Starting phenix.real_space_refine on Thu Mar 5 04:07:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oep_20033/03_2026/6oep_20033.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oep_20033/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6oep_20033/03_2026/6oep_20033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oep_20033/03_2026/6oep_20033.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oep_20033/03_2026/6oep_20033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oep_20033/03_2026/6oep_20033.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 5.70, per 1000 atoms: 0.30 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: 1.94 Conformation dependent library (CDL) restraints added in 893.5 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: 2.61 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: 5.10 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 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=" N VAL C 605 " pdb=" CA VAL C 605 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.51e+00 bond pdb=" N ILE C 953 " pdb=" CA ILE C 953 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.47e+00 bond pdb=" N VAL C 615 " pdb=" CA VAL C 615 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.23e-02 6.61e+03 6.97e+00 bond pdb=" N GLU C 607 " pdb=" CA GLU C 607 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.16e-02 7.43e+03 6.72e+00 bond pdb=" N HIS C 609 " pdb=" CA HIS C 609 " ideal model delta sigma weight residual 1.459 1.488 -0.030 1.16e-02 7.43e+03 6.58e+00 ... (remaining 20034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 27034 2.38 - 4.75: 849 4.75 - 7.13: 78 7.13 - 9.51: 22 9.51 - 11.88: 5 Bond angle restraints: 27988 Sorted by residual: angle pdb=" C GLU A 803 " pdb=" N PHE A 804 " pdb=" CA PHE A 804 " ideal model delta sigma weight residual 122.06 111.99 10.07 1.86e+00 2.89e-01 2.93e+01 angle pdb=" C ASN D 268 " pdb=" N ASP D 269 " pdb=" CA ASP D 269 " ideal model delta sigma weight residual 122.46 129.43 -6.97 1.41e+00 5.03e-01 2.44e+01 angle pdb=" N VAL A 742 " pdb=" CA VAL A 742 " pdb=" C VAL A 742 " ideal model delta sigma weight residual 106.42 113.82 -7.40 1.51e+00 4.39e-01 2.40e+01 angle pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.24e+01 angle pdb=" C PRO A 819 " pdb=" N ASN A 820 " pdb=" CA ASN A 820 " ideal model delta sigma weight residual 122.82 129.51 -6.69 1.42e+00 4.96e-01 2.22e+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: 2409 0.063 - 0.127: 566 0.127 - 0.190: 101 0.190 - 0.253: 18 0.253 - 0.317: 2 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=" 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 chirality pdb=" CA VAL A 943 " pdb=" N VAL A 943 " pdb=" C VAL A 943 " pdb=" CB VAL A 943 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.58e+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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 26.300 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.189 20047 Z= 0.372 Angle : 1.003 20.307 27992 Z= 0.572 Chirality : 0.057 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 covalent geometry : bond 0.00799 (20039) covalent geometry : angle 0.99251 (27988) hydrogen bonds : bond 0.15254 ( 854) hydrogen bonds : angle 6.61384 ( 2244) metal coordination : bond 0.11388 ( 8) metal coordination : angle 11.98558 ( 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 : 0.600 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: 3 residues processed: 191 average time/residue: 0.1597 time to fit residues: 45.5046 Evaluate side-chains 134 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 8.9990 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 836 HIS A 876 HIS A 975 ASN A1007 ASN B 101 ASN B 222 HIS C1004 ASN D 4 GLN D 89 HIS D 94 HIS D 222 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072213 restraints weight = 53867.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.073291 restraints weight = 34302.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073445 restraints weight = 23494.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073721 restraints weight = 21332.