Starting phenix.real_space_refine on Sun Oct 25 15:06:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.cif" model { file = "/net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbx_7853/10_2026/6dbx_7853.map" } 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-2.3rc1-6221/lib/python3.11/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: 4.69, per 1000 atoms: 0.27 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.05 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: 3.74 Time building geometry restraints manager: 2.30 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=" C3' DC E 24 " pdb=" C2' DC E 24 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.65e+01 bond pdb=" C3' DA E 36 " pdb=" C2' DA E 36 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.65e+01 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=" C1' DC F 18 " pdb=" N1 DC F 18 " ideal model delta sigma weight residual 1.468 1.523 -0.055 1.40e-02 5.10e+03 1.55e+01 bond pdb=" C1' DT F 31 " pdb=" N1 DT F 31 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.40e+01 ... (remaining 18006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 24383 2.78 - 5.56: 331 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=" O4' DA E 41 " pdb=" C4' DA E 41 " pdb=" C3' DA E 41 " ideal model delta sigma weight residual 106.00 102.86 3.14 6.00e-01 2.78e+00 2.73e+01 angle pdb=" O4' DG F 38 " pdb=" C1' DG F 38 " pdb=" N9 DG F 38 " ideal model delta sigma weight residual 108.00 111.63 -3.63 7.00e-01 2.04e+00 2.69e+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 ... (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 - 0.039: 1700 0.039 - 0.078: 717 0.078 - 0.117: 211 0.117 - 0.156: 58 0.156 - 0.196: 9 Chirality restraints: 2695 Sorted by residual: chirality pdb=" C3' DA E 18 " pdb=" C4' DA E 18 " pdb=" O3' DA E 18 " pdb=" C2' DA E 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.57e-01 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 ... (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: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.410 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 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 : 0.007 0.327 18016 Z= 0.395 Angle : 0.889 13.889 24750 Z= 0.583 Chirality : 0.048 0.196 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/Z covalent geometry : bond 0.00540 / 0.37 (18011) covalent geometry : angle 0.88851 / 0.58 (24750) hydrogen bonds : bond 0.19982 / 13.47 ( 721) hydrogen bonds : angle 8.08323 / 5.62 ( 2020) metal coordination : bond 0.24554 / 23.82 ( 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 : 0.630 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 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: 0.6906 (mp) REVERT: A 869 MET cc_start: 0.8645 (ptm) cc_final: 0.8221 (tmm) REVERT: A 891 LEU cc_start: 0.8933 (mt) cc_final: 0.8665 (mt) REVERT: A 1007 GLU cc_start: 0.9492 (tt0) cc_final: 0.9156 (mt-10) REVERT: B 64 ASN cc_start: 0.9022 (m-40) cc_final: 0.8394 (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: 0.9025 (ttpp) REVERT: C 907 LEU cc_start: 0.8604 (mt) cc_final: 0.8000 (mm) REVERT: D 306 GLN cc_start: 0.8592 (mp10) cc_final: 0.8089 (pp30) outliers start: 0 outliers final: 0 residues processed: 357 average time/residue: 0.1453 time to fit residues: 77.4061 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 : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [98, 194, 107, 10, 66, 130, 124, 103, 200, 77, 122] chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 964 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS B 100 ASN B 170 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN C 959 HIS C 983 ASN C1012 HIS 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061053 restraints weight = 151666.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063286 restraints weight = 66283.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064700 restraints weight = 39263.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.065595 restraints weight = 27755.