Starting phenix.real_space_refine on Sat Sep 12 15:37:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.cif" model { file = "/net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oes_20036/09_2026/6oes_20036.map" } resolution = 3.06 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= 0.008 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 2 9.91 5 Zn 2 6.06 5 P 126 5.49 5 S 103 5.16 5 C 10243 2.51 5 N 2954 2.21 5 O 3399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 16829 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4411 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} Conformer: "B" Number of residues, atoms: 548, 4405 Classifications: {'peptide': 548} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 522} bond proxies already assigned to first conformer: 4495 Chain: "B" Number of atoms: 2708 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2679 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 344, 2679 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 2714 Chain: "C" Number of atoms: 4397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4397 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 521} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2687 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2677 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 345, 2677 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2733 Chain: "F" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 722 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "J" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 303 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 695 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "L" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 307 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Chain: "M" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 77.316 60.140 63.274 1.00 35.24 S ATOM 2095 SG CYS A 730 79.566 57.590 65.579 1.00 38.04 S ATOM 9193 SG CYS C 727 24.484 103.311 59.410 1.00 35.23 S ATOM 9214 SG CYS C 730 21.682 105.123 61.104 1.00 37.28 S Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ACYS A 907 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 907 " occ=0.50 residue: pdb=" N AHIS B 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 47 " occ=0.50 residue: pdb=" N AARG B 237 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 237 " occ=0.50 residue: pdb=" N AASN B 268 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN B 268 " occ=0.50 residue: pdb=" N AHIS D 47 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS D 47 " occ=0.50 residue: pdb=" P DT J 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT J 15 " occ=0.85 residue: pdb=" P DT I 15 " occ=0.85 ... (18 atoms not shown) pdb=" C6 DT I 15 " occ=0.85 Time building chain proxies: 4.92, per 1000 atoms: 0.29 Number of scatterers: 16829 At special positions: 0 Unit cell: (105.93, 159.43, 119.84, 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 2 19.99 S 103 16.00 P 126 15.00 O 3399 8.00 N 2954 7.00 C 10243 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: 1.39 Conformation dependent library (CDL) restraints added in 962.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " Number of angles added : 4 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 17 sheets defined 34.2% alpha, 24.3% beta 61 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.787A pdb=" N LYS A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 558 through 581 removed outlier: 5.440A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP A 573 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 682 Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 683 through 685 No H-bonds generated for 'chain 'A' and resid 683 through 685' Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.648A pdb=" N GLN A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 822 through 841 removed outlier: 3.658A pdb=" N ARG A 826 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 Processing helix chain 'A' and resid 859 through 868 Processing helix chain 'A' and resid 873 through 890 Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 908 through 923 Processing helix chain 'A' and resid 933 through 942 removed outlier: 3.614A pdb=" N HIS A 942 " --> pdb=" O LYS A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.663A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A 970 " --> pdb=" O LYS A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 removed outlier: 3.537A pdb=" N ASP A 986 " --> pdb=" O TYR A 982 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 995 " --> pdb=" O HIS A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1001 removed outlier: 3.593A pdb=" N LYS A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1005 removed outlier: 3.621A pdb=" N ALA A1005 " --> pdb=" O PHE A1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1002 through 1005' Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.661A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 15 " --> pdb=" O ILE B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.838A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 477 through 493 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.531A pdb=" N LYS C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.503A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) 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 733 through 740 Processing helix chain 'C' and resid 749 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 813 removed outlier: 3.658A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 840 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 867 removed outlier: 3.568A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 removed outlier: 3.630A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.518A pdb=" N CYS C 902 " --> pdb=" O PRO C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.726A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 923 Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.540A pdb=" N HIS C 942 " --> pdb=" O LYS C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 950 Processing helix chain 'C' and resid 958 through 975 removed outlier: 4.050A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 removed outlier: 3.546A pdb=" N ASP C 986 " --> pdb=" O TYR C 982 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 995 " --> pdb=" O HIS C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1001 Processing helix chain 'C' and resid 1002 through 1005 removed outlier: 3.688A pdb=" N ALA C1005 " --> pdb=" O PHE C1002 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1002 through 1005' Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.662A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.838A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.702A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.702A pdb=" N ILE A 694 " --> pdb=" O MET A 691 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 591 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR A 705 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU A 597 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE A 631 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.564A pdb=" N SER B 2 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.783A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 removed outlier: 4.268A pdb=" N ILE B 107 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR B 121 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS B 115 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.719A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER B 141 " --> pdb=" O PHE B 156 " (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 211 removed outlier: 4.010A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267 removed outlier: 3.511A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 298 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.544A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 3.544A pdb=" N ILE C 694 " --> pdb=" O MET C 691 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR C 705 " --> pdb=" O GLU C 597 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS C 599 " --> pdb=" O THR C 705 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C 632 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 628 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LYS C 596 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL C 626 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 636 " --> pdb=" O HIS C 633 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.189A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 58 " --> pdb=" O AHIS D 47 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LEU D 55 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER D 2 " --> pdb=" O ARG D 349 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL D 8 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N PHE D 343 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE D 318 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 80 removed outlier: 4.268A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.718A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS D 191 " --> pdb=" O ASP D 186 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER D 141 " --> pdb=" O PHE D 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.011A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 262 through 267 removed outlier: 3.510A pdb=" N THR D 266 " --> pdb=" O GLU D 270 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 298 " --> pdb=" O SER D 291 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 