Starting phenix.real_space_refine on Tue Jun 17 09:27:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dbt_7849/06_2025/6dbt_7849_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dbt_7849/06_2025/6dbt_7849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dbt_7849/06_2025/6dbt_7849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dbt_7849/06_2025/6dbt_7849.map" model { file = "/net/cci-nas-00/data/ceres_data/6dbt_7849/06_2025/6dbt_7849_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dbt_7849/06_2025/6dbt_7849_neut.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 222 5.49 5 S 112 5.16 5 C 11800 2.51 5 N 3553 2.21 5 O 4203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19896 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4955 Classifications: {'peptide': 614} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 588} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 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: 4956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4956 Classifications: {'peptide': 614} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1023 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "F" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1027 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "G" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1245 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "H" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1256 Classifications: {'DNA': 61} Link IDs: {'rna3p': 60} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2636 SG CYS A 749 106.665 99.076 96.537 1.00123.70 S ATOM 2657 SG CYS A 752 108.556 101.879 97.372 1.00227.41 S ATOM 10306 SG CYS C 749 47.965 32.858 95.607 1.00 60.43 S Residues with excluded nonbonded symmetry interactions: 26 residue: pdb=" P DA E 39 " occ=0.90 ... (19 atoms not shown) pdb=" C4 DA E 39 " occ=0.90 residue: pdb=" P DA E 40 " occ=0.91 ... (19 atoms not shown) pdb=" C4 DA E 40 " occ=0.91 residue: pdb=" P DA E 41 " occ=0.97 ... (19 atoms not shown) pdb=" C4 DA E 41 " occ=0.97 residue: pdb=" P DA E 42 " occ=0.92 ... (19 atoms not shown) pdb=" C4 DA E 42 " occ=0.92 residue: pdb=" P DC E 44 " occ=0.84 ... (17 atoms not shown) pdb=" C6 DC E 44 " occ=0.84 residue: pdb=" P DG F 7 " occ=0.73 ... (20 atoms not shown) pdb=" C4 DG F 7 " occ=0.73 residue: pdb=" P DG F 8 " occ=0.76 ... (20 atoms not shown) pdb=" C4 DG F 8 " occ=0.76 residue: pdb=" P DT F 9 " occ=0.82 ... (18 atoms not shown) pdb=" C6 DT F 9 " occ=0.82 residue: pdb=" P DT F 10 " occ=0.91 ... (18 atoms not shown) pdb=" C6 DT F 10 " occ=0.91 residue: pdb=" P DT F 11 " occ=0.87 ... (18 atoms not shown) pdb=" C6 DT F 11 " occ=0.87 residue: pdb=" P DT F 12 " occ=0.82 ... (18 atoms not shown) pdb=" C6 DT F 12 " occ=0.82 residue: pdb=" P DT F 13 " occ=0.93 ... (18 atoms not shown) pdb=" C6 DT F 13 " occ=0.93 ... (remaining 14 not shown) Time building chain proxies: 11.54, per 1000 atoms: 0.58 Number of scatterers: 19896 At special positions: 0 Unit cell: (156.88, 132.5, 150.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 112 16.00 P 222 15.00 O 4203 8.00 N 3553 7.00 C 11800 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: 4.97 Conformation dependent library (CDL) restraints added in 2.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 752 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " Number of angles added : 2 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 19 sheets defined 37.7% alpha, 19.8% beta 96 base pairs and 174 stacking pairs defined. Time for finding SS restraints: 8.11 Creating SS restraints... Processing helix chain 'A' and resid 414 through 418 Processing helix chain 'A' and resid 419 through 442 removed outlier: 5.508A pdb=" N ASP A 429 " --> pdb=" O HIS A 425 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 496 through 511 Processing helix chain 'A' and resid 518 through 528 removed outlier: 3.977A pdb=" N GLU A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 600 removed outlier: 5.304A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.717A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix removed outlier: 3.570A pdb=" N MET A 705 " --> pdb=" O ARG A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 757 through 762 removed outlier: 3.826A 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 846 through 863 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 895 through 912 removed outlier: 3.608A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 4.101A pdb=" N ARG A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 924 Processing helix chain 'A' and resid 924 through 947 removed outlier: 3.530A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.753A pdb=" N HIS A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.517A pdb=" N TRP A 978 " --> pdb=" O ILE A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 3.511A pdb=" N ASN A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.559A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1025 removed outlier: 3.626A pdb=" N PHE A1024 " --> pdb=" O TYR A1020 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A1025 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.797A pdb=" N LEU B 14 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 15 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 419 through 441 removed outlier: 5.274A pdb=" N