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066156 restraints weight = 22204.706| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- 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: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 28 (41 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.768 18016 Z= 0.280 Angle : 0.824 9.305 24750 Z= 0.447 Chirality : 0.051 0.328 2695 Planarity : 0.006 0.069 2857 Dihedral : 21.516 178.892 3231 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.34 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: -3.44 (0.16), residues: 1923 helix: -1.55 (0.18), residues: 630 sheet: -2.02 (0.25), residues: 366 loop : -2.93 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 922 TYR 0.030 0.003 TYR C 500 PHE 0.033 0.002 PHE C 993 TRP 0.021 0.002 TRP A 782 HIS 0.013 0.002 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (18011) covalent geometry : angle 0.82442 / 0.45 (24750) hydrogen bonds : bond 0.06246 / 4.24 ( 721) hydrogen bonds : angle 6.32301 / 4.40 ( 2020) metal coordination : bond 0.34349 / 42.39 ( 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 297 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 CYS cc_start: 0.8974 (m) cc_final: 0.8558 (m) REVERT: A 497 CYS cc_start: 0.7853 (m) cc_final: 0.7602 (m) REVERT: A 539 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 570 ASP cc_start: 0.7454 (p0) cc_final: 0.7061 (p0) REVERT: A 647 MET cc_start: 0.8990 (mmm) cc_final: 0.8599 (mmm) REVERT: A 867 PRO cc_start: 0.8392 (Cg_exo) cc_final: 0.8067 (Cg_endo) REVERT: A 919 CYS cc_start: 0.7910 (t) cc_final: 0.7536 (t) REVERT: A 960 LYS cc_start: 0.9079 (mttp) cc_final: 0.8823 (mtmm) REVERT: A 1007 GLU cc_start: 0.8731 (tt0) cc_final: 0.8090 (mt-10) REVERT: B 23 ASP cc_start: 0.7451 (t0) cc_final: 0.7248 (t0) REVERT: B 64 ASN cc_start: 0.8831 (m-40) cc_final: 0.8184 (m-40) REVERT: B 86 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8438 (mmtt) REVERT: C 474 MET cc_start: 0.2589 (mmp) cc_final: 0.2348 (mmp) REVERT: C 517 GLN cc_start: 0.8795 (mm110) cc_final: 0.8552 (mp10) REVERT: C 524 ASN cc_start: 0.8971 (m-40) cc_final: 0.8510 (m-40) REVERT: C 598 ARG cc_start: 0.8787 (mmt-90) cc_final: 0.8340 (mmp80) REVERT: C 677 LEU cc_start: 0.9249 (tt) cc_final: 0.9027 (tp) REVERT: C 807 MET cc_start: 0.8384 (tmm) cc_final: 0.7965 (tmm) REVERT: C 906 ASP cc_start: 0.9210 (t70) cc_final: 0.8677 (m-30) REVERT: D 91 LEU cc_start: 0.9091 (mp) cc_final: 0.8749 (mp) REVERT: D 306 GLN cc_start: 0.8811 (mp10) cc_final: 0.8266 (pp30) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1500 time to fit residues: 66.4277 Evaluate side-chains 193 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [59, 14, 123, 86, 199, 118, 145, 158, 60, 130, 185] chunk 59 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 199 optimal weight: 30.0000 chunk 118 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 60 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 937 GLN A1013 HIS ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 775 ASN ** C 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN C 934 ASN D 64 ASN D 100 ASN ** 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 = 0.3699 r_free = 0.3699 target = 0.085004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.059989 restraints weight = 176531.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.062388 restraints weight = 71323.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063894 restraints weight = 40731.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.064840 restraints weight = 28168.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065457 restraints weight = 22074.297| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 55 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (15 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18016 Z= 0.164 Angle : 0.733 10.064 24750 Z= 0.397 Chirality : 0.047 0.325 2695 Planarity : 0.005 0.051 2857 Dihedral : 21.438 179.306 3231 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: -2.62 (0.17), residues: 1923 helix: -0.66 (0.19), residues: 632 sheet: -1.78 (0.25), residues: 374 loop : -2.49 (0.18), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 999 TYR 0.026 0.002 TYR C 500 PHE 0.030 0.002 PHE C 938 TRP 0.024 0.002 TRP A 782 HIS 0.014 0.001 HIS C 964 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (18011) covalent geometry : angle 0.73297 / 0.40 (24750) hydrogen bonds : bond 0.05243 / 3.56 ( 721) hydrogen bonds : angle 