157 hydrogen bonds 314 hydrogen bond angles 0 basepair planarities 61 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 1.87 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: 3963 1.33 - 1.45: 4431 1.45 - 1.58: 8674 1.58 - 1.70: 249 1.70 - 1.82: 157 Bond restraints: 17474 Sorted by residual: bond pdb=" C1' DC G 47 " pdb=" N1 DC G 47 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.47e+01 bond pdb=" O3' DC L 17 " pdb=" P DA L 18 " ideal model delta sigma weight residual 1.607 1.565 0.042 1.20e-02 6.94e+03 1.23e+01 bond pdb=" C3' DG G 41 " pdb=" C2' DG G 41 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.20e+01 bond pdb=" N GLU B 341 " pdb=" CA GLU B 341 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 1.00e+01 bond pdb=" N GLU D 341 " pdb=" CA GLU D 341 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.16e+00 ... (remaining 17469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 23252 1.94 - 3.88: 829 3.88 - 5.82: 67 5.82 - 7.76: 19 7.76 - 9.70: 11 Bond angle restraints: 24178 Sorted by residual: angle pdb=" O4' DT F 29 " pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " ideal model delta sigma weight residual 106.00 102.62 3.38 6.00e-01 2.78e+00 3.17e+01 angle pdb=" CB GLN D 201 " pdb=" CG GLN D 201 " pdb=" CD GLN D 201 " ideal model delta sigma weight residual 112.60 122.00 -9.40 1.70e+00 3.46e-01 3.06e+01 angle pdb=" CB GLN B 201 " pdb=" CG GLN B 201 " pdb=" CD GLN B 201 " ideal model delta sigma weight residual 112.60 121.99 -9.39 1.70e+00 3.46e-01 3.05e+01 angle pdb=" O4' DA M 18 " pdb=" C4' DA M 18 " pdb=" C3' DA M 18 " ideal model delta sigma weight residual 106.00 102.79 3.21 6.00e-01 2.78e+00 2.85e+01 angle pdb=" O4' DA L 18 " pdb=" C4' DA L 18 " pdb=" C3' DA L 18 " ideal model delta sigma weight residual 106.00 102.80 3.20 6.00e-01 2.78e+00 2.85e+01 ... (remaining 24173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8407 17.90 - 35.79: 1039 35.79 - 53.69: 571 53.69 - 71.58: 110 71.58 - 89.48: 15 Dihedral angle restraints: 10142 sinusoidal: 4936 harmonic: 5206 Sorted by residual: dihedral pdb=" C ASP C 569 " pdb=" N ASP C 569 " pdb=" CA ASP C 569 " pdb=" CB ASP C 569 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 dihedral pdb=" C ASN D 335 " pdb=" N ASN D 335 " pdb=" CA ASN D 335 " pdb=" CB ASN D 335 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 dihedral pdb=" N ASN D 335 " pdb=" C ASN D 335 " pdb=" CA ASN D 335 " pdb=" CB ASN D 335 " ideal model delta harmonic sigma weight residual 122.80 133.37 -10.57 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 10139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2332 0.083 - 0.165: 294 0.165 - 0.248: 13 0.248 - 0.330: 0 0.330 - 0.413: 2 Chirality restraints: 2641 Sorted by residual: chirality pdb=" CA ASP C 569 " pdb=" N ASP C 569 " pdb=" C ASP C 569 " pdb=" CB ASP C 569 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ASN D 335 " pdb=" N ASN D 335 " pdb=" C ASN D 335 " pdb=" CB ASN D 335 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA LYS D 336 " pdb=" N LYS D 336 " pdb=" C LYS D 336 " pdb=" CB LYS D 336 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 2638 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.018 2.00e-02 2.50e+03 1.68e-02 7.08e+00 pdb=" CG TRP D 317 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 317 " 0.018 2.00e-02 2.50e+03 1.67e-02 6.97e+00 pdb=" CG TRP B 317 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 317 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 317 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 317 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 317 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 317 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 331 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ILE D 331 " -0.039 2.00e-02 2.50e+03 pdb=" O ILE D 331 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO D 332 " 0.013 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2485 2.76 - 3.30: 13805 3.30 - 3.83: 29361 3.83 - 4.37: 35133 4.37 - 4.90: 58523 Nonbonded interactions: 139307 Sorted by model distance: nonbonded pdb=" O SER B 340 " pdb=" OG SER B 340 " model vdw 2.226 3.040 nonbonded pdb=" N GLY B 333 " pdb=" O ALA B 342 " model vdw 2.263 3.120 nonbonded pdb=" OD1 ASP B 143 " pdb=" OG SER B 209 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP D 143 " pdb=" OG SER D 209 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 805 " pdb=" OD1 ASP C 834 " model vdw 2.314 3.040 ... (remaining 139302 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 461 through 906 or resid 908 through 1006 or (resid 1007 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1101 through 11 \ 02)) selection = (chain 'C' and (resid 461 through 906 or resid 908 through 1102)) } ncs_group { reference = (chain 'B' and (resid 1 through 46 