ASP C 429 " --> pdb=" O HIS C 425 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 461 Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.565A pdb=" N ALA C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 496 through 511 removed outlier: 3.626A pdb=" N SER C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.641A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix removed outlier: 3.535A pdb=" N MET C 705 " --> pdb=" O ARG C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 738 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.879A 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 798 Processing helix chain 'C' and resid 819 through 835 removed outlier: 3.867A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 844 through 862 removed outlier: 3.692A pdb=" N ARG C 848 " --> pdb=" O SER C 844 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ARG C 849 " --> pdb=" O ARG C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 892 Processing helix chain 'C' and resid 895 through 917 removed outlier: 4.027A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 927 through 945 removed outlier: 4.638A pdb=" N SER C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR C 933 " --> pdb=" O CYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 949 Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.775A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 960 " --> pdb=" O ASN C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 972 Processing helix chain 'C' and resid 975 through 979 removed outlier: 3.625A pdb=" N TRP C 978 " --> pdb=" O ILE C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 980 through 997 removed outlier: 3.510A pdb=" N GLU C 984 " --> pdb=" O SER C 980 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C 986 " --> pdb=" O GLY C 982 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 991 " --> pdb=" O ASN C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1017 removed outlier: 4.498A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.559A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 539 removed outlier: 6.559A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG A 725 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 615 " --> pdb=" O ARG A 725 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR A 727 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLU A 617 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS A 616 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 646 " --> pdb=" O LYS A 616 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N SER A 618 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N PHE A 644 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASP A 620 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE A 642 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N MET A 622 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL A 640 " --> pdb=" O MET A 622 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.934A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 22 removed outlier: 4.107A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.756A pdb=" N SER B 61 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N CYS B 124 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B 106 " --> pdb=" O LYS B 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.684A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 612 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.928A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL C 640 " --> pdb=" O MET C 622 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N MET C 622 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE C 642 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP C 620 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N PHE C 644 " --> pdb=" O SER C 618 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER C 618 " --> pdb=" O PHE C 644 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE C 646 " --> pdb=" O LYS C 616 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LYS C 616 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER C 648 " --> pdb=" O VAL C 614 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 612 " --> pdb=" O SER C 650 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLY C 726 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU C 617 " --> pdb=" O GLY C 726 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 5.650A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 22 removed outlier: 4.506A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 75 through 80 Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 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 265 672 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 240 hydrogen bonds 480 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 174 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 5.88 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: 5273 1.34 - 1.46: 5875 1.46 - 1.58: 9015 1.58 - 1.71: 440 1.71 - 1.83: 168 Bond restraints: 20771 Sorted by residual: bond pdb=" C LYS A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.361 -0.024 9.80e-03 1.04e+04 5.97e+00 bond pdb=" C LYS A 840 " pdb=" N PRO A 841 " ideal model delta sigma weight residual 1.334 1.350 -0.017 8.40e-03 1.42e+04 3.99e+00 bond pdb=" CA PRO B 70 " pdb=" C PRO B 70 " ideal model delta sigma