5.79424 / 4.02 ( 2020) metal coordination : bond 0.03168 / 3.52 ( 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 262 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 0.643 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 497 CYS cc_start: 0.7971 (m) cc_final: 0.7678 (p) REVERT: A 539 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 570 ASP cc_start: 0.7546 (p0) cc_final: 0.7182 (p0) REVERT: A 647 MET cc_start: 0.9048 (mmm) cc_final: 0.8422 (mmm) REVERT: A 869 MET cc_start: 0.7624 (ppp) cc_final: 0.5885 (ppp) REVERT: A 891 LEU cc_start: 0.8679 (mt) cc_final: 0.8425 (mt) REVERT: A 905 MET cc_start: 0.8703 (tpp) cc_final: 0.8437 (tpt) REVERT: A 906 ASP cc_start: 0.8825 (t70) cc_final: 0.8175 (t70) REVERT: A 960 LYS cc_start: 0.9131 (mttp) cc_final: 0.8887 (mtmm) REVERT: A 1007 GLU cc_start: 0.8800 (tt0) cc_final: 0.8329 (mt-10) REVERT: B 64 ASN cc_start: 0.8783 (m-40) cc_final: 0.8133 (m-40) REVERT: B 69 LEU cc_start: 0.9283 (tp) cc_final: 0.9041 (tp) REVERT: B 86 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8441 (mmtt) REVERT: C 473 MET cc_start: 0.4110 (tpp) cc_final: 0.3707 (tpt) REVERT: C 517 GLN cc_start: 0.8821 (mm110) cc_final: 0.8341 (mp10) REVERT: C 598 ARG cc_start: 0.8773 (mmt-90) cc_final: 0.8355 (mmp80) REVERT: C 807 MET cc_start: 0.8464 (tmm) cc_final: 0.7759 (tmm) REVERT: C 906 ASP cc_start: 0.9200 (t70) cc_final: 0.8666 (m-30) REVERT: D 145 ILE cc_start: 0.9364 (pt) cc_final: 0.9117 (mm) REVERT: D 306 GLN cc_start: 0.8886 (mp10) cc_final: 0.8316 (pp30) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.1283 time to fit residues: 51.6212 Evaluate side-chains 180 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [144, 52, 89, 137, 78, 30, 159, 108, 177, 0, 170] chunk 144 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 177 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 170 optimal weight: 7.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 810 GLN C 930 GLN C1013 HIS D 278 GLN ** 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 = 0.3683 r_free = 0.3683 target = 0.084103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.059557 restraints weight = 155060.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.062499 restraints weight = 69240.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.063283 restraints weight = 34928.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.063601 restraints weight = 24320.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.063766 restraints weight = 24593.786| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (16 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18016 Z= 0.181 Angle : 0.727 16.750 24750 Z= 0.389 Chirality : 0.046 0.334 2695 Planarity : 0.005 0.049 2857 Dihedral : 21.438 179.875 3231 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.73 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % 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: -2.23 (0.18), residues: 1923 helix: -0.38 (0.20), residues: 642 sheet: -1.48 (0.25), residues: 371 loop : -2.29 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 675 TYR 0.024 0.002 TYR C 500 PHE 0.025 0.002 PHE C 938 TRP 0.014 0.002 TRP C 915 HIS 0.008 0.001 HIS B 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (18011) covalent geometry : angle 0.72715 / 0.39 (24750) hydrogen bonds : bond 0.05008 / 3.40 ( 721) hydrogen bonds : angle 5.52504 / 3.85 ( 2020) metal coordination : bond 0.00699 / 0.74 ( 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: 0 poor density : 225 time to evaluate : 0.627 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: A 497 CYS cc_start: 0.7929 (m) cc_final: 0.7602 (p) REVERT: A 570 ASP cc_start: 0.7539 (p0) cc_final: 0.7163 (p0) REVERT: A 647 MET cc_start: 0.8978 (mmm) cc_final: 0.8291 (mmm) REVERT: A 891 LEU cc_start: 0.8743 (mt) cc_final: 0.8533 (mt) REVERT: A 909 LEU cc_start: 0.8614 (pp) cc_final: 0.8377 (pp) REVERT: A 960 LYS cc_start: 0.9222 (mttp) cc_final: 0.8950 (mtmm) REVERT: B 64 ASN cc_start: 0.8799 (m-40) cc_final: 0.8187 (m-40) REVERT: B 69 LEU cc_start: 0.9236 (tp) cc_final: 0.9029 (tp) REVERT: B 86 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8525 (mmtt) REVERT: C 473 MET cc_start: 0.3735 (tpp) cc_final: 0.3220 (tpt) REVERT: C 517 GLN cc_start: 