Starting phenix.real_space_refine on Sat Sep 12 22:59:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.map" model { file = "/net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oep_20033/09_2026/6oep_20033.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 3 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 106 5.16 5 C 11503 2.51 5 N 3384 2.21 5 O 3996 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19198 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4791 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 604, 4788 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 578} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 604, 4788 Classifications: {'peptide': 604} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 578} Chain breaks: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 4883 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4859 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 586} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2671 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2520 SG CYS A 727 95.273 49.915 96.252 1.00 86.00 S ATOM 2541 SG CYS A 730 97.682 47.308 97.987 1.00 93.67 S ATOM 10043 SG CYS C 727 35.644 107.070 98.576 1.00 79.44 S ATOM 10064 SG CYS C 730 33.216 109.426 99.791 1.00 87.30 S Time building chain proxies: 4.33, per 1000 atoms: 0.23 Number of scatterers: 19198 At special positions: 0 Unit cell: (126.26, 159.43, 160.5, 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 3 19.99 S 106 16.00 P 204 15.00 O 3996 8.00 N 3384 7.00 C 11503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 886.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 20 sheets defined 36.7% alpha, 20.4% beta 96 base pairs and 172 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 401 through 408 removed outlier: 3.899A pdb=" N LEU A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 426 through 441 removed outlier: 3.546A pdb=" N ALA A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.832A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 473 Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.664A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 505 Processing helix chain 'A' and resid 559 through 568 removed outlier: 3.697A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'A' and resid 733 through 738 removed outlier: 3.876A pdb=" N SER A 738 " --> pdb=" O ARG A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 Processing helix chain 'A' and resid 768 through 777 removed outlier: 3.998A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 813 removed outlier: 3.630A pdb=" N ASP A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 842 removed outlier: 3.985A pdb=" N ARG A 828 " --> pdb=" O GLU A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 removed outlier: 3.600A pdb=" N ALA A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.746A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.534A pdb=" N SER A 895 " --> pdb=" O PRO A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 923 removed outlier: 5.347A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.591A pdb=" N HIS A 937 " --> pdb=" O THR A 933 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 950 removed outlier: 4.292A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 964 Processing helix chain 'A' and resid 964 through 975 removed outlier: 3.549A pdb=" N PHE A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.786A pdb=" N VAL A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 988 " --> pdb=" O MET A 984 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.773A pdb=" N GLN A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.698A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 400 through 408 Processing helix chain 'C' and resid 408 through 422 Processing helix chain 'C' and resid 426 through 441 Processing helix chain 'C' and resid 444 through 457 removed outlier: 4.004A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 removed outlier: 3.849A pdb=" N CYS C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 499 through 509 removed outlier: 3.952A pdb=" N VAL C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 682 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 683 through 685 No H-bonds generated for 'chain 'C' and resid 683 through 685' Processing helix chain 'C' and resid 708 through 716 removed outlier: 3.691A pdb=" N ARG C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 812 removed outlier: 3.573A pdb=" N CYS C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS C 806 " --> pdb=" O ALA C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 841 Processing helix chain 'C' and resid 850 through 858 removed outlier: 3.735A pdb=" N MET C 858 " --> pdb=" O ALA C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 867 Processing helix chain 'C' and resid 868 through 870 No H-bonds generated for 'chain 'C' and resid 868 through 870' Processing helix chain 'C' and resid 873 through 890 Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.623A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 907 Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.844A pdb=" N ILE C 946 " --> pdb=" O HIS C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 974 removed outlier: 3.523A pdb=" N MET C 974 " --> pdb=" O ARG C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 994 Processing helix chain 'C' and resid 996 through 1004 removed outlier: 