Starting phenix.real_space_refine on Sat Sep 12 23:52:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oer_20035/09_2026/6oer_20035.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 108 5.16 5 C 11682 2.51 5 N 3436 2.21 5 O 4046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19482 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4844 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 608, 4829 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Conformer: "B" Number of residues, atoms: 608, 4829 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 bond proxies already assigned to first conformer: 4912 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: 4866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4866 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 590} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2674 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 927 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DT:plan': 2} Unresolved non-hydrogen planarities: 18 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: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1143 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' DT:plan': 2} Unresolved non-hydrogen planarities: 18 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: "H" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 242 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 33} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2551 SG CYS A 727 100.836 25.668 65.811 1.00 60.61 S ATOM 2572 SG CYS A 730 102.666 22.653 64.452 1.00 60.71 S ATOM 10094 SG CYS C 727 55.520 91.294 61.039 1.00 63.75 S ATOM 10115 SG CYS C 730 53.507 93.903 59.647 1.00 65.17 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 816 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 816 " occ=0.50 Time building chain proxies: 4.10, per 1000 atoms: 0.21 Number of scatterers: 19482 At special positions: 0 Unit cell: (157.29, 118.77, 159.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 108 16.00 P 204 15.00 O 4046 8.00 N 3436 7.00 C 11682 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: 1.61 Conformation dependent library (CDL) restraints added in 631.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 730 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 730 " Number of angles added : 4 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 37.8% alpha, 19.6% beta 93 base pairs and 155 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 401 through 424 removed outlier: 5.056A pdb=" N GLU A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU A 411 " --> pdb=" O ARG A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 removed outlier: 4.049A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 463 through 473 removed outlier: 3.522A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 508 Processing helix chain 'A' and resid 558 through 568 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 717 removed outlier: 3.590A pdb=" N GLY A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 740 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.577A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.223A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 813 removed outlier: 3.652A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 842 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 867 Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 874 through 895 removed outlier: 4.179A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Proline residue: A 891 - end of helix Processing helix chain 'A' and resid 897 through 901 removed outlier: 3.783A pdb=" N GLU A 901 " --> pdb=" O PRO A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 924 removed outlier: 4.960A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 4.403A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 4.152A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.676A pdb=" N GLY A 964 " --> pdb=" O GLY A 960 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 996 removed outlier: 4.070A pdb=" N GLU A 985 " --> pdb=" O CYS A 981 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1004 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 423 Processing helix chain 'C' and resid 427 through 441 Processing helix chain 'C' and resid 444 through 456 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 500 through 509 removed outlier: 3.517A pdb=" N ALA C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 3.739A 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 683 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 735 through 740 removed outlier: 3.533A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 removed outlier: 4.265A pdb=" N ASP C 774 " --> pdb=" O GLU C 770 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 813 Processing helix chain 'C' and resid 824 through 841 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.782A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) 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 