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.073917 restraints weight = 20027.067| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20047 Z= 0.143 Angle : 0.622 9.736 27992 Z= 0.345 Chirality : 0.041 0.202 3096 Planarity : 0.005 0.058 2883 Dihedral : 25.474 174.832 4343 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.40 % Rotamer: Outliers : 1.54 % Allowed : 13.98 % Favored : 84.48 % 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: -2.84 (0.17), residues: 1893 helix: -1.19 (0.19), residues: 648 sheet: -1.18 (0.26), residues: 374 loop : -2.76 (0.18), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.020 0.001 TYR C 886 PHE 0.020 0.001 PHE A 804 TRP 0.020 0.001 TRP B 317 HIS 0.008 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00306 (20039) covalent geometry : angle 0.62146 (27988) hydrogen bonds : bond 0.04614 ( 854) hydrogen bonds : angle 4.73106 ( 2244) metal coordination : bond 0.00611 ( 8) metal coordination : angle 2.93542 ( 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 191 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8728 (ptp) cc_final: 0.8522 (ptm) REVERT: A 602 MET cc_start: 0.8262 (ptm) cc_final: 0.7154 (ppp) REVERT: A 691 MET cc_start: 0.7506 (mmt) cc_final: 0.7303 (tpt) REVERT: A 716 GLU cc_start: 0.7745 (tp30) cc_final: 0.7460 (tp30) REVERT: B 270 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6624 (tm-30) REVERT: C 451 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8487 (mp) REVERT: C 503 LEU cc_start: 0.9095 (tp) cc_final: 0.8877 (tp) REVERT: C 609 HIS cc_start: 0.6852 (OUTLIER) cc_final: 0.6349 (m-70) REVERT: C 662 GLU cc_start: 0.8593 (tt0) cc_final: 0.8222 (tm-30) REVERT: D 126 GLU cc_start: 0.8498 (pp20) cc_final: 0.8249 (pp20) REVERT: D 152 MET cc_start: 0.8279 (tpp) cc_final: 0.7872 (mmm) REVERT: D 287 CYS cc_start: 0.7816 (m) cc_final: 0.7357 (m) REVERT: D 298 GLU cc_start: 0.7746 (tp30) cc_final: 0.7453 (tp30) outliers start: 25 outliers final: 11 residues processed: 181 average time/residue: 0.1172 time to fit residues: 34.9833 Evaluate side-chains 144 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 274 VAL Chi-restraints excluded: chain D residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 21 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 101 optimal weight: 0.0870 chunk 93 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 ASN B 89 HIS C 637 ASN ** C 908 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 = 0.3830 r_free = 0.3830 target = 0.108283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073314 restraints weight = 59381.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.074306 restraints weight = 36119.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.074741 restraints weight = 24606.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.074974 restraints weight = 22022.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.075172 restraints weight = 20375.538| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1889 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= 0.134 Angle : 0.595 11.435 27992 Z= 0.328 Chirality : 0.040 0.224 3096 Planarity : 0.004 0.048 2883 Dihedral : 25.249 177.274 4342 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 2.65 % Allowed : 15.58 % Favored : 81.77 % 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: -2.17 (0.18), residues: 1893 helix: -0.50 (0.20), residues: 656 sheet: -0.84 (0.26), residues: 384 loop : -2.50 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 123 TYR 0.014 0.001 TYR C 886 PHE 0.015 0.001 PHE A 804 TRP 0.016 0.001 TRP B 317 HIS 0.006 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00291 (20039) covalent geometry : angle 0.59444 (27988) hydrogen bonds : bond 0.04122 ( 854) hydrogen bonds : angle 4.40797 ( 2244) metal coordination : bond 0.00453 ( 8) metal coordination : angle 2.42414 ( 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 192 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8254 (ptm) cc_final: 0.7197 (ppp) REVERT: A 691 MET cc_start: 0.7483 (mmt) cc_final: 0.7255 (tpt) REVERT: A 716 GLU cc_start: 0.7895 (tp30) cc_final: 0.7513 (tp30) REVERT: B 281 ASN cc_start: 0.8733 (t0) cc_final: 0.8487 (t0) REVERT: C 662 GLU cc_start: 0.8597 (tt0) cc_final: 0.8220 (tm-30) REVERT: D 126 GLU cc_start: 0.8421 (pp20) cc_final: 0.8085 (pp20) REVERT: D 152 MET cc_start: 0.8212 (tpp) cc_final: 0.7762 (mmm) REVERT: D 287 CYS cc_start: 0.7371 (m) cc_final: 0.6938 (m) REVERT: D 298 GLU cc_start: 0.7735 (tp30) cc_final: 0.7419 (tp30) REVERT: D 303 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7457 (pm20) outliers start: 43 outliers final: 20 residues processed: 180 average time/residue: 0.1147 time to fit residues: 34.2523 Evaluate side-chains 153 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU 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 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 263 LEU 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: 2.9990 chunk 91 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 172 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS C 445 HIS C 515 HIS ** C 908 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 = 0.3792 r_free = 0.3792 target = 0.105984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.070833 restraints weight = 55073.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072261 restraints weight = 33994.