3.646A pdb=" N GLN C1000 " --> pdb=" O SER C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1008 removed outlier: 3.875A pdb=" N ALA C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1005 through 1008' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.877A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.956A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.174A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 6.174A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 600 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 621 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.657A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.155A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 75 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 7.329A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) 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 208 through 212 removed outlier: 4.448A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 267 removed outlier: 7.227A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.830A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 705 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU C 597 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.830A pdb=" N GLU C 518 " --> pdb=" O THR C 688 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR C 705 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLU C 597 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 598 " --> pdb=" O PHE C 624 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE C 624 " --> pdb=" O SER C 598 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASP C 600 " --> pdb=" O PHE C 622 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE C 622 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.981A pdb=" N TYR D 346 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 20 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 50 through 51 removed outlier: 4.214A pdb=" N LYS D 51 " --> pdb=" O HIS D 54 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 80 Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.237A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.629A pdb=" N ILE D 210 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 234 through 235 Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.800A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 638 hydrogen bonds defined for protein. 1772 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 238 hydrogen bonds 472 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 172 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4680 1.33 - 1.46: 5947 1.46 - 1.58: 8848 1.58 - 1.71: 403 1.71 - 1.83: 161 Bond restraints: 20039 Sorted by residual: bond pdb=" C5' DG F 3 " pdb=" C4' DG F 3 " ideal model delta sigma weight residual 1.512 1.540 -0.028 7.00e-03 2.04e+04 1.58e+01 bond pdb=" C3' DG F 34 " pdb=" O3' DG F 34 " ideal model delta sigma weight residual 1.435 1.387 0.048 1.30e-02 5.92e+03 1.39e+01 bond pdb=" C3' DG F 43 " pdb=" C2' DG F 43 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C1' DC J 43 " pdb=" N1 DC J 43 " ideal model delta sigma weight residual 1.468 1.519 -0.051 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C3' DG I 46 " pdb=" C2' DG I 46 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 ... (remaining 20034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 26846 2.38 - 4.75: 1027 4.75 - 7.13: 88 7.13 - 9.51: 22 9.51 - 11.88: 5 Bond angle restraints: 27988 Sorted by residual: angle pdb=" O4' DT G 42 " pdb=" C4' DT G 42 " pdb=" C3' DT G 42 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.59e+01 angle pdb=" O4' DA F 13 " pdb=" C4' DA F 13 " pdb=" C3' DA F 13 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.58e+01 angle pdb=" O4' DC I 30 " pdb=" C1' DC I 30 " pdb=" N1 DC I 30 " ideal model delta sigma weight residual 108.00 111.96 -3.96 7.00e-01 2.04e+00 3.20e+01 angle pdb=" O4' DG J 35 " pdb=" C4' DG J 35 " pdb=" C3' DG J 35 " ideal model delta sigma weight residual 106.00 102.69 3.31 6.00e-01 2.78e+00 3.05e+01 angle pdb=" O4' DA I 40 " pdb=" C1' DA I 40 " pdb=" N9 DA I 40 " ideal model delta sigma weight residual 108.00 111.82 -3.82 7.00e-01 2.04e+00 2.98e+01 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 10393 35.65 - 71.31: 1096 71.31 - 106.96: 18 106.96 - 142.61: 2 142.61 - 178.27: 3 Dihedral angle restraints: 11512 sinusoidal: 5966 harmonic: 5546 Sorted by residual: dihedral pdb=" CA GLN C 520 " pdb=" C GLN C 520 " pdb=" N PRO C 521 " pdb=" CA PRO C 521 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA THR B 169 " pdb=" C THR B 169 " pdb=" N GLU B 170 " pdb=" CA GLU B 170 " ideal model delta harmonic sigma weight residual 180.00 154.51 25.49 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 11509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2325 0.063 - 0.127: 637 0.127 - 0.190: 113 0.190 - 0.253: 18 0.253 - 0.317: 3 Chirality restraints: 3096 Sorted by residual: chirality pdb=" CB VAL A 943 " pdb=" CA VAL A 943 " pdb=" CG1 VAL A 943 " pdb=" CG2 VAL A 943 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C3' DT I 22 " pdb=" C4' DT I 22 " pdb=" O3' DT I 22 " pdb=" C2' DT I 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA PHE A 804 " pdb=" N PHE A 804 " pdb=" C PHE A 804 " pdb=" CB PHE A 804 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 3093 not shown) Planarity restraints: 2883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 