weight residual 1.514 1.504 0.010 5.50e-03 3.31e+04 3.64e+00 bond pdb=" C HIS C 482 " pdb=" N PRO C 483 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.65e+00 bond pdb=" C PRO D 17 " pdb=" N GLY D 18 " ideal model delta sigma weight residual 1.332 1.340 -0.008 5.00e-03 4.00e+04 2.49e+00 ... (remaining 20766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 28640 2.67 - 5.33: 340 5.33 - 8.00: 25 8.00 - 10.66: 2 10.66 - 13.33: 4 Bond angle restraints: 29011 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 127.00 140.33 -13.33 2.40e+00 1.74e-01 3.08e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CA PRO D 340 " ideal model delta sigma weight residual 127.00 140.21 -13.21 2.40e+00 1.74e-01 3.03e+01 angle pdb=" C PRO D 339 " pdb=" N PRO D 340 " pdb=" CD PRO D 340 " ideal model delta sigma weight residual 120.60 109.10 11.50 2.20e+00 2.07e-01 2.73e+01 angle pdb=" C PRO B 339 " pdb=" N PRO B 340 " pdb=" CD PRO B 340 " ideal model delta sigma weight residual 120.60 109.57 11.03 2.20e+00 2.07e-01 2.51e+01 angle pdb=" C TYR C1016 " pdb=" N THR C1017 " pdb=" CA THR C1017 " ideal model delta sigma weight residual 123.17 116.22 6.95 1.49e+00 4.50e-01 2.18e+01 ... (remaining 29006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.28: 10593 35.28 - 70.55: 1310 70.55 - 105.83: 34 105.83 - 141.10: 0 141.10 - 176.38: 5 Dihedral angle restraints: 11942 sinusoidal: 6368 harmonic: 5574 Sorted by residual: 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 180.00 142.81 37.19 0 5.00e+00 4.00e-02 5.53e+01 dihedral pdb=" CA SER C 511 " pdb=" C SER C 511 " pdb=" N GLY C 512 " pdb=" CA GLY C 512 " ideal model delta harmonic sigma weight residual 180.00 148.91 31.09 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA SER B 147 " pdb=" C SER B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 11939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2016 0.035 - 0.070: 839 0.070 - 0.105: 234 0.105 - 0.140: 79 0.140 - 0.175: 10 Chirality restraints: 3178 Sorted by residual: chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 chirality pdb=" CA ASP A 624 " pdb=" N ASP A 624 " pdb=" C ASP A 624 " pdb=" CB ASP A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" C3' DA G 18 " pdb=" C4' DA G 18 " pdb=" O3' DA G 18 " pdb=" C2' DA G 18 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 3175 not shown) Planarity restraints: 2969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 197 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO D 198 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 198 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 198 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 338 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO B 339 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG E 34 " -0.028 2.00e-02 2.50e+03 1.22e-02 4.48e+00 pdb=" N9 DG E 34 " 0.028 2.00e-02 2.50e+03 pdb=" C8 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG E 34 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DG E 34 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG E 34 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG E 34 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG E 34 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG E 34 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG E 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG E 34 " 0.002 2.00e-02 2.50e+03 ... (remaining 2966 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 152 2.47 - 3.08: 13626 3.08 - 3.68: 33277 3.68 - 4.29: 44787 4.29 - 4.90: 67298 Nonbonded interactions: 159140 Sorted by model distance: nonbonded pdb=" NZ LYS C 638 " pdb=" OD2 ASP C 683 " model vdw 1.860 3.120 nonbonded pdb=" OE2 GLU A 463 " pdb=" NZ LYS C 447 " model vdw 1.900 3.120 nonbonded pdb=" NE2 HIS D 222 " pdb=" OE2 GLU D 280 " model vdw 1.961 3.120 nonbonded pdb=" NZ LYS A 804 " pdb=" OE1 GLU B 101 " model vdw 1.976 3.120 nonbonded pdb=" NH1 ARG C 575 " pdb=" O PHE C 576 " model vdw 1.999 3.120 ... (remaining 159135 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and (resid 408 through 459 or (resid 460 and (name N or name CA or na \ me C or name CB )) or resid 461 through 1028 or resid 1101 through 1103)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.900 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 56.320 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.008 0.598 20778 Z= 0.321 Angle : 0.845 35.800 29013 Z= 0.468 Chirality : 0.043 0.175 3178 Planarity : 0.005 0.060 2969 Dihedral : 24.264 176.378 8354 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.18 % Favored : 90.62 % Rotamer: Outliers : 0.12 % Allowed : 37.59 % Favored : 62.