or resid 48 through 117 or (resid 118 and (na \ me N or name CA or name C or name O or name CB )) or resid 119 through 236 or re \ sid 238 through 267 or resid 269 through 333 or (resid 334 and (name N or name C \ A or name C or name O or name CB )) or resid 335 through 350)) selection = (chain 'D' and (resid 1 through 46 or resid 48 through 236 or resid 238 through \ 267 or resid 269 through 350)) } ncs_group { reference = (chain 'F' and (resid 19 through 20 or resid 22 through 32 or resid 34 through 5 \ 0)) selection = (chain 'G' and (resid 30 through 31 or resid 33 through 43 or resid 45 through 6 \ 1)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.230 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 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 0.167 17482 Z= 0.403 Angle : 0.834 17.581 24182 Z= 0.570 Chirality : 0.052 0.413 2641 Planarity : 0.006 0.055 2672 Dihedral : 19.675 89.477 6792 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.39 % Favored : 96.44 % Rotamer: Outliers : 2.87 % Allowed : 4.47 % Favored : 92.66 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.27 % 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: -3.12 (0.16), residues: 1787 helix: -2.15 (0.15), residues: 558 sheet: -1.02 (0.26), residues: 349 loop : -2.43 (0.17), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 734 TYR 0.019 0.002 TYR A 757 PHE 0.016 0.002 PHE A 916 TRP 0.045 0.003 TRP D 317 HIS 0.005 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.39 (17474) covalent geometry : angle 0.81381 / 0.57 (24178) hydrogen bonds : bond 0.17389 / 11.13 ( 768) hydrogen bonds : angle 6.98746 / 4.88 ( 2129) metal coordination : bond 0.14798 / 10.53 ( 8) metal coordination : angle 14.28898 / 7.33 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 253 time to evaluate : 0.597 Fit side-chains REVERT: A 602 MET cc_start: 0.8385 (mtp) cc_final: 0.8083 (mtp) REVERT: A 970 ARG cc_start: 0.8261 (ttt180) cc_final: 0.8055 (ttt180) REVERT: B 22 MET cc_start: 0.8383 (ptp) cc_final: 0.8134 (ptp) REVERT: B 223 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8530 (m) REVERT: B 347 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8178 (m) REVERT: C 568 MET cc_start: 0.8204 (mmm) cc_final: 0.7989 (tpt) REVERT: C 617 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7488 (mt-10) REVERT: C 649 GLU cc_start: 0.7847 (pm20) cc_final: 0.7613 (pm20) REVERT: C 889 MET cc_start: 0.8490 (mtp) cc_final: 0.8138 (mtp) REVERT: D 22 MET cc_start: 0.8876 (ptp) cc_final: 0.8650 (ptp) REVERT: D 114 CYS cc_start: 0.7703 (p) cc_final: 0.7457 (p) REVERT: D 300 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7837 (m) outliers start: 43 outliers final: 11 residues processed: 282 average time/residue: 0.1529 time to fit residues: 63.2364 Evaluate side-chains 176 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 300 SER Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN A 753 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 101 ASN B 181 HIS ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 750 HIS C 820 ASN C 961 ASN C 965 ASN C1004 ASN D 54 HIS D 181 HIS D 268 ASN D 282 GLN D 321 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105617 restraints weight = 61735.999| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.96 r_work: 0.3081 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17482 Z= 0.142 Angle : 0.595 6.989 24182 Z= 0.340 Chirality : 0.044 0.186 2641 Planarity : 0.005 0.064 2672 Dihedral : 21.289 65.285 3334 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.61 % Rotamer: Outliers : 1.66 % Allowed : 8.56 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.18), residues: 1787 helix: -0.10 (0.20), residues: 569 sheet: -0.21 (0.28), residues: 336 loop : -1.83 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 696 TYR 0.015 0.001 TYR A 757 PHE 0.021 0.001 PHE A 911 TRP 0.029 0.002 TRP B 317 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (17474) covalent geometry : angle 0.59315 / 0.34 (24178) hydrogen bonds : bond 0.04617 / 2.98 ( 768) hydrogen bonds : angle 4.91795 / 3.47 ( 2129) metal coordination : bond 0.02109 / 1.52 ( 8) metal coordination : angle 3.67643 / 1.51 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.468 Fit side-chains REVERT: A 602 MET cc_start: 0.8678 (mtp) cc_final: 0.8385 (mtp) REVERT: A 939 THR cc_start: 0.9021 (m) cc_final: 0.8773 (p) REVERT: C 649 GLU cc_start: 0.8214 (pm20) cc_final: 0.7952 (pm20) REVERT: C 889 MET cc_start: 0.8614 (mtp) cc_final: 0.8291 (mtp) REVERT: D 22 MET cc_start: 0.8840 (ptp) cc_final: 0.8504 (ptp) REVERT: D 114 CYS cc_start: 0.7927 (p) cc_final: 0.7672 (p) outliers start: 24 outliers final: 15 residues processed: 186 average time/residue: 0.1456 time to fit residues: 40.6019 Evaluate side-chains 164 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 