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 923 removed outlier: 4.631A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 958 through 964 removed outlier: 3.914A pdb=" N GLY C 964 " --> pdb=" O GLY C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 975 Processing helix chain 'C' and resid 981 through 995 removed outlier: 4.161A pdb=" N GLU C 985 " --> pdb=" O CYS C 981 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1004 Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'H' and resid 102 through 107 removed outlier: 4.132A pdb=" N SER H 107 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 115 Processing helix chain 'H' and resid 123 through 136 removed outlier: 3.966A pdb=" N LYS H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU H 129 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR H 136 " --> pdb=" O MET H 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 519 removed outlier: 10.017A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 655 " --> pdb=" O PHE A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 519 removed outlier: 10.017A pdb=" N PHE A 591 " --> pdb=" O PHE A 700 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N PHE A 702 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 10.299A pdb=" N VAL A 593 " --> pdb=" O PHE A 702 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N GLY A 704 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 10.722A pdb=" N VAL A 595 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N GLY A 706 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 597 " --> pdb=" O GLY A 706 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP A 600 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE A 622 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A 631 " --> pdb=" O LYS A 639 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYS A 639 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS A 633 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ASN A 637 " --> pdb=" O HIS A 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 24 removed outlier: 5.483A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N LEU B 55 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG B 349 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR B 346 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.826A pdb=" N TYR B 108 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LYS B 127 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N MET B 110 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 125 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VAL B 112 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG B 123 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.842A pdb=" N GLU B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.460A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.028A 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: 3.631A pdb=" N ARG B 212 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 267 removed outlier: 5.803A pdb=" N GLN B 265 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 272 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 277 through 279 removed outlier: 6.418A pdb=" N GLN B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 517 through 520 removed outlier: 6.798A pdb=" N ILE C 631 " --> pdb=" O LYS C 639 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS C 639 " --> pdb=" O ILE C 631 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 534 through 536 removed outlier: 7.199A pdb=" N LEU C 655 " --> pdb=" O PHE C 557 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.962A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 7 through 8 removed outlier: 7.244A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 80 removed outlier: 5.165A pdb=" N TYR D 108 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS D 127 " --> pdb=" O TYR D 108 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET D 110 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR D 125 " --> pdb=" O MET D 110 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL D 112 " --> pdb=" O ARG D 123 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG D 123 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.767A pdb=" N GLU D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.440A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 156 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.876A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 262 through 267 removed outlier: 6.972A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 229 hydrogen bonds 454 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 155 stacking parallelities Total time for adding SS restraints: 4.59 Time building geometry restraints manager: 2.11 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: 4914 1.33 - 1.45: 4819 1.45 - 1.57: 10028 1.57 - 1.69: 406 1.69 - 1.81: 164 Bond restraints: 20331 Sorted by residual: bond pdb=" C3' DA I 35 " pdb=" C2' DA I 35 