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.15), residues: 1918 helix: -2.41 (0.16), residues: 631 sheet: -1.82 (0.27), residues: 312 loop : -3.40 (0.16), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1014 HIS 0.016 0.002 HIS A 687 PHE 0.024 0.003 PHE D 274 TYR 0.021 0.003 TYR C 500 ARG 0.010 0.001 ARG D 284 Details of bonding type rmsd hydrogen bonds : bond 0.13853 ( 896) hydrogen bonds : angle 7.30431 ( 2346) metal coordination : bond 0.35998 ( 7) metal coordination : angle 25.52318 ( 2) covalent geometry : bond 0.00527 (20771) covalent geometry : angle 0.81804 (29011) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 622 MET cc_start: 0.9315 (ttm) cc_final: 0.8982 (mtm) REVERT: A 671 GLU cc_start: 0.9464 (pm20) cc_final: 0.8972 (pt0) REVERT: A 869 MET cc_start: 0.8612 (ttt) cc_final: 0.8196 (tpp) REVERT: A 947 LYS cc_start: 0.8763 (tttt) cc_final: 0.8456 (tppt) REVERT: B 43 THR cc_start: 0.9574 (m) cc_final: 0.9348 (p) REVERT: C 427 LEU cc_start: 0.9237 (mt) cc_final: 0.8903 (mm) REVERT: C 617 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8546 (mm-30) REVERT: C 737 MET cc_start: 0.8588 (mmt) cc_final: 0.8174 (mmt) REVERT: D 52 LYS cc_start: 0.8525 (ptpt) cc_final: 0.7959 (ptpt) REVERT: D 91 LEU cc_start: 0.7785 (mt) cc_final: 0.7480 (mt) REVERT: D 129 LEU cc_start: 0.9399 (mt) cc_final: 0.8986 (tp) outliers start: 2 outliers final: 0 residues processed: 278 average time/residue: 0.4322 time to fit residues: 170.4767 Evaluate side-chains 151 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 167 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS A 669 ASN A 687 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 GLN B 79 HIS B 83 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 ASN C 772 HIS C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 910 GLN C 983 ASN ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.070288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.050937 restraints weight = 110410.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052159 restraints weight = 59902.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052951 restraints weight = 40295.336| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 53 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20778 Z= 0.187 Angle : 0.757 11.582 29013 Z= 0.416 Chirality : 0.044 0.176 3178 Planarity : 0.006 0.053 2969 Dihedral : 26.229 174.914 4556 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 0.12 % Allowed : 3.25 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.17), residues: 1918 helix: -0.94 (0.19), residues: 645 sheet: -1.64 (0.28), residues: 323 loop : -2.65 (0.18), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 915 HIS 0.018 0.002 HIS B 237 PHE 0.028 0.002 PHE A 993 TYR 0.022 0.002 TYR D 268 ARG 0.010 0.001 ARG A 999 Details of bonding type rmsd hydrogen bonds : bond 0.04924 ( 896) hydrogen bonds : angle 5.30100 ( 2346) metal coordination : bond 0.01534 ( 7) metal coordination : angle 8.34227 ( 2) covalent geometry : bond 0.00403 (20771) covalent geometry : angle 0.75369 (29011) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 270 time to evaluate : 1.936 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: A 471 GLU cc_start: 0.9266 (tp30) cc_final: 0.8926 (tp30) REVERT: A 557 LEU cc_start: 0.9022 (mp) cc_final: 0.8595 (mt) REVERT: A 671 GLU cc_start: 0.8782 (pm20) cc_final: 0.8563 (pt0) REVERT: A 870 ARG cc_start: 0.8150 (ptt90) cc_final: 0.7908 (ptp-170) REVERT: A 902 LEU cc_start: 0.9323 (mt) cc_final: 0.9087 (mt) REVERT: A 905 MET cc_start: 0.8920 (tpp) cc_final: 0.8613 (tpp) REVERT: A 1014 TRP cc_start: 0.9139 (t-100) cc_final: 0.8936 (t-100) REVERT: B 43 THR cc_start: 0.9303 (m) cc_final: 0.9043 (p) REVERT: B 56 LYS cc_start: 0.8830 (tptm) cc_final: 0.8388 (tptp) REVERT: B 162 MET cc_start: 0.8043 (mtm) cc_final: 0.7223 (mtm) REVERT: B 271 TYR cc_start: 0.8240 (m-80) cc_final: 0.8002 (m-10) REVERT: C 436 THR cc_start: 0.9180 (p) cc_final: 0.8829 (p) REVERT: C 524 ASN cc_start: 0.9041 (t0) cc_final: 0.8742 (t0) REVERT: C 606 MET cc_start: 0.6361 (tpt) cc_final: 0.6136 (tpt) REVERT: C 652 ARG cc_start: 0.7589 (tpt90) cc_final: 0.6893 (tpt90) REVERT: C 704 MET cc_start: 0.8414 (tpp) cc_final: 0.7821 (tpp) REVERT: C 905 MET cc_start: 0.8986 (tpp) cc_final: 0.8633 (tpp) REVERT: D 52 LYS cc_start: 0.8729 (ptpt) cc_final: 0.8403 (ptpt) REVERT: D 146 ASN cc_start: 0.8859 (m-40) cc_final: 0.8545 (p0) outliers start: 2 outliers final: 0 residues processed: 271 average time/residue: 0.4125 time to fit residues: 158.9158 Evaluate side-chains 148 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 39 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 158 optimal weight: 0.2980 chunk 35 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 199 optimal weight: 8.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 146 ASN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** 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 = 0.3555 r_free = 0.3555 target = 0.068078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.048592 restraints weight = 111559.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049795 restraints weight = 61652.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.050576 restraints weight = 42213.533| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 80 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20778 Z= 0.207 Angle : 0.714 11.882 29013 Z= 0.392 Chirality : 0.042 0.159 3178 Planarity : 0.005 0.052 2969 Dihedral : 25.981 173.711 4556 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 0.06 % Allowed : 4.02 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 1918 helix: -0.48 (0.19), residues: 640 sheet: -1.45 (0.28), residues: 343 loop : -2.25 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 915 HIS 0.011 0.002 HIS B 237 PHE 0.024 0.002 PHE A 993 TYR 0.017 0.002 TYR C 500 ARG 0.017 0.001 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.04598 ( 896) hydrogen bonds : angle 5.09340 ( 2346) metal coordination : bond 0.01240 ( 7) metal coordination : angle 4.62043 ( 