0.8790 (mm110) cc_final: 0.8389 (mp10) REVERT: C 598 ARG cc_start: 0.8878 (mmt-90) cc_final: 0.8445 (mmp80) REVERT: C 606 MET cc_start: 0.7561 (ppp) cc_final: 0.7354 (ppp) REVERT: C 617 GLU cc_start: 0.8490 (pt0) cc_final: 0.8282 (pt0) REVERT: C 704 MET cc_start: 0.8685 (mmm) cc_final: 0.8449 (tpp) REVERT: C 737 MET cc_start: 0.7794 (tmm) cc_final: 0.7491 (tmm) REVERT: C 906 ASP cc_start: 0.9218 (t70) cc_final: 0.8689 (m-30) REVERT: D 218 PHE cc_start: 0.8741 (m-80) cc_final: 0.8487 (m-80) REVERT: D 285 MET cc_start: 0.7815 (mmp) cc_final: 0.7398 (mmt) REVERT: D 306 GLN cc_start: 0.8831 (mp10) cc_final: 0.8277 (pp30) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1199 time to fit residues: 42.3711 Evaluate side-chains 170 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [26, 110, 197, 89, 133, 44, 47, 193, 10, 200, 98] chunk 26 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 197 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 193 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 930 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.083144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058319 restraints weight = 137964.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060446 restraints weight = 61306.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.061782 restraints weight = 36785.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062636 restraints weight = 26328.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.063180 restraints weight = 21201.036| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (14 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18016 Z= 0.197 Angle : 0.723 9.996 24750 Z= 0.388 Chirality : 0.047 0.340 2695 Planarity : 0.005 0.055 2857 Dihedral : 21.386 179.972 3231 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.51 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: -2.10 (0.18), residues: 1923 helix: -0.29 (0.20), residues: 641 sheet: -1.40 (0.25), residues: 374 loop : -2.20 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 159 TYR 0.024 0.002 TYR C 500 PHE 0.028 0.002 PHE D 206 TRP 0.015 0.002 TRP A 782 HIS 0.006 0.001 HIS A 534 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (18011) covalent geometry : angle 0.72269 / 0.39 (24750) hydrogen bonds : bond 0.04894 / 3.32 ( 721) hydrogen bonds : angle 5.48277 / 3.82 ( 2020) metal coordination : bond 0.00562 / 0.52 ( 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 : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.7852 (m) cc_final: 0.7512 (p) REVERT: A 570 ASP cc_start: 0.7492 (p0) cc_final: 0.7159 (p0) REVERT: A 647 MET cc_start: 0.9100 (mmm) cc_final: 0.8891 (mmm) REVERT: A 825 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8270 (tp30) REVERT: A 872 ASN cc_start: 0.7773 (p0) cc_final: 0.7566 (p0) REVERT: A 950 TYR cc_start: 0.8301 (m-10) cc_final: 0.7687 (m-10) REVERT: A 960 LYS cc_start: 0.9236 (mttp) cc_final: 0.8938 (mtmm) REVERT: B 64 ASN cc_start: 0.8795 (m-40) cc_final: 0.8146 (m-40) REVERT: B 69 LEU cc_start: 0.9296 (tp) cc_final: 0.9033 (tp) REVERT: B 86 LYS cc_start: 0.8880 (ttmm) cc_final: 0.8528 (mmtt) REVERT: C 473 MET cc_start: 0.3124 (tpp) cc_final: 0.2480 (tpt) REVERT: C 517 GLN cc_start: 0.8921 (mm110) cc_final: 0.8389 (mp10) REVERT: C 598 ARG cc_start: 0.8799 (mmt-90) cc_final: 0.8348 (mmp80) REVERT: C 617 GLU cc_start: 0.8580 (pt0) cc_final: 0.8298 (pt0) REVERT: C 700 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8448 (tt0) REVERT: C 704 MET cc_start: 0.8705 (mmm) cc_final: 0.8469 (tpp) REVERT: C 906 ASP cc_start: 0.9224 (t70) cc_final: 0.8661 (m-30) REVERT: D 93 HIS cc_start: 0.8388 (t70) cc_final: 0.7596 (t70) REVERT: D 218 PHE cc_start: 0.8579 (m-80) cc_final: 0.8370 (m-80) REVERT: D 306 GLN cc_start: 0.8752 (mp10) cc_final: 0.8259 (pp30) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1251 time to fit residues: 43.4930 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 : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [6, 58, 89, 132, 113, 52, 154, 121, 146, 144, 104] chunk 6 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 121 optimal weight: 0.0010 chunk 146 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 539 GLN A 997 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.084006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.058513 restraints weight = 169045.