212 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ARG B 212 " 0.065 2.00e-02 2.50e+03 pdb=" O ARG B 212 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 213 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.024 2.00e-02 2.50e+03 2.36e-02 1.39e+01 pdb=" CG TRP B 317 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO D 99 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.046 5.00e-02 4.00e+02 ... (remaining 2880 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 995 2.70 - 3.25: 16638 3.25 - 3.80: 32825 3.80 - 4.35: 38797 4.35 - 4.90: 62265 Nonbonded interactions: 151520 Sorted by model distance: nonbonded pdb=" OD2 ASP A 600 " pdb="CA CA A1101 " model vdw 2.147 2.510 nonbonded pdb=" OE1 GLN A 962 " pdb="CA CA A1101 " model vdw 2.238 2.510 nonbonded pdb=" OG SER B 147 " pdb=" OD1 ASP B 214 " model vdw 2.248 3.040 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1101 " model vdw 2.260 2.510 nonbonded pdb=" OH TYR A 559 " pdb=" OE2 GLU A 597 " model vdw 2.268 3.040 ... (remaining 151515 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 401 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 or resid 4 \ 32 through 457 or (resid 458 and (name N or name CA or name C or name O or name \ CB )) or resid 459 through 519 or (resid 520 and (name N or name CA or name C or \ name O or name CB )) or resid 521 through 584 or (resid 585 and (name N or name \ CA or name C or name O or name CB )) or resid 586 through 607 or (resid 608 and \ (name N or name CA or name C or name O or name CB )) or resid 613 through 846 o \ r (resid 847 through 848 and (name N or name CA or name C or name O or name CB ) \ ) or resid 849 through 903 or (resid 904 and (name N or name CA or name C or nam \ e O or name CB )) or resid 905 through 913 or (resid 914 and (name N or name CA \ or name C or name O or name CB )) or resid 915 through 917 or (resid 918 and (na \ me N or name CA or name C or name O or name CB )) or resid 919 through 924 or (r \ esid 925 and (name N or name CA or name C or name O or name CB )) or resid 926 t \ hrough 958 or (resid 961 and (name N or name CA or name C or name O or name CB ) \ ) or resid 962 through 1102)) selection = (chain 'C' and (resid 401 through 430 or resid 432 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 568 o \ r (resid 569 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 70 through 571 or (resid 572 and (name N or name CA or name C or name O or name \ CB )) or resid 573 through 603 or (resid 604 and (name N or name CA or name C or \ name O or name CB )) or resid 605 through 608 or resid 613 through 631 or (resi \ d 632 and (name N or name CA or name C or name O or name CB )) or resid 633 thro \ ugh 813 or (resid 814 and (name N or name CA or name C or name O or name CB )) o \ r resid 815 through 816 or (resid 817 and (name N or name CA or name C or name O \ or name CB )) or resid 818 through 822 or (resid 823 through 824 and (name N or \ name CA or name C or name O or name CB )) or resid 825 through 826 or (resid 82 \ 7 through 828 and (name N or name CA or name C or name O or name CB )) or resid \ 829 through 834 or (resid 835 and (name N or name CA or name C or name O or name \ CB )) or resid 836 through 838 or (resid 839 and (name N or name CA or name C o \ r name O or name CB )) or resid 840 through 854 or (resid 855 and (name N or nam \ e CA or name C or name O or name CB )) or resid 856 through 860 or (resid 861 an \ d (name N or name CA or name C or name O or name CB )) or resid 862 through 867 \ or (resid 868 and (name N or name CA or name C or name O or name CB )) or resid \ 869 through 947 or (resid 948 and (name N or name CA or name C or name O or name \ CB )) or resid 949 through 979 or (resid 980 and (name N or name CA or name C o \ r name O or name CB )) or resid 981 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 334 or (resid 335 through 338 and (name N or nam \ e CA or name C or name O or name CB )) or resid 339 through 351)) selection = (chain 'D' and (resid 1 through 339 or (resid 340 through 342 and (name N or nam \ e CA or name C or name O or name CB )) or resid 343 through 351)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 21.910 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.009 0.189 20047 Z= 0.548 Angle : 1.062 20.307 27992 Z= 0.737 Chirality : 0.060 0.317 3096 Planarity : 0.007 0.084 2883 Dihedral : 22.733 178.268 7936 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.61 % Favored : 92.07 % Rotamer: Outliers : 0.55 % Allowed : 10.78 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 1.15 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.10 (0.15), residues: 1893 helix: -2.87 (0.14), residues: 633 sheet: -1.54 (0.26), residues: 333 loop : -3.08 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 558 TYR 0.027 0.002 TYR C 998 PHE 0.024 0.003 PHE C 591 TRP 0.062 0.003 TRP B 317 HIS 0.009 0.002 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00846 / 0.54 (20039) covalent geometry : angle 1.05227 / 0.74 (27988) hydrogen bonds : bond 0.15254 / 10.36 ( 854) hydrogen bonds : angle 6.61384 / 4.70 ( 2244) metal coordination : bond 0.11388 / 5.92 ( 8) metal coordination : angle 11.98558 / 5.65 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.9122 (ptp) cc_final: 0.8769 (ptm) REVERT: A 602 MET cc_start: 0.8397 (ptm) cc_final: 0.7570 (ppp) REVERT: A 962 GLN cc_start: 0.8240 (tp40) cc_final: 0.7999 (tm-30) REVERT: B 162 