2) covalent geometry : bond 0.00441 (20771) covalent geometry : angle 0.71257 (29011) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 1.985 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 453 LEU cc_start: 0.9357 (mm) cc_final: 0.9151 (mm) REVERT: A 471 GLU cc_start: 0.9277 (tp30) cc_final: 0.8892 (tp30) REVERT: A 474 MET cc_start: 0.8964 (tpp) cc_final: 0.8404 (tpp) REVERT: A 869 MET cc_start: 0.8093 (tmm) cc_final: 0.7477 (tpp) REVERT: A 882 ARG cc_start: 0.9135 (tmm160) cc_final: 0.8764 (ttp80) REVERT: A 902 LEU cc_start: 0.9343 (mt) cc_final: 0.9064 (mt) REVERT: B 244 SER cc_start: 0.8928 (t) cc_final: 0.8727 (m) REVERT: B 271 TYR cc_start: 0.8370 (m-80) cc_final: 0.8063 (m-10) REVERT: C 436 THR cc_start: 0.8923 (p) cc_final: 0.8231 (p) REVERT: C 524 ASN cc_start: 0.9134 (t0) cc_final: 0.8821 (t0) REVERT: C 737 MET cc_start: 0.8873 (tpp) cc_final: 0.8613 (tpt) REVERT: C 807 MET cc_start: 0.8488 (ttm) cc_final: 0.8187 (ttp) REVERT: C 880 MET cc_start: 0.8708 (ppp) cc_final: 0.8268 (ppp) REVERT: C 905 MET cc_start: 0.9069 (tpp) cc_final: 0.8603 (tpp) REVERT: D 52 LYS cc_start: 0.8662 (ptpt) cc_final: 0.8340 (ptpt) REVERT: D 129 LEU cc_start: 0.9155 (mm) cc_final: 0.8802 (tp) REVERT: D 150 LYS cc_start: 0.8450 (pttm) cc_final: 0.8184 (ptpp) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.3754 time to fit residues: 114.9489 Evaluate side-chains 137 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 0 optimal weight: 50.0000 chunk 56 optimal weight: 6.9990 chunk 208 optimal weight: 40.0000 chunk 60 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 514 GLN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 HIS B 83 GLN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** 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 = 0.3527 r_free = 0.3527 target = 0.066812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047718 restraints weight = 114672.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048873 restraints weight = 64314.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049573 restraints weight = 44299.068| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 20778 Z= 0.204 Angle : 0.707 18.841 29013 Z= 0.384 Chirality : 0.042 0.158 3178 Planarity : 0.005 0.051 2969 Dihedral : 25.774 173.419 4556 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 1918 helix: -0.26 (0.20), residues: 641 sheet: -1.34 (0.29), residues: 340 loop : -2.17 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 915 HIS 0.010 0.001 HIS D 79 PHE 0.020 0.002 PHE A 993 TYR 0.021 0.002 TYR A 500 ARG 0.007 0.001 ARG A 523 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 896) hydrogen bonds : angle 5.01630 ( 2346) metal coordination : bond 0.04294 ( 7) metal coordination : angle 14.19307 ( 2) covalent geometry : bond 0.00437 (20771) covalent geometry : angle 0.69710 (29011) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 1.954 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 453 LEU cc_start: 0.9386 (mm) cc_final: 0.9159 (mm) REVERT: A 468 ASP cc_start: 0.9209 (t70) cc_final: 0.9003 (t0) REVERT: A 471 GLU cc_start: 0.9210 (tp30) cc_final: 0.8790 (tp30) REVERT: A 474 MET cc_start: 0.8901 (tpp) cc_final: 0.8396 (tpp) REVERT: A 704 MET cc_start: 0.9115 (tpp) cc_final: 0.8810 (tpt) REVERT: A 882 ARG cc_start: 0.9100 (tmm160) cc_final: 0.8821 (ttp80) REVERT: A 902 LEU cc_start: 0.9342 (mt) cc_final: 0.9044 (mt) REVERT: B 271 TYR cc_start: 0.8258 (m-80) cc_final: 0.8009 (m-10) REVERT: C 503 MET cc_start: 0.8952 (tmm) cc_final: 0.8633 (tmm) REVERT: C 524 ASN cc_start: 0.9060 (t0) cc_final: 0.8750 (t0) REVERT: C 880 MET cc_start: 0.8692 (ppp) cc_final: 0.8188 (ppp) REVERT: C 905 MET cc_start: 0.9063 (tpp) cc_final: 0.8809 (tpp) REVERT: C 931 TYR cc_start: 0.8452 (t80) cc_final: 0.8250 (t80) REVERT: D 52 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8276 (ptpt) REVERT: D 65 ASN cc_start: 0.7788 (p0) cc_final: 0.7575 (p0) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.3758 time to fit residues: 100.4348 Evaluate side-chains 125 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 132 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 158 optimal weight: 0.2980 chunk 183 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 100 ASN ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 817 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 HIS ** D 100 ASN ** 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 = 0.3574 r_free = 0.3574 target = 0.068752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049711 restraints weight = 112411.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050908 restraints weight = 62678.