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072363 restraints weight = 22632.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.072622 restraints weight = 20438.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072790 restraints weight = 19480.561| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 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 = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20047 Z= 0.214 Angle : 0.657 11.911 27992 Z= 0.354 Chirality : 0.042 0.240 3096 Planarity : 0.004 0.047 2883 Dihedral : 25.290 176.604 4340 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 2.59 % Allowed : 17.00 % Favored : 80.42 % 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: -1.73 (0.19), residues: 1893 helix: -0.10 (0.20), residues: 651 sheet: -0.33 (0.29), residues: 332 loop : -2.30 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 556 TYR 0.019 0.002 TYR C 757 PHE 0.014 0.002 PHE D 206 TRP 0.021 0.002 TRP B 317 HIS 0.005 0.001 HIS A 942 Details of bonding type rmsd covalent geometry : bond 0.00488 (20039) covalent geometry : angle 0.65653 (27988) hydrogen bonds : bond 0.04591 ( 854) hydrogen bonds : angle 4.44961 ( 2244) metal coordination : bond 0.02049 ( 8) metal coordination : angle 1.83169 ( 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 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: A 602 MET cc_start: 0.8276 (ptm) cc_final: 0.7014 (ppp) REVERT: A 691 MET cc_start: 0.7574 (mmt) cc_final: 0.7373 (tpt) REVERT: A 716 GLU cc_start: 0.8086 (tp30) cc_final: 0.7659 (tp30) REVERT: B 5 MET cc_start: 0.8282 (tmm) cc_final: 0.8033 (tmm) REVERT: B 270 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7044 (tm-30) REVERT: D 126 GLU cc_start: 0.8426 (pp20) cc_final: 0.8082 (pp20) REVERT: D 287 CYS cc_start: 0.7528 (m) cc_final: 0.7091 (m) REVERT: D 298 GLU cc_start: 0.7770 (tp30) cc_final: 0.7465 (tp30) REVERT: D 303 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7589 (pm20) outliers start: 42 outliers final: 29 residues processed: 165 average time/residue: 0.1087 time to fit residues: 30.6044 Evaluate side-chains 154 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 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 863 VAL Chi-restraints excluded: chain B residue 12 ILE 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 258 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 472 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 933 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 274 VAL Chi-restraints excluded: chain D residue 280 GLU 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: 10.0000 chunk 89 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 200 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 443 ASN ** 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 = 0.3812 r_free = 0.3812 target = 0.107302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.072464 restraints weight = 66309.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073375 restraints weight = 38694.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073949 restraints weight = 26399.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.074220 restraints weight = 22932.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074378 restraints weight = 20902.002| |-----------------------------------------------------------------------------| 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 = 0.14 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 = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20047 Z= 0.152 Angle : 0.606 13.421 27992 Z= 0.329 Chirality : 0.040 0.234 3096 Planarity : 0.004 0.048 2883 Dihedral : 25.178 175.997 4340 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 2.46 % Allowed : 18.35 % Favored : 79.19 % 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: -1.43 (0.19), residues: 1893 helix: 0.18 (0.20), residues: 652 sheet: -0.19 (0.29), residues: 348 loop : -2.18 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 972 TYR 0.014 0.001 TYR C 998 PHE 0.045 0.001 PHE C 418 TRP 0.017 0.001 TRP B 317 HIS 0.005 0.001 HIS C 445 Details of bonding type rmsd covalent geometry : bond 0.00339 (20039) covalent geometry : angle 0.60600 (27988) hydrogen bonds : bond 0.04054 ( 854) hydrogen bonds : angle 4.25072 ( 2244) metal coordination : bond 0.00797 ( 8) metal coordination : angle 2.13131 ( 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 177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 602 MET cc_start: 0.8209 (ptm) cc_final: 0.7076 (ppp) REVERT: A 691 MET cc_start: 0.7563 (mmt) cc_final: 0.7351 (tpt) REVERT: A 716 GLU cc_start: 0.7934 (tp30) cc_final: 0.7493 (tp30) REVERT: A 841 MET cc_start: 0.7751 (mtt) cc_final: 0.7516 (mtp) REVERT: A 847 MET cc_start: 0.7809 (mpp) cc_final: 0.7435 (mpp) REVERT: A 