MET cc_start: 0.8803 (mmt) cc_final: 0.8393 (mmm) REVERT: C 445 HIS cc_start: 0.8541 (m-70) cc_final: 0.8282 (m-70) REVERT: C 597 GLU cc_start: 0.7545 (tp30) cc_final: 0.7225 (tp30) REVERT: D 249 CYS cc_start: 0.8683 (t) cc_final: 0.8045 (t) REVERT: D 287 CYS cc_start: 0.7967 (m) cc_final: 0.7243 (m) REVERT: D 298 GLU cc_start: 0.7687 (tp30) cc_final: 0.7395 (tp30) outliers start: 9 outliers final: 4 residues processed: 191 average time/residue: 0.1508 time to fit residues: 43.4691 Evaluate side-chains 135 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 952 SER Chi-restraints excluded: chain C residue 962 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 HIS A 876 HIS A 975 ASN A1007 ASN B 101 ASN B 222 HIS B 281 ASN C1004 ASN D 4 GLN D 89 HIS D 94 HIS D 222 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.106521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071735 restraints weight = 54381.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072721 restraints weight = 34200.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.072913 restraints weight = 23609.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073220 restraints weight = 21535.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073397 restraints weight = 20202.427| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20047 Z= 0.152 Angle : 0.689 8.957 27992 Z= 0.386 Chirality : 0.048 0.246 3096 Planarity : 0.005 0.060 2883 Dihedral : 25.858 176.809 4346 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 1.48 % Allowed : 13.67 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.17), residues: 1893 helix: -1.35 (0.18), residues: 646 sheet: -1.08 (0.26), residues: 367 loop : -2.88 (0.17), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.018 0.001 TYR C 998 PHE 0.026 0.001 PHE A 804 TRP 0.025 0.001 TRP B 317 HIS 0.006 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (20039) covalent geometry : angle 0.68761 / 0.39 (27988) hydrogen bonds : bond 0.05563 / 3.85 ( 854) hydrogen bonds : angle 5.02456 / 3.57 ( 2244) metal coordination : bond 0.01024 / 0.66 ( 8) metal coordination : angle 3.85810 / 1.94 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8854 (ptp) cc_final: 0.8633 (ptm) REVERT: A 602 MET cc_start: 0.8303 (ptm) cc_final: 0.7169 (ppp) REVERT: A 716 GLU cc_start: 0.7694 (tp30) cc_final: 0.7345 (tp30) REVERT: B 270 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6976 (tm-30) REVERT: B 285 MET cc_start: 0.8370 (mmm) cc_final: 0.8141 (mmt) REVERT: C 445 HIS cc_start: 0.8499 (m-70) cc_final: 0.8279 (m90) REVERT: C 451 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8517 (mp) REVERT: C 503 LEU cc_start: 0.9101 (tp) cc_final: 0.8825 (tp) REVERT: C 597 GLU cc_start: 0.7766 (tp30) cc_final: 0.7503 (mm-30) REVERT: D 126 GLU cc_start: 0.8583 (pp20) cc_final: 0.8251 (pp20) REVERT: D 152 MET cc_start: 0.8407 (tpp) cc_final: 0.8205 (mmp) REVERT: D 287 CYS cc_start: 0.7953 (m) cc_final: 0.7393 (m) REVERT: D 298 GLU cc_start: 0.7814 (tp30) cc_final: 0.7495 (tp30) outliers start: 24 outliers final: 11 residues processed: 168 average time/residue: 0.1205 time to fit residues: 33.4029 Evaluate side-chains 140 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 263 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 101 optimal weight: 0.1980 chunk 93 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 128 optimal weight: 0.0770 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 753 ASN B 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.107439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072224 restraints weight = 58479.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.073311 restraints weight = 35957.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073680 restraints weight = 23886.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073918 restraints weight = 21382.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074148 restraints weight = 19801.001| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20047 Z= 0.147 Angle : 0.640 11.073 27992 Z= 0.359 Chirality : 0.045 0.247 3096 Planarity : 0.004 0.049 2883 Dihedral : 25.650 179.875 4342 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.60 % Rotamer: Outliers : 2.65 % Allowed : 16.01 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.18), residues: 1893 helix: -0.73 (0.19), residues: 652 sheet: -0.84 (0.27), residues: 374 loop : -2.56 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 409 TYR 0.015 0.001 TYR C 757 PHE 0.029 0.001 PHE C 418 TRP 0.017 0.001 TRP B 317 HIS 0.007 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (20039) covalent geometry : angle 0.63972 / 0.36 (27988) hydrogen bonds : bond 0.04887 / 3.38 ( 854) hydrogen bonds : angle 4.64641 / 3.28 ( 2244) metal coordination : bond 0.00639 / 0.35 ( 8) metal coordination : angle 2.48595 / 1.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 570 MET cc_start: 0.8752 (ptp) cc_final: 0.8549 (ptm) REVERT: A 602 MET cc_start: 0.8290 (ptm) cc_final: 0.7154 (ppp) REVERT: A 716 GLU cc_start: 0.7826 (tp30) cc_final: 0.7483 (tp30) REVERT: A 876 HIS cc_start: 0.5341 (m-70) cc_final: 0.5056 (m-70) REVERT: B 285 MET cc_start: 0.8312 (mmm) cc_final: 0.7437 (mmm) REVERT: C 609 HIS cc_start: 0.6804 (OUTLIER) cc_final: 0.6326 (m-70) REVERT: D 5 MET cc_start: 0.8184 (tpp) cc_final: 0.7944 (tpp) REVERT: D 126 GLU cc_start: 0.8509 (pp20) cc_final: 0.8163 (pp20) REVERT: D 152 MET cc_start: 0.8297 (tpp) cc_final: 0.7853 (mmm) REVERT: D 287 CYS cc_start: 0.7636 (m) cc_final: 0.7264 (m) REVERT: D 298 GLU cc_start: 0.7789 (tp30) cc_final: 0.7491 (tp30) REVERT: D 303 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7458 (pm20) outliers start: 43 outliers final: 19 residues processed: 173 average time/residue: 0.1095 time to fit residues: 32.4562 Evaluate side-chains 146 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 157 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 199 optimal weight: 30.