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051657 restraints weight = 42927.671| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.691 20778 Z= 0.217 Angle : 0.678 11.703 29013 Z= 0.369 Chirality : 0.041 0.182 3178 Planarity : 0.004 0.050 2969 Dihedral : 25.548 172.598 4556 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.19), residues: 1918 helix: 0.04 (0.20), residues: 639 sheet: -1.03 (0.29), residues: 333 loop : -1.90 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 915 HIS 0.007 0.001 HIS D 79 PHE 0.029 0.002 PHE A 993 TYR 0.016 0.001 TYR A 747 ARG 0.007 0.000 ARG D 232 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 896) hydrogen bonds : angle 4.77073 ( 2346) metal coordination : bond 0.26131 ( 7) metal coordination : angle 5.90161 ( 2) covalent geometry : bond 0.00311 (20771) covalent geometry : angle 0.67575 (29011) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 LEU cc_start: 0.9378 (mm) cc_final: 0.9133 (mm) REVERT: A 468 ASP cc_start: 0.9117 (t70) cc_final: 0.8897 (t0) REVERT: A 471 GLU cc_start: 0.9146 (tp30) cc_final: 0.8704 (tp30) REVERT: A 474 MET cc_start: 0.8908 (tpp) cc_final: 0.8255 (tpp) REVERT: A 622 MET cc_start: 0.8405 (tmm) cc_final: 0.7944 (tmm) REVERT: A 680 MET cc_start: 0.8056 (mpp) cc_final: 0.7665 (mpp) REVERT: A 882 ARG cc_start: 0.9067 (tmm160) cc_final: 0.8795 (ttp80) REVERT: A 902 LEU cc_start: 0.9288 (mt) cc_final: 0.8969 (mt) REVERT: B 244 SER cc_start: 0.8810 (t) cc_final: 0.8585 (m) REVERT: B 271 TYR cc_start: 0.8223 (m-80) cc_final: 0.7993 (m-10) REVERT: C 503 MET cc_start: 0.8965 (tmm) cc_final: 0.8579 (tmm) REVERT: C 524 ASN cc_start: 0.9054 (t0) cc_final: 0.8740 (t0) REVERT: C 652 ARG cc_start: 0.7432 (tpt90) cc_final: 0.7147 (tpt90) REVERT: C 737 MET cc_start: 0.8653 (tpt) cc_final: 0.8225 (tpt) REVERT: C 863 MET cc_start: 0.8671 (mmm) cc_final: 0.8367 (mmt) REVERT: C 880 MET cc_start: 0.8675 (ppp) cc_final: 0.8164 (ppp) REVERT: C 905 MET cc_start: 0.9001 (tpp) cc_final: 0.8750 (tpp) REVERT: D 65 ASN cc_start: 0.7843 (p0) cc_final: 0.7548 (p0) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.3759 time to fit residues: 111.9391 Evaluate side-chains 135 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 3 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 ASN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.066961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047652 restraints weight = 113113.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048794 restraints weight = 63582.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.049526 restraints weight = 43921.427| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20778 Z= 0.206 Angle : 0.703 14.489 29013 Z= 0.382 Chirality : 0.041 0.170 3178 Planarity : 0.005 0.050 2969 Dihedral : 25.462 172.702 4556 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.06 % Allowed : 2.19 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.19), residues: 1918 helix: 0.01 (0.20), residues: 655 sheet: -0.96 (0.30), residues: 328 loop : -1.86 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 915 HIS 0.008 0.002 HIS D 79 PHE 0.032 0.002 PHE A 993 TYR 0.022 0.002 TYR C 500 ARG 0.006 0.001 ARG A 477 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 896) hydrogen bonds : angle 4.79913 ( 2346) metal coordination : bond 0.02139 ( 7) metal coordination : angle 7.58605 ( 2) covalent geometry : bond 0.00444 (20771) covalent geometry : angle 0.70067 (29011) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 185 time to evaluate : 2.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 LEU cc_start: 0.8817 (mt) cc_final: 0.8609 (tt) REVERT: A 468 ASP cc_start: 0.9124 (t70) cc_final: 0.8921 (t0) REVERT: A 471 GLU cc_start: 0.9215 (tp30) cc_final: 0.8810 (tp30) REVERT: A 474 MET cc_start: 0.8890 (tpp) cc_final: 0.7956 (tpp) REVERT: A 622 MET cc_start: 0.8483 (tmm) cc_final: 0.8048 (tmm) REVERT: A 680 MET cc_start: 0.8294 (mpp) cc_final: 0.7894 (mpp) REVERT: A 882 ARG cc_start: 0.9065 (tmm160) cc_final: 0.8832 (ttp80) REVERT: A 902 LEU cc_start: 0.9330 (mt) cc_final: 0.8999 (mt) REVERT: A 947 LYS cc_start: 0.9150 (tttm) cc_final: 0.8555 (tppt) REVERT: B 271 TYR cc_start: 0.8477 (m-80) cc_final: 0.8242 (m-10) REVERT: C 524 ASN cc_start: 0.9145 (t0) cc_final: 0.8837 (t0) REVERT: C 704 MET cc_start: 0.9035 (mmm) cc_final: 0.8787 (mmt) REVERT: C 737 MET cc_start: 0.8517 (tpt) cc_final: 0.8293 (tpt) REVERT: C 863 MET cc_start: 0.8719 (mmm) cc_final: 0.8423 (mmt) REVERT: C 880 MET cc_start: 0.8734 (ppp) cc_final: 0.8213 (ppp) REVERT: C 905 MET cc_start: 0.9052 (tpp) cc_final: 0.8801 (tpp) REVERT: C 945 MET cc_start: 0.8662 (tpt) cc_final: 0.8417 (tpp) REVERT: D 65 ASN cc_start: 0.7989 (p0) cc_final: 0.7682 (p0) REVERT: D 129 LEU cc_start: 0.9192 (mm) cc_final: 0.8870 (tt) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 0.3777 time to fit residues: 103.4664 Evaluate side-chains 128 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 114 optimal weight: 7.9990 chunk 197 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 109 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 GLN ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.066231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047261 restraints weight = 114296.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048456 restraints weight = 62363.