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060863 restraints weight = 67851.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062343 restraints weight = 38824.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063254 restraints weight = 26984.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.063770 restraints weight = 21473.593| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 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 = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18016 Z= 0.150 Angle : 0.681 8.694 24750 Z= 0.366 Chirality : 0.045 0.341 2695 Planarity : 0.004 0.049 2857 Dihedral : 21.301 179.776 3231 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.52 % Favored : 94.38 % Rotamer: Outliers : 0.06 % Allowed : 1.94 % Favored : 98.00 % 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: -1.83 (0.18), residues: 1923 helix: -0.02 (0.20), residues: 642 sheet: -1.23 (0.26), residues: 372 loop : -2.08 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 523 TYR 0.021 0.002 TYR C 500 PHE 0.020 0.001 PHE D 206 TRP 0.014 0.001 TRP A 915 HIS 0.005 0.001 HIS C 964 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (18011) covalent geometry : angle 0.68051 / 0.37 (24750) hydrogen bonds : bond 0.04602 / 3.14 ( 721) hydrogen bonds : angle 5.25098 / 3.67 ( 2020) metal coordination : bond 0.00385 / 0.32 ( 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 232 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 0.532 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: 0.8102 (m) cc_final: 0.7601 (p) REVERT: A 570 ASP cc_start: 0.7549 (p0) cc_final: 0.7203 (p0) REVERT: A 698 VAL cc_start: 0.9398 (t) cc_final: 0.9192 (p) REVERT: A 872 ASN cc_start: 0.7772 (p0) cc_final: 0.7558 (p0) REVERT: A 891 LEU cc_start: 0.8699 (mt) cc_final: 0.8497 (mt) REVERT: A 950 TYR cc_start: 0.8314 (m-10) cc_final: 0.7817 (m-10) REVERT: A 960 LYS cc_start: 0.9240 (mttp) cc_final: 0.8967 (mtmm) REVERT: B 64 ASN cc_start: 0.8809 (m-40) cc_final: 0.8162 (m-40) REVERT: B 86 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8615 (mmtt) REVERT: B 127 LYS cc_start: 0.9203 (tppt) cc_final: 0.8715 (tptt) REVERT: B 174 SER cc_start: 0.9019 (t) cc_final: 0.8776 (p) REVERT: C 473 MET cc_start: 0.3089 (tpp) cc_final: 0.2464 (tpt) REVERT: C 517 GLN cc_start: 0.8921 (mm110) cc_final: 0.8250 (mp10) REVERT: C 594 MET cc_start: 0.9537 (mmp) cc_final: 0.8829 (mmp) REVERT: C 598 ARG cc_start: 0.8817 (mmt-90) cc_final: 0.8355 (mmp80) REVERT: C 617 GLU cc_start: 0.8524 (pt0) cc_final: 0.8208 (pt0) REVERT: C 700 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8525 (tt0) REVERT: C 737 MET cc_start: 0.8050 (tmm) cc_final: 0.6989 (tmm) REVERT: C 906 ASP cc_start: 0.9225 (t70) cc_final: 0.8672 (m-30) REVERT: C 947 LYS cc_start: 0.9509 (tttt) cc_final: 0.9180 (tptt) REVERT: C 1010 LEU cc_start: 0.9592 (tp) cc_final: 0.9390 (tp) REVERT: D 93 HIS cc_start: 0.8410 (t70) cc_final: 0.7654 (t70) REVERT: D 306 GLN cc_start: 0.8745 (mp10) cc_final: 0.8200 (pp30) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1300 time to fit residues: 45.5982 Evaluate side-chains 169 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [195, 102, 77, 110, 82, 149, 156, 25, 140, 63, 106] chunk 195 optimal weight: 50.0000 chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.083421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.058138 restraints weight = 156031.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.060386 restraints weight = 65043.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.061793 restraints weight = 37916.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062696 restraints weight = 26707.