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.105283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.070177 restraints weight = 54961.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.070570 restraints weight = 39577.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071007 restraints weight = 27112.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071368 restraints weight = 22723.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071514 restraints weight = 20872.340| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20047 Z= 0.247 Angle : 0.718 15.125 27992 Z= 0.389 Chirality : 0.046 0.248 3096 Planarity : 0.005 0.048 2883 Dihedral : 25.668 179.881 4342 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 3.02 % Allowed : 17.86 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.18), residues: 1893 helix: -0.39 (0.20), residues: 648 sheet: -0.65 (0.28), residues: 366 loop : -2.48 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 237 TYR 0.018 0.002 TYR C 757 PHE 0.053 0.002 PHE C 418 TRP 0.021 0.002 TRP B 317 HIS 0.007 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.25 (20039) covalent geometry : angle 0.71723 / 0.39 (27988) hydrogen bonds : bond 0.05225 / 3.60 ( 854) hydrogen bonds : angle 4.67049 / 3.28 ( 2244) metal coordination : bond 0.02546 / 1.28 ( 8) metal coordination : angle 2.01017 / 0.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 127 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 602 MET cc_start: 0.8345 (ptm) cc_final: 0.7066 (ppp) REVERT: A 716 GLU cc_start: 0.8072 (tp30) cc_final: 0.7684 (tp30) REVERT: A 876 HIS cc_start: 0.5480 (m-70) cc_final: 0.5164 (m-70) REVERT: B 270 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7071 (tm-30) REVERT: B 285 MET cc_start: 0.8266 (mmm) cc_final: 0.8002 (mmt) REVERT: C 597 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7765 (mm-30) REVERT: C 609 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.6460 (m-70) REVERT: C 948 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: D 126 GLU cc_start: 0.8492 (pp20) cc_final: 0.8142 (pp20) REVERT: D 152 MET cc_start: 0.8261 (tpp) cc_final: 0.7804 (mmm) REVERT: D 287 CYS cc_start: 0.7820 (m) cc_final: 0.7327 (m) REVERT: D 298 GLU cc_start: 0.7816 (tp30) cc_final: 0.7496 (tp30) REVERT: D 303 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7512 (pm20) outliers start: 49 outliers final: 33 residues processed: 163 average time/residue: 0.1125 time to fit residues: 31.4043 Evaluate side-chains 157 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 194 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 184 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 200 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 HIS C 515 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.104868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.069632 restraints weight = 66181.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.070695 restraints weight = 38262.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.071157 restraints weight = 25128.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.071516 restraints weight = 22322.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.071665 restraints weight = 20452.055| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3089 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20047 Z= 0.250 Angle : 0.710 12.044 27992 Z= 0.386 Chirality : 0.047 0.261 3096 Planarity : 0.004 0.051 2883 Dihedral : 25.650 178.541 4342 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer: Outliers : 3.26 % Allowed : 18.90 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.18), residues: 1893 helix: -0.23 (0.20), residues: 648 sheet: -0.35 (0.30), residues: 334 loop : -2.36 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 123 TYR 0.019 0.002 TYR C 998 PHE 0.039 0.002 PHE C 418 TRP 0.022 0.002 TRP B 317 HIS 0.007 0.001 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (20039) covalent geometry : angle 0.70981 / 0.39 (27988) hydrogen bonds : bond 0.05184 / 3.57 ( 854) hydrogen bonds : angle 4.65381 / 3.26 ( 2244) metal coordination : bond 0.02465 / 1.25 ( 8) metal coordination : angle 2.02483 / 0.96 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 123 time to evaluate : 0.695 Fit side-chains REVERT: A 602 MET cc_start: 0.8378 (ptm) cc_final: 0.7087 (ppp) REVERT: A 716 GLU cc_start: 0.8110 (tp30) cc_final: 0.7779 (tp30) REVERT: A 983 GLU cc_start: 0.8688 (tt0) cc_final: 0.8367 (tm-30) REVERT: B 5 MET cc_start: 0.8319 (tmm) cc_final: 0.8104 (tmm) REVERT: B 285 MET cc_start: 0.8279 (mmm) cc_final: 0.8039 (mmt) REVERT: C 451 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 597 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7796 (mm-30) REVERT: C 772 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8533 (tm) REVERT: D 126 GLU cc_start: 0.8473 (pp20) cc_final: 0.8130 (pp20) REVERT: D 298 GLU cc_start: 0.7872 (tp30) cc_final: 0.7543 (tp30) REVERT: D 303 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7615 (pm20) outliers start: 53 outliers final: 35 residues processed: 162 average time/residue: 0.1061 time to fit residues: 29.5526 Evaluate side-chains 157 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 249 CYS Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 131 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 180 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 206 optimal weight: 50.0000 chunk 50 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 203 optimal weight: 40.0000 chunk 96 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 HIS ** C 908 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 = 0.3819 r_free = 0.3819 target = 0.107636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.072430 restraints weight = 56636.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073798 restraints weight = 33655.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.073930 restraints weight = 22271.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074212 restraints weight = 20185.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074392 restraints weight = 19082.558| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 20047 Z= 0.128 Angle : 0.633 13.781 27992 Z= 0.348 Chirality : 0.044 0.263 3096 Planarity : 0.004 0.049 2883 Dihedral : 25.441 178.392 4340 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 2.40 % Allowed : 20.50 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.19), residues: 1893 helix: 0.05 (0.20), residues: 649 sheet: -0.34 (0.28), residues: 358 loop : -2.19 (0.19), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 972 TYR 0.014 0.001 TYR A 757 PHE 0.034 0.001 PHE C 418 TRP 0.013 0.001 TRP B 36 HIS 0.003 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (20039) covalent geometry : angle 0.63202 / 0.35 (27988) hydrogen bonds : bond 0.04363 / 3.01 ( 854) hydrogen bonds : angle 4.35620 / 3.05 ( 2244) metal coordination : bond 0.00559 / 0.30 ( 8) metal coordination : angle 2.64803 / 1.32 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 138 time to evaluate : 0.597 Fit side-chains REVERT: A 602 MET cc_start: 0.8283 (ptm) cc_final: 0.7056 (ppp) REVERT: A 627 MET cc_start: 0.8335 (ttm) cc_final: 0.7936 (mtm) REVERT: A 716 GLU cc_start: 0.7909 (tp30) cc_final: 0.7506 (tp30) REVERT: A 983 GLU cc_start: 0.8533 (tt0) cc_final: 0.8299 (tm-30) REVERT: B 285 MET cc_start: 0.8281 (mmm) cc_final: 0.8043 (mmt) REVERT: C 597 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7591 (mm-30) REVERT: C 662 GLU cc_start: 0.8609 (tt0) cc_final: 0.8256 (tm-30) REVERT: C 772 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8410 (tm) REVERT: D 126 GLU cc_start: 0.8379 (pp20) cc_final: 0.8018 (pp20) REVERT: D 137 ARG cc_start: 0.8702 (ptp-170) cc_final: 0.8437 (ptp90) REVERT: D 152 MET cc_start: 0.7757 (mmm) cc_final: 0.7452 (mmm) REVERT: D 298 GLU cc_start: 0.7812 (tp30) cc_final: 0.7471 (tp30) REVERT: D 303 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7636 (pm20) outliers start: 39 outliers final: 27 residues processed: 162 average time/residue: 0.1104 time to fit residues: 30.8201 Evaluate side-chains 160 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 609 HIS Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 124 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 164 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 161 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 198 optimal weight: 50.0000 chunk 115 optimal weight: 10.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 HIS ** C 908 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 = 0.3788 r_free = 0.3788 target = 0.105771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.070580 restraints weight = 54186.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.071873 restraints weight = 34318.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072008 restraints weight = 23005.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072269 restraints weight = 20921.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072433 restraints weight = 19804.735| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20047 Z= 0.212 Angle : 0.678 12.193 27992 Z= 0.366 Chirality : 0.045 0.254 3096 Planarity : 0.004 0.046 2883 Dihedral : 25.476 179.566 4340 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.19 % Favored : 92.76 % Rotamer: Outliers : 2.89 % Allowed : 20.44 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.19), residues: 1893 helix: 0.14 (0.20), residues: 651 sheet: -0.09 (0.30), residues: 338 loop : -2.15 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 556 TYR 0.016 0.001 TYR C 757 PHE 0.027 0.002 PHE C 418 TRP 0.017 0.002 TRP B 317 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (20039) covalent geometry : angle 0.67767 / 0.37 (27988) hydrogen bonds : bond 0.04896 / 3.36 ( 854) hydrogen bonds : angle 4.43907 / 3.10 ( 2244) metal coordination : bond 0.02146 / 1.08 ( 8) metal coordination : angle 1.88059 / 0.93 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 0.653 Fit side-chains REVERT: A 602 MET cc_start: 0.8365 (ptm) cc_final: 0.7080 (ppp) REVERT: A 716 GLU cc_start: 0.8111 (tp30) cc_final: 0.7715 (tp30) REVERT: A 862 THR cc_start: 0.8381 (m) cc_final: 0.8040 (p) REVERT: A 983 GLU cc_start: 0.8657 (tt0) cc_final: 0.8385 (tm-30) REVERT: B 270 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7058 (tm-30) REVERT: B 285 MET cc_start: 0.8263 (mmm) cc_final: 0.8047 (mmt) REVERT: C 597 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 772 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8543 (tm) REVERT: D 126 GLU cc_start: 0.8384 (pp20) cc_final: 0.8013 (pp20) REVERT: D 137 ARG cc_start: 0.8911 (ptp-170) cc_final: 0.8647 (ptp90) REVERT: D 152 MET cc_start: 0.7698 (mmm) cc_final: 0.7406 (mmm) REVERT: D 298 GLU cc_start: 0.7818 (tp30) cc_final: 0.7492 (tp30) REVERT: D 303 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7493 (pm20) outliers start: 47 outliers final: 32 residues processed: 162 average time/residue: 0.1114 time to fit residues: 30.9430 Evaluate side-chains 159 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 HIS ** C 908 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 = 0.3799 r_free = 0.3799 target = 0.106450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071706 restraints weight = 79333.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.072709 restraints weight = 45674.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073501 restraints weight = 27525.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.073852 restraints weight = 22634.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.074025 restraints weight = 20454.213| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20047 Z= 0.163 Angle : 0.645 12.292 27992 Z= 0.351 Chirality : 0.044 0.260 3096 Planarity : 0.004 0.048 2883 Dihedral : 25.424 179.054 4340 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.60 % Rotamer: Outliers : 2.34 % Allowed : 21.80 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.19), residues: 1893 helix: 0.28 (0.20), residues: 649 sheet: -0.00 (0.29), residues: 348 loop : -2.10 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 556 TYR 0.014 0.001 TYR C 998 PHE 0.027 0.001 PHE C 418 TRP 0.015 0.001 TRP B 317 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (20039) covalent geometry : angle 0.64502 / 0.35 (27988) hydrogen bonds : bond 0.04561 / 3.12 ( 854) hydrogen bonds : angle 4.32920 / 3.02 ( 2244) metal coordination : bond 0.01224 / 0.63 ( 8) metal coordination : angle 1.94094 / 0.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.648 Fit side-chains REVERT: A 602 MET cc_start: 0.8262 (ptm) cc_final: 0.7045 (ppp) REVERT: A 716 GLU cc_start: 0.7963 (tp30) cc_final: 0.7622 (tp30) REVERT: A 856 LYS cc_start: 0.8339 (mttt) cc_final: 0.7946 (mtmm) REVERT: A 862 THR cc_start: 0.8350 (m) cc_final: 0.8021 (p) REVERT: B 102 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: B 270 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 597 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7725 (mm-30) REVERT: C 662 GLU cc_start: 0.8637 (tt0) cc_final: 0.8279 (tm-30) REVERT: C 772 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8551 (tm) REVERT: D 126 GLU cc_start: 0.8360 (pp20) cc_final: 0.7999 (pp20) REVERT: D 137 ARG cc_start: 0.8799 (ptp-170) cc_final: 0.8525 (ptp90) REVERT: D 152 MET cc_start: 0.7626 (mmm) cc_final: 0.7371 (mmm) REVERT: D 287 CYS cc_start: 0.6909 (m) cc_final: 0.6695 (m) REVERT: D 298 GLU cc_start: 0.7690 (tp30) cc_final: 0.7379 (tp30) REVERT: D 303 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7589 (pm20) outliers start: 38 outliers final: 27 residues processed: 156 average time/residue: 0.1141 time to fit residues: 30.2137 Evaluate side-chains 157 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 68 optimal weight: 7.9990 chunk 69 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 128 optimal weight: 0.3980 chunk 108 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 445 HIS C 637 ASN ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.107489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072216 restraints weight = 66132.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073308 restraints weight = 39537.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073751 restraints weight = 25880.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.074182 restraints weight = 22804.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.074301 restraints weight = 20714.753| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20047 Z= 0.134 Angle : 0.620 12.273 27992 Z= 0.340 Chirality : 0.043 0.259 3096 Planarity : 0.004 0.048 2883 Dihedral : 25.364 179.873 4340 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 2.09 % Allowed : 22.35 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.19), residues: 1893 helix: 0.32 (0.20), residues: 664 sheet: -0.01 (0.29), residues: 352 loop : -2.07 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 972 TYR 0.013 0.001 TYR A 757 PHE 0.025 0.001 PHE C 418 TRP 0.014 0.001 TRP B 317 HIS 0.003 0.001 HIS C 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (20039) covalent geometry : angle 0.61990 / 0.34 (27988) hydrogen bonds : bond 0.04355 / 2.98 ( 854) hydrogen bonds : angle 4.23032 / 2.95 ( 2244) metal coordination : bond 0.00701 / 0.38 ( 8) metal coordination : angle 2.03477 / 1.