraints weight = 24493.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.064454 restraints weight = 19602.365| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 60 | |-----------------------------------------------------------------------------| r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18016 Z= 0.136 Angle : 0.636 8.577 24750 Z= 0.337 Chirality : 0.041 0.178 2695 Planarity : 0.004 0.050 2857 Dihedral : 20.618 179.876 3231 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.19), residues: 1923 helix: 0.69 (0.21), residues: 644 sheet: -0.77 (0.28), residues: 348 loop : -1.67 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.020 0.001 TYR C 500 PHE 0.030 0.001 PHE C 938 TRP 0.043 0.002 TRP A 915 HIS 0.006 0.001 HIS A 959 Details of bonding type rmsd covalent geometry : bond 0.00299 (18011) covalent geometry : angle 0.63635 (24750) hydrogen bonds : bond 0.03978 ( 721) hydrogen bonds : angle 4.75828 ( 2020) metal coordination : bond 0.00289 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.78 seconds wall clock time: 66 minutes 36.02 seconds (3996.02 seconds total)