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.063267 restraints weight = 21260.561| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 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 = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18016 Z= 0.163 Angle : 0.680 8.512 24750 Z= 0.364 Chirality : 0.045 0.344 2695 Planarity : 0.004 0.062 2857 Dihedral : 21.215 179.908 3231 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: -1.71 (0.18), residues: 1923 helix: 0.07 (0.20), residues: 636 sheet: -1.13 (0.27), residues: 370 loop : -2.02 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 949 TYR 0.022 0.002 TYR C 500 PHE 0.017 0.001 PHE D 206 TRP 0.015 0.002 TRP A 915 HIS 0.006 0.001 HIS C 964 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (18011) covalent geometry : angle 0.67968 / 0.36 (24750) hydrogen bonds : bond 0.04593 / 3.10 ( 721) hydrogen bonds : angle 5.20368 / 3.64 ( 2020) metal coordination : bond 0.00343 / 0.25 ( 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 218 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.506 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: 0.7971 (m) cc_final: 0.7570 (p) REVERT: A 570 ASP cc_start: 0.7575 (p0) cc_final: 0.7235 (p0) REVERT: A 960 LYS cc_start: 0.9282 (mttp) cc_final: 0.8987 (mtmm) REVERT: B 64 ASN cc_start: 0.8811 (m-40) cc_final: 0.8130 (m-40) REVERT: B 86 LYS cc_start: 0.8937 (ttmm) cc_final: 0.8640 (mmtt) REVERT: B 127 LYS cc_start: 0.9213 (tppt) cc_final: 0.8695 (tptt) REVERT: B 174 SER cc_start: 0.9029 (t) cc_final: 0.8742 (p) REVERT: C 473 MET cc_start: 0.3091 (tpp) cc_final: 0.2420 (tpt) REVERT: C 517 GLN cc_start: 0.8949 (mm110) cc_final: 0.8355 (mp10) REVERT: C 598 ARG cc_start: 0.8829 (mmt-90) cc_final: 0.8338 (mmp80) REVERT: C 617 GLU cc_start: 0.8584 (pt0) cc_final: 0.8234 (pt0) REVERT: C 906 ASP cc_start: 0.9286 (t70) cc_final: 0.8729 (m-30) REVERT: C 1010 LEU cc_start: 0.9602 (tp) cc_final: 0.9396 (tp) REVERT: D 218 PHE cc_start: 0.8590 (m-80) cc_final: 0.8361 (m-80) REVERT: D 306 GLN cc_start: 0.8735 (mp10) cc_final: 0.8191 (pp30) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1312 time to fit residues: 44.1439 Evaluate side-chains 169 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [24, 165, 176, 1, 79, 74, 81, 14, 152, 38, 148] chunk 24 optimal weight: 10.0000 chunk 165 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 152 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 462 ASN A 775 ASN A 934 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 535 GLN ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN C 839 GLN C 936 GLN ** C 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.078392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053344 restraints weight = 163425.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055438 restraints weight = 69018.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056773 restraints weight = 40745.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057620 restraints weight = 28827.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058136 restraints weight = 23040.534| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 58 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.5170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.101 18016 Z= 0.396 Angle : 0.926 11.832 24750 Z= 0.486 Chirality : 0.051 0.362 2695 Planarity : 0.006 0.076 2857 Dihedral : 21.388 178.831 3231 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.33 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.06 % 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: -2.37 (0.18), residues: 1923 helix: -0.65 (0.19), residues: 645 sheet: -1.45 (0.26), residues: 357 loop : -2.29 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 232 TYR 0.030 0.003 TYR C 500 PHE 0.028 0.003 PHE A 946 TRP 0.040 0.003 TRP A 782 HIS 0.013 0.003 HIS C 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.40 (18011) covalent geometry : angle 0.92561 / 0.49 (24750) hydrogen bonds : bond 0.05881 / 3.95 ( 721) hydrogen bonds : angle 5.81418 / 4.08 ( 2020) metal coordination : bond 0.01161 / 0.99 ( 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 189 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.8125 (m) cc_final: 0.7740 (p) REVERT: A 570 ASP cc_start: 0.7688 (p0) cc_final: 0.7306 (p0) REVERT: A 594 MET cc_start: 0.9378 (mmt) cc_final: 0.9145 (mmp) REVERT: B 64 ASN cc_start: 0.8571 (m-40) cc_final: 0.8067 (m-40) REVERT: B 86 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8752 (mmtt) REVERT: B 189 PHE cc_start: 0.8442 (m-80) cc_final: 0.8146 (m-80) REVERT: C 473 MET cc_start: 0.3197 (tpp) cc_final: 0.2432 (tpt) REVERT: C 528 GLU cc_start: 0.8941 (tt0) cc_final: 0.8720 (tm-30) REVERT: C 598 ARG cc_start: 0.8860 (mmt-90) cc_final: 0.8362 (mmp80) REVERT: C 617 GLU cc_start: 0.8876 (pt0) cc_final: 0.8231 (pt0) REVERT: C 807 MET cc_start: 0.8866 (tmm) cc_final: 0.8480 (tmm) REVERT: C 1010 LEU cc_start: 0.9657 (tp) cc_final: 0.9437 (tp) REVERT: D 272 ILE cc_start: 0.8250 (tp) cc_final: 0.8032 (tp) REVERT: D 306 GLN cc_start: 0.8766 (mp10) cc_final: 0.8276 (pp30) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1324 time to fit residues: 38.2877 Evaluate side-chains 147 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [97, 38, 140, 8, 43, 23, 86, 15, 12, 30, 17] chunk 97 optimal weight: 0.0020 chunk 38 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN ** D 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.056976 restraints weight = 177028.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059309 restraints weight = 70513.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.060792 restraints weight = 40197.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061726 restraints weight = 27820.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062324 restraints weight = 21915.920| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 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 = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18016 Z= 0.147 Angle : 0.717 8.529 24750 Z= 0.384 Chirality : 0.046 0.347 2695 Planarity : 0.005 0.047 2857 Dihedral : 21.221 179.869 3231 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.82 (0.18), residues: 1923 helix: -0.07 (0.20), residues: 639 sheet: -1.18 (0.27), residues: 353 loop : -2.05 (0.19), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 167 TYR 0.023 0.002 TYR C 500 PHE 0.030 0.002 PHE A 993 TRP 0.035 0.002 TRP A 915 HIS 0.007 0.001 HIS C 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (18011) covalent geometry : angle 0.71688 / 0.38 (24750) hydrogen bonds : bond 0.04626 / 3.17 ( 721) hydrogen bonds : angle 5.38704 / 3.76 ( 2020) metal coordination : bond 0.00425 / 0.26 ( 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 214 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.7963 (m) cc_final: 0.7508 (p) REVERT: A 570 ASP cc_start: 0.7562 (p0) cc_final: 0.7207 (p0) REVERT: A 647 MET cc_start: 0.8519 (mmm) cc_final: 0.7939 (mtt) REVERT: A 891 LEU cc_start: 0.8685 (mt) cc_final: 0.8469 (mt) REVERT: A 960 LYS cc_start: 0.9321 (mttp) cc_final: 0.8973 (mtmm) REVERT: B 1 MET cc_start: 0.6007 (mpp) cc_final: 0.5783 (mpp) REVERT: B 64 ASN cc_start: 0.8700 (m-40) cc_final: 0.8100 (m-40) REVERT: B 86 LYS cc_start: 0.8891 (ttmm) cc_final: 0.8608 (mmtt) REVERT: B 174 SER cc_start: 0.9032 (t) cc_final: 0.8824 (t) REVERT: B 189 PHE cc_start: 0.8411 (m-80) cc_final: 0.8131 (m-80) REVERT: C 473 MET cc_start: 0.3266 (tpp) cc_final: 0.2605 (tpt) REVERT: C 528 GLU cc_start: 0.8926 (tt0) cc_final: 0.8608 (tm-30) REVERT: C 594 MET cc_start: 0.9476 (mmp) cc_final: 0.8702 (mmp) REVERT: C 598 ARG cc_start: 0.8809 (mmt-90) cc_final: 0.8261 (mmp80) REVERT: C 617 GLU cc_start: 0.8794 (pt0) cc_final: 0.8309 (pt0) REVERT: C 875 TYR cc_start: 0.7854 (t80) cc_final: 0.7399 (t80) REVERT: C 947 LYS cc_start: 0.9603 (tttt) cc_final: 0.9223 (tptp) REVERT: C 1010 LEU cc_start: 0.9671 (tp) cc_final: 0.9413 (tp) REVERT: D 218 PHE cc_start: 0.8606 (m-80) cc_final: 0.8378 (m-80) REVERT: D 306 GLN cc_start: 0.8751 (mp10) cc_final: 0.8179 (pp30) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1329 time to fit residues: 43.7911 Evaluate side-chains 160 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [200, 158, 153, 96, 47, 48, 84, 76, 170, 60, 36] chunk 200 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 170 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 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 = 0.3623 r_free = 0.3623 target = 0.081361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055799 restraints weight = 165856.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058087 restraints weight = 67011.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059551 restraints weight = 38576.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060472 restraints weight = 26841.