983 GLU cc_start: 0.8534 (tt0) cc_final: 0.8173 (tm-30) REVERT: B 270 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 445 HIS cc_start: 0.8534 (m90) cc_final: 0.8259 (m-70) REVERT: C 451 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8425 (mp) REVERT: C 662 GLU cc_start: 0.8619 (tt0) cc_final: 0.8278 (tm-30) REVERT: C 752 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7854 (tt0) REVERT: C 772 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8429 (tm) REVERT: D 287 CYS cc_start: 0.7404 (m) cc_final: 0.7058 (m) REVERT: D 298 GLU cc_start: 0.7723 (tp30) cc_final: 0.7423 (tp30) REVERT: D 303 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7563 (pm20) outliers start: 40 outliers final: 26 residues processed: 165 average time/residue: 0.1097 time to fit residues: 30.7758 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 : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 LEU 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 451 LEU Chi-restraints excluded: chain C residue 564 VAL 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 752 GLU Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain D residue 8 VAL 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 280 GLU 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: 0.9990 chunk 44 optimal weight: 0.0370 chunk 180 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 203 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.108655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.073849 restraints weight = 58155.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.074677 restraints weight = 35408.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075030 restraints weight = 24900.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075307 restraints weight = 22193.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.075506 restraints weight = 20588.613| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20047 Z= 0.127 Angle : 0.589 13.234 27992 Z= 0.318 Chirality : 0.040 0.208 3096 Planarity : 0.004 0.047 2883 Dihedral : 25.056 177.334 4340 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 2.46 % Allowed : 18.66 % Favored : 78.88 % 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: -1.10 (0.19), residues: 1893 helix: 0.50 (0.21), residues: 645 sheet: -0.23 (0.29), residues: 364 loop : -1.92 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 972 TYR 0.013 0.001 TYR A 757 PHE 0.041 0.001 PHE C 418 TRP 0.012 0.001 TRP B 317 HIS 0.003 0.001 HIS A 876 Details of bonding type rmsd covalent geometry : bond 0.00278 (20039) covalent geometry : angle 0.58807 (27988) hydrogen bonds : bond 0.03811 ( 854) hydrogen bonds : angle 4.11058 ( 2244) metal coordination : bond 0.00358 ( 8) metal coordination : angle 1.99319 ( 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 188 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.556 Fit side-chains REVERT: A 602 MET cc_start: 0.8370 (ptm) cc_final: 0.7284 (ppp) REVERT: A 691 MET cc_start: 0.7389 (mmt) cc_final: 0.7164 (tpt) REVERT: A 716 GLU cc_start: 0.7976 (tp30) cc_final: 0.7530 (tp30) REVERT: A 847 MET cc_start: 0.7816 (mpp) cc_final: 0.7368 (mpp) REVERT: A 856 LYS cc_start: 0.8344 (mttt) cc_final: 0.7959 (mtmm) REVERT: A 983 GLU cc_start: 0.8264 (tt0) cc_final: 0.8014 (tm-30) REVERT: B 102 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 270 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 303 GLU cc_start: 0.8495 (pm20) cc_final: 0.7962 (pm20) REVERT: B 322 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: C 445 HIS cc_start: 0.8551 (m90) cc_final: 0.8271 (m-70) REVERT: C 446 ARG cc_start: 0.7479 (ptm160) cc_final: 0.7273 (ptm160) REVERT: C 772 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8273 (tm) REVERT: D 152 MET cc_start: 0.8190 (tpp) cc_final: 0.7769 (mmm) REVERT: D 287 CYS cc_start: 0.7216 (m) cc_final: 0.6832 (m) REVERT: D 298 GLU cc_start: 0.7719 (tp30) cc_final: 0.7385 (tp30) REVERT: D 303 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7454 (pm20) outliers start: 40 outliers final: 25 residues processed: 173 average time/residue: 0.1154 time to fit residues: 33.2343 Evaluate side-chains 163 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 662 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 168 THR 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 B residue 322 MET Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 569 ASP 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 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS 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 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: 1.9990 chunk 64 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 198 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.107419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.072346 restraints weight = 54278.