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC G 47 " pdb=" C2' DC G 47 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DC J 44 " pdb=" C2' DC J 44 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA F 35 " pdb=" O3' DA F 35 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.03e+01 bond pdb=" C3' DG F 15 " pdb=" C2' DG F 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 20326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 26920 1.81 - 3.61: 1348 3.61 - 5.42: 86 5.42 - 7.22: 23 7.22 - 9.03: 6 Bond angle restraints: 28383 Sorted by residual: angle pdb=" N ILE H 113 " pdb=" CA ILE H 113 " pdb=" C ILE H 113 " ideal model delta sigma weight residual 113.71 108.78 4.93 9.50e-01 1.11e+00 2.69e+01 angle pdb=" O4' DT F 27 " pdb=" C4' DT F 27 " pdb=" C3' DT F 27 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 angle pdb=" N3 DT J 38 " pdb=" C4 DT J 38 " pdb=" O4 DT J 38 " ideal model delta sigma weight residual 119.90 122.82 -2.92 6.00e-01 2.78e+00 2.37e+01 angle pdb=" N3 DT G 7 " pdb=" C4 DT G 7 " pdb=" O4 DT G 7 " ideal model delta sigma weight residual 119.90 122.74 -2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" N3 DT G 18 " pdb=" C4 DT G 18 " pdb=" O4 DT G 18 " ideal model delta sigma weight residual 119.90 122.73 -2.83 6.00e-01 2.78e+00 2.22e+01 ... (remaining 28378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 10788 35.86 - 71.72: 879 71.72 - 107.57: 10 107.57 - 143.43: 0 143.43 - 179.29: 5 Dihedral angle restraints: 11682 sinusoidal: 6012 harmonic: 5670 Sorted by residual: dihedral pdb=" CA ARG A 458 " pdb=" C ARG A 458 " pdb=" N GLY A 459 " pdb=" CA GLY A 459 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA ARG C 838 " pdb=" C ARG C 838 " pdb=" N LYS C 839 " pdb=" CA LYS C 839 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+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 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 11679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2309 0.053 - 0.106: 678 0.106 - 0.160: 131 0.160 - 0.213: 13 0.213 - 0.266: 2 Chirality restraints: 3133 Sorted by residual: chirality pdb=" C3' DT G 42 " pdb=" C4' DT G 42 " pdb=" O3' DT G 42 " pdb=" C2' DT G 42 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' DC I 17 " pdb=" C4' DC I 17 " pdb=" O3' DC I 17 " pdb=" C2' DC I 17 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CG LEU C 411 " pdb=" CB LEU C 411 " pdb=" CD1 LEU C 411 " pdb=" CD2 LEU C 411 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 3130 not shown) Planarity restraints: 2944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 18 " 0.043 2.00e-02 2.50e+03 1.71e-02 8.08e+00 pdb=" N9 DA I 18 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 18 " -0.014 2.00e-02 2.50e+03 pdb=" N7 DA I 18 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 18 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 18 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 18 " 0.018 2.00e-02 2.50e+03 pdb=" N1 DA I 18 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 18 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I 18 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DA I 18 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 515 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO C 516 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 18 " 0.035 2.00e-02 2.50e+03 1.42e-02 5.55e+00 pdb=" N9 DA J 18 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA J 18 " -0.010 2.00e-02 2.50e+03 pdb=" N7 DA J 18 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 18 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA J 18 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA J 18 " 0.013 2.00e-02 2.50e+03 pdb=" N1 DA J 18 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 18 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J 18 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DA J 18 " -0.009 2.00e-02 2.50e+03 ... (remaining 2941 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 40 2.35 - 2.99: 10011 2.99 - 3.62: 29724 3.62 - 4.26: 47253 4.26 - 4.90: 73921 Nonbonded interactions: 160949 Sorted by model distance: nonbonded pdb=" OD2 ASP A 708 " pdb="CA CA A1102 " model vdw 1.709 2.510 nonbonded pdb=" OD2 ASP C 708 " pdb="CA CA C1102 " model vdw 1.920 2.510 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1103 " model vdw 1.966 2.510 nonbonded pdb=" O GLN A 962 " pdb=" NE2 GLN A 962 " model vdw 2.165 3.120 nonbonded pdb=" NH2 ARG D 73 " pdb=" OD1 ASN D 101 " model vdw 2.196 3.120 ... (remaining 160944 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 451 or (resid 452 through 453 and (name N or name CA or name C or nam \ e O or name CB )) or resid 454 or (resid 455 through 456 and (name N or name CA \ or name C or name O or name CB )) or resid 457 or (resid 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 through 523 or (resid 524 and \ (name N or name CA or name C or name O or name CB )) or resid 525 through 815 o \ r resid 817 through 1103)) selection = (chain 'C' and (resid 401 through 430 or