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061051 restraints weight = 21275.910| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 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 = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 18016 Z= 0.187 Angle : 0.717 8.349 24750 Z= 0.381 Chirality : 0.046 0.354 2695 Planarity : 0.005 0.049 2857 Dihedral : 21.191 179.488 3231 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.76 (0.18), residues: 1923 helix: -0.05 (0.20), residues: 643 sheet: -1.07 (0.27), residues: 354 loop : -2.04 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 795 TYR 0.027 0.002 TYR C 500 PHE 0.022 0.002 PHE C 938 TRP 0.035 0.002 TRP A 915 HIS 0.009 0.001 HIS C 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (18011) covalent geometry : angle 0.71676 / 0.38 (24750) hydrogen bonds : bond 0.04775 / 3.21 ( 721) hydrogen bonds : angle 5.40007 / 3.77 ( 2020) metal coordination : bond 0.00508 / 0.42 ( 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 203 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 497 CYS cc_start: 0.8132 (m) cc_final: 0.7539 (p) REVERT: A 570 ASP cc_start: 0.7598 (p0) cc_final: 0.7240 (p0) REVERT: A 647 MET cc_start: 0.8569 (mmm) cc_final: 0.7956 (mtt) REVERT: A 709 LEU cc_start: 0.8753 (tp) cc_final: 0.8133 (tp) REVERT: A 891 LEU cc_start: 0.8771 (mt) cc_final: 0.8548 (mt) REVERT: A 960 LYS cc_start: 0.9308 (mttp) cc_final: 0.8999 (mtmm) REVERT: B 1 MET cc_start: 0.6154 (mpp) cc_final: 0.5874 (mpp) REVERT: B 64 ASN cc_start: 0.8716 (m-40) cc_final: 0.8097 (m-40) REVERT: B 86 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8641 (mmtt) REVERT: B 174 SER cc_start: 0.9020 (t) cc_final: 0.8803 (t) REVERT: B 189 PHE cc_start: 0.8464 (m-80) cc_final: 0.8169 (m-80) REVERT: C 473 MET cc_start: 0.3277 (tpp) cc_final: 0.2620 (tpt) REVERT: C 528 GLU cc_start: 0.8959 (tt0) cc_final: 0.8653 (tm-30) REVERT: C 592 ASP cc_start: 0.8026 (p0) cc_final: 0.7538 (p0) REVERT: C 594 MET cc_start: 0.9458 (mmp) cc_final: 0.8723 (mmp) REVERT: C 598 ARG cc_start: 0.8851 (mmt-90) cc_final: 0.8291 (mmp80) REVERT: C 617 GLU cc_start: 0.8872 (pt0) cc_final: 0.8193 (pt0) REVERT: C 733 MET cc_start: 0.9345 (mmm) cc_final: 0.9084 (tpp) REVERT: C 875 TYR cc_start: 0.7854 (t80) cc_final: 0.7314 (t80) REVERT: C 1008 ASP cc_start: 0.7822 (m-30) cc_final: 0.7597 (m-30) REVERT: D 218 PHE cc_start: 0.8525 (m-80) cc_final: 0.8323 (m-80) REVERT: D 272 ILE cc_start: 0.8397 (tp) cc_final: 0.8165 (tp) REVERT: D 285 MET cc_start: 0.7482 (mmt) cc_final: 0.7194 (tpp) REVERT: D 306 GLN cc_start: 0.8758 (mp10) cc_final: 0.8193 (pp30) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1288 time to fit residues: 40.1164 Evaluate side-chains 155 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: [135, 180, 31, 20, 37, 11, 132, 167, 160, 184, 176] chunk 135 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 11 optimal weight: 0.0000 chunk 132 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 687 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 839 GLN C 930 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057955 restraints weight = 132403.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060112 restraints weight = 57949.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.061505 restraints weight = 34567.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062375 restraints weight = 24558.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062939 restraints weight = 19666.321| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 59 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18016 Z= 0.137 Angle : 0.701 8.301 24750 Z= 0.372 Chirality : 0.046 0.349 2695 Planarity : 0.004 0.050 2857 Dihedral : 21.108 179.987 3231 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.53 (0.19), residues: 1923 helix: 0.14 (0.20), residues: 640 sheet: -0.94 (0.28), residues: 357 loop : -1.88 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 735 TYR 0.029 0.002 TYR A 908 PHE 0.026 0.002 PHE C 938 TRP 0.028 0.002 TRP A 915 HIS 0.006 0.001 HIS C 959 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (18011) covalent geometry : angle 0.70081 / 0.37 (24750) hydrogen bonds : bond 0.04420 / 2.98 ( 721) hydrogen bonds : angle 5.27473 / 3.69 ( 2020) metal coordination : bond 0.00410 / 0.26 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3670.39 seconds wall clock time: 63 minutes 55.30 seconds (3835.30 seconds total)