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.073771 restraints weight = 33627.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.073900 restraints weight = 22305.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.074161 restraints weight = 20360.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.074321 restraints weight = 19288.438| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 20047 Z= 0.166 Angle : 0.620 12.392 27992 Z= 0.331 Chirality : 0.041 0.274 3096 Planarity : 0.004 0.045 2883 Dihedral : 25.065 177.212 4340 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.76 % Rotamer: Outliers : 2.65 % Allowed : 19.15 % Favored : 78.20 % 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: -1.00 (0.19), residues: 1893 helix: 0.54 (0.21), residues: 650 sheet: 0.12 (0.30), residues: 342 loop : -1.93 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 409 TYR 0.014 0.001 TYR C 757 PHE 0.036 0.001 PHE C 418 TRP 0.021 0.001 TRP A 956 HIS 0.003 0.001 HIS C 937 Details of bonding type rmsd covalent geometry : bond 0.00377 (20039) covalent geometry : angle 0.61963 (27988) hydrogen bonds : bond 0.04111 ( 854) hydrogen bonds : angle 4.15699 ( 2244) metal coordination : bond 0.01324 ( 8) metal coordination : angle 1.65644 ( 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 178 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 135 time to evaluate : 0.666 Fit side-chains REVERT: A 602 MET cc_start: 0.8378 (ptm) cc_final: 0.7202 (ppp) REVERT: A 716 GLU cc_start: 0.8018 (tp30) cc_final: 0.7428 (tp30) REVERT: A 847 MET cc_start: 0.7784 (mpp) cc_final: 0.7267 (mpp) REVERT: A 856 LYS cc_start: 0.8375 (mttt) cc_final: 0.7969 (mtmm) REVERT: A 858 MET cc_start: 0.7020 (mmp) cc_final: 0.4686 (ptt) REVERT: A 862 THR cc_start: 0.8208 (m) cc_final: 0.7864 (p) REVERT: B 102 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7900 (mt-10) REVERT: C 445 HIS cc_start: 0.8512 (m90) cc_final: 0.8202 (m-70) REVERT: C 772 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8389 (tm) REVERT: C 948 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: D 126 GLU cc_start: 0.8306 (pp20) cc_final: 0.8076 (pp20) REVERT: D 152 MET cc_start: 0.8114 (tpp) cc_final: 0.7687 (mmm) REVERT: D 287 CYS cc_start: 0.7420 (m) cc_final: 0.6996 (m) REVERT: D 298 GLU cc_start: 0.7818 (tp30) cc_final: 0.7438 (tp30) REVERT: D 303 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7377 (pm20) outliers start: 43 outliers final: 28 residues processed: 165 average time/residue: 0.1070 time to fit residues: 30.1884 Evaluate side-chains 161 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 LEU 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 152 MET 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 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 ASP 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 933 THR Chi-restraints excluded: chain C residue 948 GLU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS 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 280 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 204 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.106872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.072658 restraints weight = 79784.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073186 restraints weight = 43596.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073993 restraints weight = 30695.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074763 restraints weight = 23766.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.074884 restraints weight = 20929.547| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20047 Z= 0.182 Angle : 0.636 12.893 27992 Z= 0.338 Chirality : 0.041 0.252 3096 Planarity : 0.004 0.046 2883 Dihedral : 25.085 176.310 4340 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 2.46 % Allowed : 19.58 % Favored : 77.96 % 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: -0.91 (0.19), residues: 1893 helix: 0.61 (0.21), residues: 647 sheet: 0.14 (0.29), residues: 354 loop : -1.89 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 972 TYR 0.015 0.001 TYR C 757 PHE 0.034 0.001 PHE C 418 TRP 0.019 0.002 TRP B 317 HIS 0.004 0.001 HIS C 937 Details of bonding type rmsd covalent geometry : bond 0.00417 (20039) covalent geometry : angle 0.63596 (27988) hydrogen bonds : bond 0.04239 ( 854) hydrogen bonds : angle 4.22470 ( 2244) metal coordination : bond 0.01444 ( 8) metal coordination : angle 1.91214 ( 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 169 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.613 Fit side-chains REVERT: A 602 MET cc_start: 0.8245 (ptm) cc_final: 0.7044 (ppp) REVERT: A 716 GLU cc_start: 0.7993 (tp30) cc_final: 0.7512 (tp30) REVERT: A 847 MET cc_start: 0.7775 (mpp) cc_final: 0.7226 (mpp) REVERT: A 856 LYS cc_start: 0.8407 (mttt) cc_final: 0.8000 (mtmm) REVERT: A 858 MET cc_start: 0.6904 (mmp) cc_final: 0.4696 (ptt) REVERT: C 445 HIS cc_start: 0.8504 (m90) cc_final: 0.8203 (m-70) REVERT: C 662 GLU cc_start: 0.8658 (tt0) cc_final: 0.8337 (tm-30) REVERT: C 772 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8477 (tm) REVERT: D 110 MET cc_start: 0.9072 (mmt) cc_final: 0.8754 (mmp) REVERT: D 126 GLU cc_start: 0.8254 (pp20) cc_final: 0.8043 (pp20) REVERT: D 152 MET cc_start: 0.8076 (tpp) cc_final: 0.7683 (mmm) REVERT: D 287 CYS cc_start: 0.7428 (m) cc_final: 0.6867 (m) REVERT: D 298 GLU cc_start: 0.7741 (tp30) cc_final: 0.7386 (tp30) REVERT: D 302 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6459 (ptt) REVERT: D 303 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7482 (pm20) outliers start: 40 outliers final: 29 residues processed: 157 average time/residue: 0.1086 time to fit residues: 29.0294 Evaluate side-chains 158 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 LEU 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 168 THR 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 436 LEU Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 569 ASP 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 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS 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 280 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 68 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.108327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.073375 restraints weight = 66859.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.074409 restraints weight = 38422.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.074835 restraints weight = 26009.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075268 restraints weight = 22887.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.075397 restraints weight = 20850.711| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20047 Z= 0.133 Angle : 0.606 12.821 27992 Z= 0.323 Chirality : 0.040 0.239 3096 Planarity : 0.004 0.047 2883 Dihedral : 24.979 177.257 4340 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 20.01 % Favored : 77.89 % 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: -0.77 (0.20), residues: 1893 helix: 0.74 (0.21), residues: 644 sheet: 0.03 (0.29), residues: 366 loop : -1.74 (0.20), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 972 TYR 0.013 0.001 TYR A 757 PHE 0.032 0.001 PHE C 418 TRP 0.011 0.001 TRP B 317 HIS 0.002 0.001 HIS C 836 Details of bonding type rmsd covalent geometry : bond 0.00298 (20039) covalent geometry : angle 0.60531 (27988) hydrogen bonds : bond 0.03864 ( 854) hydrogen bonds : angle 4.07968 ( 2244) metal coordination : bond 0.00477 ( 8) metal coordination : angle 2.00640 ( 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 : 0.630 Fit side-chains REVERT: A 602 MET cc_start: 0.8357 (ptm) cc_final: 0.7199 (ppp) REVERT: A 716 GLU cc_start: 0.7960 (tp30) cc_final: 0.7376 (tp30) REVERT: A 847 MET cc_start: 0.7741 (mpp) cc_final: 0.7170 (mpp) REVERT: A 856 LYS cc_start: 0.8357 (mttt) cc_final: 0.7969 (mtmm) REVERT: A 858 MET cc_start: 0.6629 (mmp) cc_final: 0.4854 (ptt) REVERT: B 102 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: C 445 HIS cc_start: 0.8563 (m90) cc_final: 0.8234 (m-70) REVERT: C 662 GLU cc_start: 0.8619 (tt0) cc_final: 0.8280 (tm-30) REVERT: C 772 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8337 (tm) REVERT: C 970 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8111 (tpt170) REVERT: D 110 MET cc_start: 0.9129 (mmt) cc_final: 0.8820 (mmp) REVERT: D 126 GLU cc_start: 0.8273 (pp20) cc_final: 0.8029 (pp20) REVERT: D 152 MET cc_start: 0.8090 (tpp) cc_final: 0.7656 (mmm) REVERT: D 287 CYS cc_start: 0.7197 (m) cc_final: 0.6743 (m) REVERT: D 298 GLU cc_start: 0.7771 (tp30) cc_final: 0.7363 (tp30) REVERT: D 302 MET cc_start: 0.6545 (OUTLIER) cc_final: 0.6301 (ptt) REVERT: D 303 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7374 (pm20) outliers start: 34 outliers final: 26 residues processed: 163 average time/residue: 0.1053 time to fit residues: 28.8538 Evaluate side-chains 160 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 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 152 MET 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 242 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 569 ASP 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 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 280 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 92 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.106683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.071630 restraints weight = 55035.