resid 432 through 815 or resid 817 thro \ ugh 860 or (resid 861 and (name N or name CA or name C or name O or name CB )) o \ r 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 1103)) } 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 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 through 339 or (resid 340 through 342 an \ d (name N or name 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 individual isotropic 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: 2.120 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 21.670 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 20339 Z= 0.463 Angle : 0.846 11.437 28387 Z= 0.606 Chirality : 0.051 0.266 3133 Planarity : 0.005 0.059 2944 Dihedral : 20.065 179.289 8030 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.45 % Favored : 90.34 % Rotamer: Outliers : 0.30 % Allowed : 2.67 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -4.65 (0.15), residues: 1940 helix: -2.29 (0.16), residues: 682 sheet: -3.15 (0.23), residues: 352 loop : -3.70 (0.16), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 409 TYR 0.034 0.003 TYR D 91 PHE 0.033 0.003 PHE A 557 TRP 0.035 0.003 TRP B 317 HIS 0.008 0.002 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.46 (20331) covalent geometry : angle 0.84076 / 0.61 (28383) hydrogen bonds : bond 0.11620 / 7.91 ( 911) hydrogen bonds : angle 6.25738 / 4.46 ( 2385) metal coordination : bond 0.06535 / 3.94 ( 8) metal coordination : angle 7.83691 / 4.24 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 298 GLU cc_start: 0.8086 (tt0) cc_final: 0.7571 (tm-30) REVERT: B 302 MET cc_start: 0.7316 (ptm) cc_final: 0.6874 (ptp) REVERT: C 416 LYS cc_start: 0.8056 (pptt) cc_final: 0.7776 (mtpp) REVERT: C 418 PHE cc_start: 0.8313 (t80) cc_final: 0.7205 (t80) REVERT: C 849 MET cc_start: 0.8599 (tpt) cc_final: 0.8318 (tpt) REVERT: D 298 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7621 (mp0) REVERT: D 303 GLU cc_start: 0.7391 (pm20) cc_final: 0.6977 (mp0) outliers start: 5 outliers final: 3 residues processed: 180 average time/residue: 0.1517 time to fit residues: 40.9082 Evaluate side-chains 115 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 602 MET Chi-restraints excluded: chain C residue 607 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN A 633 HIS A 739 GLN A 750 HIS ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN A 990 HIS B 100 ASN B 222 HIS B 282 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN C 991 HIS D 181 HIS D 282 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.103053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.067381 restraints weight = 62936.088| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.08 r_work: 0.2898 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 20339 Z= 0.231 Angle : 0.736 8.776 28387 Z= 0.406 Chirality : 0.048 0.371 3133 Planarity : 0.005 0.050 2944 Dihedral : 25.245 177.797 4395 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.33 % Favored : 92.56 % Rotamer: Outliers : 1.22 % Allowed : 5.59 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.17), residues: 1940 helix: -0.98 (0.19), residues: 695 sheet: -2.65 (0.24), residues: 354 loop : -2.98 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 713 TYR 0.024 0.002 TYR C 928 PHE 0.027 0.002 PHE A 557 TRP 0.026 0.002 TRP H 133 HIS 0.006 0.001 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (20331) covalent geometry : angle 0.73436 / 0.41 (28383) hydrogen bonds : bond 0.04919 / 3.30 ( 911) hydrogen bonds : angle 5.23386 / 3.75 ( 2385) metal coordination : bond 0.01172 / 0.61 ( 8) metal coordination : angle 3.75410 / 1.95 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7393 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 298 GLU cc_start: 0.8275 (tt0) cc_final: 0.7620 (tm-30) REVERT: B 302 MET cc_start: 0.7257 (ptm) cc_final: 0.6934 (ptp) REVERT: C 416 LYS cc_start: 0.8077 (pptt) cc_final: 0.7760 (mtpp) REVERT: C 662 GLU cc_start: 0.8820 (pt0) cc_final: 0.8563 (pm20) REVERT: C 847 MET cc_start: 0.5916 (mtm) cc_final: 0.5702 (mtm) REVERT: C 988 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9181 (tp) REVERT: D 298 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7756 (mp0) REVERT: D 303 GLU cc_start: 0.7410 (pm20) cc_final: 0.7042 (mp0) REVERT: D 322 MET cc_start: 0.9253 (mtm) cc_final: 0.9028 (mtm) outliers start: 20 outliers final: 7 residues processed: 131 average time/residue: 0.1463 time to fit residues: 30.2974 Evaluate side-chains 116 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 988 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 206 optimal weight: 50.0000 chunk 143 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 179 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 HIS D 222 HIS H 117 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.100610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065804 restraints weight = 74448.720| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.22 r_work: 0.2825 