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049184 restraints weight = 42276.090| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20778 Z= 0.207 Angle : 0.694 13.872 29013 Z= 0.378 Chirality : 0.041 0.231 3178 Planarity : 0.004 0.051 2969 Dihedral : 25.441 172.261 4556 Min Nonbonded Distance : 1.619 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.19), residues: 1918 helix: 0.18 (0.20), residues: 652 sheet: -0.82 (0.30), residues: 322 loop : -1.83 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 915 HIS 0.008 0.001 HIS D 79 PHE 0.018 0.002 PHE D 62 TYR 0.023 0.002 TYR C 931 ARG 0.014 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 896) hydrogen bonds : angle 4.77790 ( 2346) metal coordination : bond 0.01071 ( 7) metal coordination : angle 5.96397 ( 2) covalent geometry : bond 0.00449 (20771) covalent geometry : angle 0.69239 (29011) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 LEU cc_start: 0.8826 (mt) cc_final: 0.8585 (tt) REVERT: A 468 ASP cc_start: 0.9139 (t70) cc_final: 0.8927 (t0) REVERT: A 471 GLU cc_start: 0.9226 (tp30) cc_final: 0.8838 (tp30) REVERT: A 474 MET cc_start: 0.9042 (tpp) cc_final: 0.7922 (tpp) REVERT: A 622 MET cc_start: 0.8542 (tmm) cc_final: 0.8123 (tmm) REVERT: A 680 MET cc_start: 0.8296 (mpp) cc_final: 0.7688 (mpp) REVERT: A 882 ARG cc_start: 0.9096 (tmm160) cc_final: 0.8865 (ttp80) REVERT: A 902 LEU cc_start: 0.9341 (mt) cc_final: 0.9007 (mt) REVERT: A 941 LEU cc_start: 0.9233 (tp) cc_final: 0.8539 (tp) REVERT: B 155 LEU cc_start: 0.9207 (tt) cc_final: 0.8881 (mt) REVERT: B 271 TYR cc_start: 0.8513 (m-80) cc_final: 0.8294 (m-10) REVERT: C 503 MET cc_start: 0.9063 (tmm) cc_final: 0.8814 (tmm) REVERT: C 524 ASN cc_start: 0.9186 (t0) cc_final: 0.8892 (t0) REVERT: C 863 MET cc_start: 0.8823 (mmm) cc_final: 0.8584 (mmt) REVERT: C 880 MET cc_start: 0.8759 (ppp) cc_final: 0.8257 (ppp) REVERT: C 905 MET cc_start: 0.9094 (tpp) cc_final: 0.8812 (tpp) REVERT: C 945 MET cc_start: 0.8737 (tpt) cc_final: 0.8486 (tpp) REVERT: D 65 ASN cc_start: 0.8032 (p0) cc_final: 0.7688 (p0) REVERT: D 129 LEU cc_start: 0.9213 (mm) cc_final: 0.8899 (tt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.3443 time to fit residues: 94.1891 Evaluate side-chains 122 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 185 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 959 HIS C 983 ASN ** D 100 ASN ** 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 = 0.3485 r_free = 0.3485 target = 0.065126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.045606 restraints weight = 114886.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046716 restraints weight = 66150.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.047413 restraints weight = 45958.219| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.946 20778 Z= 0.351 Angle : 0.776 15.320 29013 Z= 0.415 Chirality : 0.043 0.181 3178 Planarity : 0.005 0.069 2969 Dihedral : 25.516 173.077 4556 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.92 % Favored : 92.02 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.18), residues: 1918 helix: -0.02 (0.20), residues: 655 sheet: -1.02 (0.28), residues: 346 loop : -1.87 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 915 HIS 0.012 0.002 HIS D 313 PHE 0.020 0.002 PHE A 993 TYR 0.024 0.002 TYR C 500 ARG 0.011 0.001 ARG A 490 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 896) hydrogen bonds : angle 4.99500 ( 2346) metal coordination : bond 0.35794 ( 7) metal coordination : angle 8.36185 ( 2) covalent geometry : bond 0.00593 (20771) covalent geometry : angle 0.77245 (29011) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 427 LEU cc_start: 0.8817 (mt) cc_final: 0.8526 (tt) REVERT: A 430 LEU cc_start: 0.9626 (tp) cc_final: 0.9421 (tp) REVERT: A 468 ASP cc_start: 0.9204 (t70) cc_final: 0.8992 (t0) REVERT: A 471 GLU cc_start: 0.9242 (tp30) cc_final: 0.8826 (tp30) REVERT: A 474 MET cc_start: 0.9035 (tpp) cc_final: 0.7751 (tpp) REVERT: A 622 MET cc_start: 0.8455 (tmm) cc_final: 0.7994 (tmm) REVERT: A 680 MET cc_start: 0.8455 (mpp) cc_final: 0.7915 (mpp) REVERT: A 807 MET cc_start: 0.8781 (tpp) cc_final: 0.8347 (ttm) REVERT: A 902 LEU cc_start: 0.9366 (mt) cc_final: 0.9042 (mt) REVERT: A 941 LEU cc_start: 0.9341 (tp) cc_final: 0.8741 (tp) REVERT: B 271 TYR cc_start: 0.8539 (m-80) cc_final: 0.8282 (m-10) REVERT: C 503 MET cc_start: 0.9063 (tmm) cc_final: 0.8776 (tmm) REVERT: C 524 ASN cc_start: 0.9253 (t0) cc_final: 0.8971 (t0) REVERT: C 905 MET cc_start: 0.9165 (tpp) cc_final: 0.8920 (tpp) REVERT: C 945 MET cc_start: 0.8783 (tpt) cc_final: 0.8525 (tpp) REVERT: D 65 ASN cc_start: 0.8088 (p0) cc_final: 0.7702 (p0) REVERT: D 129 LEU cc_start: 0.9211 (mm) cc_final: 0.8938 (tt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.3450 time to fit residues: 88.6850 Evaluate side-chains 125 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 209 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 77 optimal weight: 0.0070 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 147 optimal weight: 0.0170 chunk 183 optimal weight: 7.9990 overall best weight: 2.0040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 959 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.066791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.047475 restraints weight = 110500.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048651 restraints weight = 61438.