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073077 restraints weight = 32701.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073230 restraints weight = 21382.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073491 restraints weight = 19515.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.073677 restraints weight = 18559.672| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- 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 = 0.26 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 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20047 Z= 0.186 Angle : 0.643 12.700 27992 Z= 0.341 Chirality : 0.041 0.239 3096 Planarity : 0.004 0.046 2883 Dihedral : 25.034 177.113 4340 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 1.91 % Allowed : 20.38 % Favored : 77.71 % 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: -0.80 (0.20), residues: 1893 helix: 0.66 (0.21), residues: 650 sheet: 0.20 (0.29), residues: 354 loop : -1.80 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 137 TYR 0.015 0.001 TYR C 757 PHE 0.015 0.001 PHE A 804 TRP 0.017 0.002 TRP B 317 HIS 0.004 0.001 HIS A 942 Details of bonding type rmsd covalent geometry : bond 0.00426 (20039) covalent geometry : angle 0.64265 (27988) hydrogen bonds : bond 0.04281 ( 854) hydrogen bonds : angle 4.20273 ( 2244) metal coordination : bond 0.01625 ( 8) metal coordination : angle 1.77689 ( 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 159 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.681 Fit side-chains REVERT: A 602 MET cc_start: 0.8279 (ptm) cc_final: 0.7034 (ppp) REVERT: A 716 GLU cc_start: 0.8017 (tp30) cc_final: 0.7503 (tp30) REVERT: A 847 MET cc_start: 0.7804 (mpp) cc_final: 0.7269 (mpp) REVERT: A 856 LYS cc_start: 0.8367 (mttt) cc_final: 0.7971 (mtmm) REVERT: A 858 MET cc_start: 0.6689 (mmp) cc_final: 0.4726 (ptt) REVERT: C 445 HIS cc_start: 0.8524 (m90) cc_final: 0.8179 (m-70) REVERT: C 772 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8462 (tm) REVERT: D 110 MET cc_start: 0.9163 (mmt) cc_final: 0.8647 (mmp) REVERT: D 126 GLU cc_start: 0.8279 (pp20) cc_final: 0.8050 (pp20) REVERT: D 287 CYS cc_start: 0.7418 (m) cc_final: 0.6854 (m) REVERT: D 298 GLU cc_start: 0.7764 (tp30) cc_final: 0.7368 (tp30) REVERT: D 302 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.6171 (ptt) REVERT: D 303 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7370 (pm20) outliers start: 31 outliers final: 25 residues processed: 150 average time/residue: 0.1108 time to fit residues: 28.5562 Evaluate side-chains 156 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 439 LEU 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 168 THR 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 569 ASP 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 98 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 124 CYS Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 280 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 101 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 184 optimal weight: 0.0020 chunk 204 optimal weight: 5.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 ASN A 633 HIS B 313 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 = 0.3805 r_free = 0.3805 target = 0.106850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.071771 restraints weight = 69981.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.072751 restraints weight = 40866.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.073409 restraints weight = 27118.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.073643 restraints weight = 23437.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.073906 restraints weight = 21372.705| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20047 Z= 0.181 Angle : 0.643 12.828 27992 Z= 0.341 Chirality : 0.041 0.235 3096 Planarity : 0.004 0.046 2883 Dihedral : 25.050 176.586 4340 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.34 % Favored : 93.60 % Rotamer: Outliers : 2.34 % Allowed : 20.32 % Favored : 77.34 % 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: -0.84 (0.20), residues: 1893 helix: 0.60 (0.21), residues: 655 sheet: 0.23 (0.29), residues: 354 loop : -1.83 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 137 TYR 0.014 0.001 TYR C 757 PHE 0.012 0.001 PHE B 30 TRP 0.015 0.001 TRP B 317 HIS 0.004 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00415 (20039) covalent geometry : angle 0.64243 (27988) hydrogen bonds : bond 0.04260 ( 854) hydrogen bonds : angle 4.22349 ( 2244) metal coordination : bond 0.01334 ( 8) metal coordination : angle 2.00337 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2989.66 seconds wall clock time: 52 minutes 49.86 seconds (3169.86 seconds total)