309 SER Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 317 TRP Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 142 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 108 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 24 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 750 HIS A 961 ASN ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN C 498 GLN C 961 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103934 restraints weight = 64022.887| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.65 r_work: 0.3038 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17482 Z= 0.175 Angle : 0.592 8.438 24182 Z= 0.331 Chirality : 0.045 0.184 2641 Planarity : 0.005 0.054 2672 Dihedral : 21.368 71.793 3326 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.72 % Allowed : 10.60 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.19), residues: 1787 helix: 0.72 (0.22), residues: 569 sheet: 0.07 (0.28), residues: 341 loop : -1.46 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.027 0.002 PHE A 911 TRP 0.037 0.002 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (17474) covalent geometry : angle 0.58776 / 0.33 (24178) hydrogen bonds : bond 0.04423 / 2.86 ( 768) hydrogen bonds : angle 4.50867 / 3.20 ( 2129) metal coordination : bond 0.01452 / 1.05 ( 8) metal coordination : angle 5.36721 / 2.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.606 Fit side-chains REVERT: A 602 MET cc_start: 0.8645 (mtp) cc_final: 0.8384 (mtp) REVERT: A 939 THR cc_start: 0.9039 (m) cc_final: 0.8742 (p) REVERT: A 1003 MET cc_start: 0.8909 (mmm) cc_final: 0.8198 (mmm) REVERT: B 5 MET cc_start: 0.8117 (ttp) cc_final: 0.7906 (ttt) REVERT: B 339 MET cc_start: 0.6313 (mtt) cc_final: 0.6034 (mtp) REVERT: C 649 GLU cc_start: 0.8222 (pm20) cc_final: 0.8002 (pm20) REVERT: C 889 MET cc_start: 0.8684 (mtp) cc_final: 0.8283 (mtt) REVERT: D 285 MET cc_start: 0.8488 (mmm) cc_final: 0.8240 (mmm) outliers start: 25 outliers final: 18 residues processed: 181 average time/residue: 0.1400 time to fit residues: 38.1114 Evaluate side-chains 164 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 645 LYS Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 317 TRP Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 137 optimal weight: 5.9990 chunk 143 optimal weight: 0.0040 chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 52 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104881 restraints weight = 60476.508| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.69 r_work: 0.3062 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17482 Z= 0.132 Angle : 0.553 8.385 24182 Z= 0.310 Chirality : 0.043 0.172 2641 Planarity : 0.004 0.045 2672 Dihedral : 21.312 73.472 3319 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 1.72 % Allowed : 11.81 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.20), residues: 1787 helix: 1.11 (0.22), residues: 566 sheet: 0.16 (0.28), residues: 331 loop : -1.32 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.027 0.001 PHE A 911 TRP 0.029 0.002 TRP D 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (17474) covalent geometry : angle 0.55055 / 0.31 (24178) hydrogen bonds : bond 0.03771 / 2.44 ( 768) hydrogen bonds : angle 4.34497 / 3.08 ( 2129) metal coordination : bond 0.00910 / 0.67 ( 8) metal coordination : angle 4.28273 / 1.99 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.528 Fit side-chains REVERT: A 602 MET cc_start: 0.8681 (mtp) cc_final: 0.8408 (mtp) REVERT: A 939 THR cc_start: 0.9071 (m) cc_final: 0.8795 (p) REVERT: B 339 MET cc_start: 0.6467 (mtt) cc_final: 0.6160 (mtp) REVERT: C 649 GLU cc_start: 0.8175 (pm20) cc_final: 0.7945 (pm20) REVERT: C 889 MET cc_start: 0.8645 (mtp) cc_final: 0.8162 (mtt) REVERT: D 285 MET cc_start: 0.8477 (mmm) cc_final: 0.8226 (mmm) outliers start: 25 outliers final: 19 residues processed: 175 average time/residue: 0.1510 time to fit residues: 39.2329 Evaluate side-chains 169 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 317 TRP Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 121 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 161 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 0.0670 chunk 17 optimal weight: 5.