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049382 restraints weight = 42054.202| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20778 Z= 0.161 Angle : 0.693 13.871 29013 Z= 0.376 Chirality : 0.041 0.179 3178 Planarity : 0.004 0.052 2969 Dihedral : 25.441 171.492 4556 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.19), residues: 1918 helix: 0.23 (0.20), residues: 651 sheet: -0.83 (0.29), residues: 326 loop : -1.72 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 915 HIS 0.008 0.001 HIS D 79 PHE 0.015 0.001 PHE A 993 TYR 0.026 0.002 TYR C 838 ARG 0.008 0.001 ARG C 897 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 896) hydrogen bonds : angle 4.73167 ( 2346) metal coordination : bond 0.01182 ( 7) metal coordination : angle 4.82186 ( 2) covalent geometry : bond 0.00351 (20771) covalent geometry : angle 0.69204 (29011) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ASP cc_start: 0.9127 (t70) cc_final: 0.8869 (t0) REVERT: A 471 GLU cc_start: 0.9203 (tp30) cc_final: 0.8934 (tm-30) REVERT: A 474 MET cc_start: 0.8995 (tpp) cc_final: 0.8242 (tpp) REVERT: A 680 MET cc_start: 0.8276 (mpp) cc_final: 0.7668 (mpp) REVERT: A 902 LEU cc_start: 0.9304 (mt) cc_final: 0.8976 (mt) REVERT: C 524 ASN cc_start: 0.9168 (t0) cc_final: 0.8894 (t0) REVERT: C 704 MET cc_start: 0.9064 (mmt) cc_final: 0.8803 (mmt) REVERT: C 880 MET cc_start: 0.8695 (ppp) cc_final: 0.8238 (ppp) REVERT: C 945 MET cc_start: 0.8686 (tpt) cc_final: 0.8446 (tpp) REVERT: D 14 LEU cc_start: 0.9106 (mt) cc_final: 0.8822 (mp) REVERT: D 65 ASN cc_start: 0.8018 (p0) cc_final: 0.7619 (p0) REVERT: D 129 LEU cc_start: 0.9165 (mm) cc_final: 0.8903 (tt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3530 time to fit residues: 92.3535 Evaluate side-chains 125 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 96 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 0.0980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 173 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 149 optimal weight: 0.0270 chunk 158 optimal weight: 3.9990 overall best weight: 2.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.066747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047231 restraints weight = 112910.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.048405 restraints weight = 62742.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.049129 restraints weight = 43201.039| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20778 Z= 0.173 Angle : 0.695 14.409 29013 Z= 0.377 Chirality : 0.040 0.159 3178 Planarity : 0.005 0.062 2969 Dihedral : 25.358 171.982 4556 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1918 helix: 0.22 (0.20), residues: 650 sheet: -0.76 (0.29), residues: 326 loop : -1.67 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 915 HIS 0.006 0.001 HIS D 79 PHE 0.017 0.002 PHE A 946 TYR 0.023 0.002 TYR D 268 ARG 0.009 0.001 ARG A 882 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 896) hydrogen bonds : angle 4.70445 ( 2346) metal coordination : bond 0.00702 ( 7) metal coordination : angle 5.14690 ( 2) covalent geometry : bond 0.00377 (20771) covalent geometry : angle 0.69324 (29011) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3836 Ramachandran restraints generated. 1918 Oldfield, 0 Emsley, 1918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 2.011 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 468 ASP cc_start: 0.9163 (t70) cc_final: 0.8918 (t0) REVERT: A 471 GLU cc_start: 0.9155 (tp30) cc_final: 0.8790 (tm-30) REVERT: A 474 MET cc_start: 0.9005 (tpp) cc_final: 0.8239 (tpp) REVERT: A 680 MET cc_start: 0.8307 (mpp) cc_final: 0.7731 (mpp) REVERT: A 807 MET cc_start: 0.8618 (tpp) cc_final: 0.8320 (ttm) REVERT: A 902 LEU cc_start: 0.9286 (mt) cc_final: 0.8935 (mt) REVERT: A 1010 LEU cc_start: 0.9638 (tp) cc_final: 0.9406 (tp) REVERT: C 606 MET cc_start: 0.4833 (tpt) cc_final: 0.4519 (tpt) REVERT: C 704 MET cc_start: 0.8986 (mmt) cc_final: 0.8782 (mmt) REVERT: C 825 GLU cc_start: 0.8782 (tp30) cc_final: 0.8550 (tp30) REVERT: C 880 MET cc_start: 0.8760 (ppp) cc_final: 0.8251 (ppp) REVERT: C 945 MET cc_start: 0.8649 (tpt) cc_final: 0.8443 (tpp) REVERT: D 65 ASN cc_start: 0.8012 (p0) cc_final: 0.7602 (p0) REVERT: D 129 LEU cc_start: 0.9185 (mm) cc_final: 0.8875 (tt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.3428 time to fit residues: 86.0773 Evaluate side-chains 126 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 207 optimal weight: 20.0000 chunk 132 optimal weight: 1.9990 chunk 212 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 161 optimal weight: 0.0070 chunk 54 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 68 optimal weight: 0.0670 chunk 185 optimal weight: 5.9990 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 HIS ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.067469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047966 restraints weight = 113300.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049147 restraints weight = 62998.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.049902 restraints weight = 43322.259| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.5315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20778 Z= 0.153 Angle : 0.685 13.915 29013 Z= 0.370 Chirality : 0.040 0.174 3178 Planarity : 0.004 0.051 2969 Dihedral : 25.283 171.852 4556 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 1.36 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1918 helix: 0.30 (0.20), residues: 646 sheet: -0.68 (0.28), residues: 326 loop : -1.63 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 915 HIS 0.006 0.001 HIS D 79 PHE 0.024 0.001 PHE A 946 TYR 0.020 0.002 TYR A 578 ARG 0.011 0.001 ARG A 897 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 896) hydrogen bonds : angle 4.58572 ( 2346) metal coordination : bond 0.00542 ( 7) metal coordination : angle 4.22791 ( 2) covalent geometry : bond 0.00334 (20771) covalent geometry : angle 0.68408 (29011) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6379.89 seconds wall clock time: 111 minutes 13.54 seconds (6673.54 seconds total)