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.154 20339 Z= 0.369 Angle : 0.813 9.677 28387 Z= 0.437 Chirality : 0.051 0.374 3133 Planarity : 0.006 0.057 2944 Dihedral : 25.354 177.793 4390 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.64 % Allowed : 6.87 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.96 (0.18), residues: 1940 helix: -0.71 (0.19), residues: 698 sheet: -2.41 (0.26), residues: 336 loop : -2.81 (0.18), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 713 TYR 0.034 0.003 TYR A 559 PHE 0.032 0.003 PHE A 784 TRP 0.023 0.003 TRP A 893 HIS 0.010 0.002 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00843 / 0.37 (20331) covalent geometry : angle 0.81106 / 0.44 (28383) hydrogen bonds : bond 0.05555 / 3.73 ( 911) hydrogen bonds : angle 5.16310 / 3.70 ( 2385) metal coordination : bond 0.02319 / 1.13 ( 8) metal coordination : angle 4.17921 / 2.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8491 (tpt) cc_final: 0.8199 (tpt) REVERT: B 270 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 298 GLU cc_start: 0.8378 (tt0) cc_final: 0.8115 (tm-30) REVERT: B 302 MET cc_start: 0.7374 (ptm) cc_final: 0.7110 (ptp) REVERT: C 416 LYS cc_start: 0.8073 (pptt) cc_final: 0.7752 (mtpp) REVERT: C 662 GLU cc_start: 0.8970 (pt0) cc_final: 0.8713 (pm20) REVERT: C 691 MET cc_start: 0.8987 (ttm) cc_final: 0.8682 (ttp) REVERT: C 988 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9215 (tp) REVERT: D 152 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7457 (mpt) REVERT: D 298 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7901 (mp0) REVERT: D 322 MET cc_start: 0.9327 (mtm) cc_final: 0.9114 (mtm) outliers start: 27 outliers final: 12 residues processed: 129 average time/residue: 0.1375 time to fit residues: 28.7942 Evaluate side-chains 117 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 297 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 184 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.103499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.068856 restraints weight = 78893.339| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.38 r_work: 0.2892 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20339 Z= 0.149 Angle : 0.669 13.156 28387 Z= 0.367 Chirality : 0.045 0.372 3133 Planarity : 0.004 0.038 2944 Dihedral : 25.147 177.425 4390 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer: Outliers : 1.22 % Allowed : 8.75 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.20 (0.18), residues: 1940 helix: 0.04 (0.20), residues: 686 sheet: -2.03 (0.26), residues: 349 loop : -2.44 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.019 0.001 TYR A 559 PHE 0.021 0.001 PHE A 557 TRP 0.014 0.001 TRP A 893 HIS 0.006 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (20331) covalent geometry : angle 0.66726 / 0.37 (28383) hydrogen bonds : bond 0.04278 / 2.88 ( 911) hydrogen bonds : angle 4.86816 / 3.48 ( 2385) metal coordination : bond 0.00813 / 0.48 ( 8) metal coordination : angle 3.66608 / 1.91 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 270 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 298 GLU cc_start: 0.8261 (tt0) cc_final: 0.7899 (tm-30) REVERT: B 302 MET cc_start: 0.7345 (ptm) cc_final: 0.7070 (ptp) REVERT: C 416 LYS cc_start: 0.8115 (pptt) cc_final: 0.7817 (mtpp) REVERT: C 451 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7842 (tt) REVERT: C 662 GLU cc_start: 0.8882 (pt0) cc_final: 0.8647 (pm20) REVERT: C 988 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9153 (tp) REVERT: D 298 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7865 (mp0) REVERT: D 303 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: D 322 MET cc_start: 0.9283 (mtm) cc_final: 0.9050 (mtm) REVERT: D 329 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8839 (mp) outliers start: 20 outliers final: 9 residues processed: 125 average time/residue: 0.1273 time to fit residues: 26.0641 Evaluate side-chains 113 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 303 GLU Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 22 optimal weight: 0.9980 chunk 190 optimal weight: 40.0000 chunk 191 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.103306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068241 restraints weight = 73445.387| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.28 r_work: 0.2886 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20339 Z= 0.166 Angle : 0.656 11.738 28387 Z= 0.358 Chirality : 0.045 0.367 3133 Planarity : 0.004 0.039 2944 Dihedral : 25.096 176.982 4390 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 2.07 % Allowed : 8.51 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.93 (0.19), residues: 1940 helix: 0.20 (0.20), residues: 700 sheet: -1.79 (0.26), residues: 349 loop : -2.30 (0.20), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.017 0.001 TYR A 559 PHE 0.018 0.001 PHE A 418 TRP 0.013 0.001 TRP A 893 HIS 0.005 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (20331) covalent geometry : angle 0.65505 / 0.36 (28383) hydrogen