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.659 Fit side-chains REVERT: A 602 MET cc_start: 0.8283 (ptm) cc_final: 0.7067 (ppp) REVERT: A 716 GLU cc_start: 0.7991 (tp30) cc_final: 0.7589 (tp30) REVERT: A 856 LYS cc_start: 0.8293 (mttt) cc_final: 0.7919 (mtmm) REVERT: A 862 THR cc_start: 0.8310 (m) cc_final: 0.7985 (p) REVERT: B 270 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7102 (tm-30) REVERT: B 285 MET cc_start: 0.8523 (mmt) cc_final: 0.8290 (mmm) REVERT: C 627 MET cc_start: 0.8881 (ttm) cc_final: 0.8430 (ttm) REVERT: C 662 GLU cc_start: 0.8631 (tt0) cc_final: 0.8258 (tm-30) REVERT: C 772 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8469 (tm) REVERT: D 126 GLU cc_start: 0.8313 (pp20) cc_final: 0.7946 (pp20) REVERT: D 152 MET cc_start: 0.7631 (mmm) cc_final: 0.7353 (mmm) REVERT: D 287 CYS cc_start: 0.7074 (m) cc_final: 0.6845 (m) REVERT: D 298 GLU cc_start: 0.7818 (tp30) cc_final: 0.7434 (tp30) REVERT: D 303 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7680 (pm20) outliers start: 34 outliers final: 26 residues processed: 159 average time/residue: 0.1157 time to fit residues: 31.0497 Evaluate side-chains 159 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 933 THR Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 92 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 152 optimal weight: 0.0670 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 168 optimal weight: 0.6980 chunk 179 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS C 443 ASN C 445 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.107986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.073176 restraints weight = 53262.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.074148 restraints weight = 32668.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.074500 restraints weight = 22363.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074715 restraints weight = 19279.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.074881 restraints weight = 18262.117| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 20047 Z= 0.129 Angle : 0.632 15.264 27992 Z= 0.342 Chirality : 0.043 0.302 3096 Planarity : 0.004 0.048 2883 Dihedral : 25.328 179.597 4340 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.97 % Rotamer: Outliers : 1.91 % Allowed : 22.66 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1893 helix: 0.45 (0.20), residues: 662 sheet: 0.04 (0.29), residues: 352 loop : -2.01 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 229 TYR 0.014 0.001 TYR A 757 PHE 0.025 0.001 PHE C 418 TRP 0.010 0.001 TRP B 317 HIS 0.004 0.001 HIS B 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (20039) covalent geometry : angle 0.63143 / 0.34 (27988) hydrogen bonds : bond 0.04250 / 2.90 ( 854) hydrogen bonds : angle 4.17863 / 2.91 ( 2244) metal coordination : bond 0.00479 / 0.27 ( 8) metal coordination : angle 2.03419 / 1.02 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.593 Fit side-chains REVERT: A 602 MET cc_start: 0.8358 (ptm) cc_final: 0.7137 (ppp) REVERT: A 716 GLU cc_start: 0.7958 (tp30) cc_final: 0.7524 (tp30) REVERT: A 856 LYS cc_start: 0.8261 (mttt) cc_final: 0.7901 (mtmm) REVERT: A 858 MET cc_start: 0.7264 (mmp) cc_final: 0.4570 (ptt) REVERT: A 862 THR cc_start: 0.8251 (m) cc_final: 0.7908 (p) REVERT: B 270 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7070 (tm-30) REVERT: B 285 MET cc_start: 0.8512 (mmt) cc_final: 0.8284 (mmm) REVERT: C 627 MET cc_start: 0.8903 (ttm) cc_final: 0.8411 (ttm) REVERT: C 662 GLU cc_start: 0.8681 (tt0) cc_final: 0.8278 (tm-30) REVERT: C 772 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8391 (tm) REVERT: D 152 MET cc_start: 0.7623 (mmm) cc_final: 0.7320 (mmm) REVERT: D 287 CYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6748 (m) REVERT: D 298 GLU cc_start: 0.7842 (tp30) cc_final: 0.7447 (tp30) REVERT: D 303 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7626 (pm20) outliers start: 31 outliers final: 24 residues processed: 152 average time/residue: 0.1127 time to fit residues: 28.8664 Evaluate side-chains 155 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 863 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 331 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 101 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 633 HIS B 313 HIS C 445 HIS ** C 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.105061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.070366 restraints weight = 69818.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.071257 restraints weight = 40996.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072048 restraints weight = 27662.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072271 restraints weight = 23179.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.072496 restraints weight = 20885.633| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 20047 Z= 0.282 Angle : 0.739 13.746 27992 Z= 0.392 Chirality : 0.047 0.302 3096 Planarity : 0.005 0.047 2883 Dihedral : 25.477 179.789 4340 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.09 % Favored : 91.86 % Rotamer: Outliers : 2.34 % Allowed : 22.54 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.19), residues: 1893 helix: 0.39 (0.20), residues: 647 sheet: 0.15 (0.30), residues: 337 loop : -2.06 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 756 TYR 0.020 0.002 TYR C 757 PHE 0.023 0.002 PHE C 418 TRP 0.020 0.002 TRP B 317 HIS 0.007 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.28 (20039) covalent geometry : angle 0.73831 / 0.39 (27988) hydrogen bonds : bond 0.05269 / 3.58 ( 854) hydrogen bonds : angle 4.48565 / 3.12 ( 2244) metal coordination : bond 0.02836 / 1.43 ( 8) metal coordination : angle 2.00794 / 1.02 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2995.85 seconds wall clock time: 52 minutes 30.95 seconds (3150.95 seconds total)