bonds : bond 0.04287 / 2.88 ( 911) hydrogen bonds : angle 4.73613 / 3.38 ( 2385) metal coordination : bond 0.00984 / 0.50 ( 8) metal coordination : angle 3.31077 / 1.70 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 691 MET cc_start: 0.8454 (ttm) cc_final: 0.8136 (ttm) REVERT: A 784 PHE cc_start: 0.8466 (t80) cc_final: 0.8139 (t80) REVERT: B 270 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7228 (tm-30) REVERT: B 298 GLU cc_start: 0.8237 (tt0) cc_final: 0.7901 (tm-30) REVERT: B 302 MET cc_start: 0.7256 (ptm) cc_final: 0.7034 (ptp) REVERT: C 416 LYS cc_start: 0.8190 (pptt) cc_final: 0.7892 (mtpp) REVERT: C 662 GLU cc_start: 0.8891 (pt0) cc_final: 0.8611 (pm20) REVERT: C 691 MET cc_start: 0.8909 (ttm) cc_final: 0.8583 (ttp) REVERT: C 988 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9169 (tp) REVERT: D 298 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7862 (mp0) REVERT: D 322 MET cc_start: 0.9318 (mtm) cc_final: 0.8968 (mtm) REVERT: D 329 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8857 (mp) outliers start: 34 outliers final: 19 residues processed: 134 average time/residue: 0.1310 time to fit residues: 29.0043 Evaluate side-chains 123 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 185 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 199 optimal weight: 30.0000 chunk 131 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 189 optimal weight: 50.0000 chunk 204 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 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 = 0.3811 r_free = 0.3811 target = 0.100675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065445 restraints weight = 77168.042| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 3.37 r_work: 0.2815 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.134 20339 Z= 0.371 Angle : 0.780 11.520 28387 Z= 0.413 Chirality : 0.050 0.365 3133 Planarity : 0.005 0.050 2944 Dihedral : 25.266 177.154 4387 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.01 % Favored : 91.94 % Rotamer: Outliers : 2.37 % Allowed : 8.94 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.19 (0.18), residues: 1940 helix: -0.08 (0.20), residues: 699 sheet: -1.94 (0.26), residues: 342 loop : -2.38 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 148 TYR 0.024 0.002 TYR A 559 PHE 0.021 0.003 PHE B 30 TRP 0.021 0.002 TRP A 893 HIS 0.008 0.002 HIS A 942 Details of bonding type rmsd/Z covalent geometry : bond 0.00850 / 0.37 (20331) covalent geometry : angle 0.77841 / 0.41 (28383) hydrogen bonds : bond 0.05184 / 3.48 ( 911) hydrogen bonds : angle 4.90177 / 3.50 ( 2385) metal coordination : bond 0.02291 / 1.11 ( 8) metal coordination : angle 4.31695 / 2.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 101 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8287 (tpt) cc_final: 0.7886 (tpt) REVERT: B 270 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7295 (tm-30) REVERT: B 298 GLU cc_start: 0.8359 (tt0) cc_final: 0.7883 (tm-30) REVERT: B 302 MET cc_start: 0.7191 (ptm) cc_final: 0.6978 (ptp) REVERT: C 416 LYS cc_start: 0.8131 (pptt) cc_final: 0.7816 (mtpp) REVERT: C 662 GLU cc_start: 0.9023 (pt0) cc_final: 0.8693 (pm20) REVERT: C 988 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9195 (tp) REVERT: D 298 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7928 (mp0) REVERT: D 322 MET cc_start: 0.9360 (mtm) cc_final: 0.9001 (mtm) REVERT: D 329 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8859 (mp) outliers start: 39 outliers final: 25 residues processed: 132 average time/residue: 0.1204 time to fit residues: 26.6861 Evaluate side-chains 127 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 163 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 HIS ** 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 = 0.3858 r_free = 0.3858 target = 0.103647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.065508 restraints weight = 90591.298| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.38 r_work: 0.2889 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20339 Z= 0.141 Angle : 0.653 11.414 28387 Z= 0.355 Chirality : 0.044 0.363 3133 Planarity : 0.004 0.037 2944 Dihedral : 25.098 177.440 4387 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 1.70 % Allowed : 10.40 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.81 (0.19), residues: 1940 helix: 0.28 (0.20), residues: 699 sheet: -1.65 (0.27), residues: 337 loop : -2.24 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.013 0.001 TYR A 559 PHE 0.018 0.001 PHE C 911 TRP 0.012 0.001 TRP A 893 HIS 0.005 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (20331) covalent geometry : angle 0.65148 / 0.35 (28383) hydrogen bonds : bond 0.04168 / 2.80 ( 911) hydrogen bonds : angle 4.71058 / 3.35 ( 2385) metal coordination : bond 0.00803 / 0.44 ( 8) metal coordination : angle 3.62780 / 1.88 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8091 (tpt) cc_final: 0.7732 (tpt) REVERT: A 988 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9274 (tp) REVERT: B 270 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 298 GLU cc_start: 0.8295 (tt0) cc_final: 0.7921 (tm-30) REVERT: B 302 MET cc_start: 0.7059 (ptm) cc_final: 0.6808 (ptp) REVERT: C 416 LYS cc_start: 0.8200 (pptt) cc_final: 0.7897 (mtpp) REVERT: C 658 MET cc_start: 0.8949 (ptp) cc_final: 0.8710 (mtm) REVERT: C 662 GLU cc_start: 0.8887 (pt0) cc_final: 0.8580 (pm20) REVERT: C 858 MET cc_start: 0.8350 (mmm) cc_final: 0.8101 (mmm) REVERT: C 915 ARG cc_start: 0.8214 (ttp-170) cc_final: 0.7897 (mmm-85) REVERT: C 988 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9149 (tp) REVERT: D 298 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7811 (mp0) REVERT: D 322 MET cc_start: 0.9307 (mtm) cc_final: 0.8895 (mtm) REVERT: D 329 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8809 (mp) outliers start: 28 outliers final: 15 residues processed: 127 average time/residue: 0.1359 time to fit residues: 27.7304 Evaluate side-chains 122 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 988 LEU Chi-restraints excluded: chain D residue 22 MET Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 200 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 127 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 29 optimal weight: 0.3980 chunk 54 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 443 ASN ** A 836 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.104840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.069171 restraints weight = 62872.838| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.12 r_work: 0.2929 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20339 Z= 0.129 Angle : 0.633 12.712 28387 Z= 0.345 Chirality : 0.043 0.358 3133 Planarity : 0.004 0.100 2944 Dihedral : 24.933 177.055 4387 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.73 % Rotamer: Outliers : 1.52 % Allowed : 10.58 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.48 (0.19), residues: 1940 helix: 0.63 (0.20), residues: 687 sheet: -1.50 (0.26), residues: 353 loop : -2.07 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 442 TYR 0.011 0.001 TYR A 559 PHE 0.021 0.001 PHE C 911 TRP 0.012 0.001 TRP B 317 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.13 (20331) covalent geometry : angle 0.63185 / 0.34 (28383) hydrogen bonds : bond 0.03968 / 2.67 ( 911) hydrogen bonds : angle 4.52493 / 3.21 ( 2385) metal coordination : bond 0.00611 / 0.36 ( 8) metal coordination : angle 3.10626 / 1.61 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8053 (tpt) cc_final: 0.7745 (tpt) REVERT: A 988 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9308 (tp) REVERT: B 135 GLU cc_start: 0.8868 (tt0) cc_final: 0.8579 (pt0) REVERT: B 270 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7318 (tm-30) REVERT: B 298 GLU cc_start: 0.8199 (tt0) cc_final: 0.7902 (tm-30) REVERT: B 302 MET cc_start: 0.6979 (ptm) cc_final: 0.6012 (ptm) REVERT: C 416 LYS cc_start: 0.8192 (pptt) cc_final: 0.7899 (mtpp) REVERT: C 658 MET cc_start: 0.8932 (ptp) cc_final: 0.8680 (mtm) REVERT: C 691 MET cc_start: 0.8941 (ttm) cc_final: 0.8572 (ttp) REVERT: C 915 ARG cc_start: 0.8243 (ttp-170) cc_final: 0.7900 (mmm-85) REVERT: D 298 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7735 (mp0) REVERT: D 322 MET cc_start: 0.9271 (mtm) cc_final: 0.8944 (mtm) REVERT: D 329 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8816 (mp) outliers start: 25 outliers final: 15 residues processed: 131 average time/residue: 0.1395 time to fit residues: 29.4721 Evaluate side-chains 122 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 183 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 202 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 94 optimal weight: 40.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 HIS ** 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 = 0.3881 r_free = 0.3881 target = 0.104875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.069067 restraints weight = 62633.021| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.12 r_work: 0.2930 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20339 Z= 0.132 Angle : 0.625 11.592 28387 Z= 0.339 Chirality : 0.043 0.356 3133 Planarity : 0.004 0.039 2944 Dihedral : 24.881 177.065 4387 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.27 % Favored : 94.68 % Rotamer: Outliers : 1.34 % Allowed : 10.88 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.36 (0.19), residues: 1940 helix: 0.66 (0.20), residues: 691 sheet: -1.31 (0.27), residues: 347 loop : -2.01 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 838 TYR 0.012 0.001 TYR A 559 PHE 0.019 0.001 PHE C 911 TRP 0.011 0.001 TRP B 317 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (20331) covalent geometry : angle 0.62374 / 0.34 (28383) hydrogen bonds : bond 0.03932 / 2.64 ( 911) hydrogen bonds : angle 4.46288 / 3.16 ( 2385) metal coordination : bond 0.00626 / 0.35 ( 8) metal coordination : angle 2.95132 / 1.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.8070 (tpt) cc_final: 0.7763 (tpt) REVERT: A 988 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9292 (tp) REVERT: B 135 GLU cc_start: 0.8838 (tt0) cc_final: 0.8543 (pt0) REVERT: B 270 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7346 (tm-30) REVERT: B 298 GLU cc_start: 0.8190 (tt0) cc_final: 0.7904 (tm-30) REVERT: C 416 LYS cc_start: 0.8191 (pptt) cc_final: 0.7910 (mtpp) REVERT: C 691 MET cc_start: 0.8938 (ttm) cc_final: 0.8535 (ttp) REVERT: C 915 ARG cc_start: 0.8242 (ttp-170) cc_final: 0.7919 (mmm-85) REVERT: D 298 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7776 (mp0) REVERT: D 322 MET cc_start: 0.9244 (mtm) cc_final: 0.8950 (mtm) REVERT: D 329 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8815 (mp) outliers start: 22 outliers final: 19 residues processed: 124 average time/residue: 0.1301 time to fit residues: 26.5347 Evaluate side-chains 127 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 113 optimal weight: 0.7980 chunk 78 optimal weight: 0.0470 chunk 138 optimal weight: 10.0000 chunk 14 optimal weight: 0.0070 chunk 77 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 45 optimal weight: 0.0050 chunk 89 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.068055 restraints weight = 85814.813| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.32 r_work: 0.2962 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20339 Z= 0.118 Angle : 0.614 12.222 28387 Z= 0.333 Chirality : 0.042 0.351 3133 Planarity : 0.004 0.040 2944 Dihedral : 24.753 177.230 4387 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.55 % Favored : 95.35 % Rotamer: Outliers : 1.22 % Allowed : 11.12 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.19 (0.19), residues: 1940 helix: 0.78 (0.20), residues: 689 sheet: -1.14 (0.27), residues: 347 loop : -1.92 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 713 TYR 0.012 0.001 TYR C 586 PHE 0.021 0.001 PHE C 911 TRP 0.015 0.001 TRP H 133 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.12 (20331) covalent geometry : angle 0.61268 / 0.33 (28383) hydrogen bonds : bond 0.03785 / 2.54 ( 911) hydrogen bonds : angle 4.37750 / 3.09 ( 2385) metal coordination : bond 0.00525 / 0.33 ( 8) metal coordination : angle 2.92491 / 1.52 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 883 MET cc_start: 0.7936 (tpt) cc_final: 0.7615 (tpt) REVERT: A 988 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9268 (tp) REVERT: B 270 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7313 (tm-30) REVERT: B 298 GLU cc_start: 0.8190 (tt0) cc_final: 0.7909 (tm-30) REVERT: C 416 LYS cc_start: 0.8173 (pptt) cc_final: 0.7924 (mtpp) REVERT: C 627 MET cc_start: 0.8852 (tpt) cc_final: 0.8594 (tpt) REVERT: C 691 MET cc_start: 0.8920 (ttm) cc_final: 0.8480 (ttp) REVERT: C 743 PHE cc_start: 0.8295 (m-80) cc_final: 0.8027 (m-10) REVERT: C 915 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7897 (mmm-85) REVERT: D 48 PHE cc_start: 0.8724 (t80) cc_final: 0.8442 (t80) REVERT: D 298 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7818 (mp0) REVERT: D 322 MET cc_start: 0.9235 (mtm) cc_final: 0.8962 (mtm) REVERT: D 329 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8797 (mp) outliers start: 20 outliers final: 17 residues processed: 133 average time/residue: 0.1340 time to fit residues: 28.8132 Evaluate side-chains 128 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 22 MET Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 625 THR Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 910 SER Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 161 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 126 optimal weight: 0.3980 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 47 optimal weight: 0.0030 chunk 90 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 HIS ** 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 = 0.3890 r_free = 0.3890 target = 0.105514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067688 restraints weight = 78302.817| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.19 r_work: 0.2957 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20339 Z= 0.129 Angle : 0.610 11.587 28387 Z= 0.330 Chirality : 0.042 0.351 3133 Planarity : 0.004 0.037 2944 Dihedral : 24.737 177.168 4387 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 1.34 % Allowed : 10.94 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.19), residues: 1940 helix: 0.84 (0.20), residues: 692 sheet: -1.02 (0.27), residues: 347 loop : -1.86 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 713 TYR 0.012 0.001 TYR A 559 PHE 0.019 0.001 PHE C 911 TRP 0.014 0.001 TRP H 133 HIS 0.004 0.001 HIS C 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (20331) covalent geometry : angle 0.60905 / 0.33 (28383) hydrogen bonds : bond 0.03840 / 2.57 ( 911) hydrogen bonds : angle 4.34206 / 3.07 ( 2385) metal coordination : bond 0.00592 / 0.32 ( 8) metal coordination : angle 2.92086 / 1.51 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5314.98 seconds wall clock time: 91 minutes 36.08 seconds (5496.08 seconds total)