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.131848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104162 restraints weight = 48170.659| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.53 r_work: 0.3072 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17482 Z= 0.147 Angle : 0.555 9.260 24182 Z= 0.309 Chirality : 0.043 0.171 2641 Planarity : 0.004 0.052 2672 Dihedral : 21.266 75.974 3317 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.79 % Allowed : 12.20 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1787 helix: 1.28 (0.22), residues: 568 sheet: 0.39 (0.29), residues: 316 loop : -1.23 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 148 TYR 0.016 0.001 TYR A 757 PHE 0.029 0.001 PHE A 911 TRP 0.030 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (17474) covalent geometry : angle 0.55223 / 0.31 (24178) hydrogen bonds : bond 0.03791 / 2.47 ( 768) hydrogen bonds : angle 4.24223 / 3.01 ( 2129) metal coordination : bond 0.00919 / 0.67 ( 8) metal coordination : angle 4.67842 / 2.17 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.599 Fit side-chains REVERT: A 602 MET cc_start: 0.8690 (mtp) cc_final: 0.8437 (mtp) REVERT: A 939 THR cc_start: 0.9090 (m) cc_final: 0.8804 (p) REVERT: B 55 LEU cc_start: 0.9121 (tp) cc_final: 0.8894 (tp) REVERT: B 339 MET cc_start: 0.6289 (mtt) cc_final: 0.5978 (mtp) REVERT: C 649 GLU cc_start: 0.8113 (pm20) cc_final: 0.7889 (pm20) REVERT: C 889 MET cc_start: 0.8634 (mtp) cc_final: 0.8243 (mtt) REVERT: D 285 MET cc_start: 0.8485 (mmm) cc_final: 0.8255 (mmm) outliers start: 26 outliers final: 22 residues processed: 183 average time/residue: 0.1421 time to fit residues: 39.3132 Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 134 optimal weight: 0.6980 chunk 160 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 0.0000 chunk 161 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104858 restraints weight = 54764.372| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.68 r_work: 0.3075 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17482 Z= 0.123 Angle : 0.534 10.144 24182 Z= 0.299 Chirality : 0.042 0.167 2641 Planarity : 0.004 0.042 2672 Dihedral : 21.216 76.936 3316 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 1.72 % Allowed : 12.71 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.20), residues: 1787 helix: 1.40 (0.22), residues: 567 sheet: 0.51 (0.30), residues: 315 loop : -1.14 (0.20), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.029 0.001 PHE A 911 TRP 0.023 0.002 TRP D 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (17474) covalent geometry : angle 0.53181 / 0.30 (24178) hydrogen bonds : bond 0.03515 / 2.28 ( 768) hydrogen bonds : angle 4.16321 / 2.95 ( 2129) metal coordination : bond 0.00751 / 0.55 ( 8) metal coordination : angle 3.91921 / 1.80 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.726 Fit side-chains REVERT: A 602 MET cc_start: 0.8691 (mtp) cc_final: 0.8466 (mtp) REVERT: A 939 THR cc_start: 0.9082 (m) cc_final: 0.8813 (p) REVERT: B 55 LEU cc_start: 0.9108 (tp) cc_final: 0.8863 (tp) REVERT: B 339 MET cc_start: 0.6249 (mtt) cc_final: 0.5933 (mtp) REVERT: C 649 GLU cc_start: 0.8082 (pm20) cc_final: 0.7846 (pm20) REVERT: C 889 MET cc_start: 0.8585 (mtp) cc_final: 0.8215 (mtt) REVERT: C 968 PHE cc_start: 0.8956 (t80) cc_final: 0.8720 (t80) REVERT: D 285 MET cc_start: 0.8352 (mmm) cc_final: 0.8127 (mmm) outliers start: 25 outliers final: 22 residues processed: 180 average time/residue: 0.1444 time to fit residues: 39.1241 Evaluate side-chains 174 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103665 restraints weight = 56506.603| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.50 r_work: 0.3034 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17482 Z= 0.166 Angle : 0.568 10.060 24182 Z= 0.313 Chirality : 0.044 0.179 2641 Planarity : 0.004 0.045 2672 Dihedral : 21.275 77.667 3316 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 1.92 % Allowed : 13.03 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1787 helix: 1.40 (0.22), residues: 568 sheet: 0.60 (0.30), residues: 310 loop : -1.13 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 529 TYR 0.015 0.001 TYR A 805 PHE 0.030 0.001 PHE A 911 TRP 0.027 0.002 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (17474) covalent geometry : angle 0.56416 / 0.31 (24178) hydrogen bonds : bond 0.03902 / 2.55 ( 768) hydrogen bonds : angle 4.18813 / 2.97 ( 2129) metal coordination : bond 0.01037 / 0.74 ( 8) metal coordination : angle 4.93905 / 2.32 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.521 Fit side-chains REVERT: A 602 MET cc_start: 0.8707 (mtp) cc_final: 0.8472 (mtp) REVERT: A 939 THR cc_start: 0.9126 (m) cc_final: 0.8803 (p) REVERT: B 339 MET cc_start: 0.6351 (mtt) cc_final: 0.6020 (mtp) REVERT: C 649 GLU cc_start: 0.8149 (pm20) cc_final: 0.7928 (pm20) REVERT: C 889 MET cc_start: 0.8611 (mtp) cc_final: 0.8261 (mtt) REVERT: C 968 PHE cc_start: 0.8965 (t80) cc_final: 0.8711 (t80) REVERT: D 285 MET cc_start: 0.8325 (mmm) cc_final: 0.8101 (mmm) outliers start: 28 outliers final: 23 residues processed: 178 average time/residue: 0.1503 time to fit residues: 40.0654 Evaluate side-chains 174 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 848 ARG Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN D 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.132831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105284 restraints weight = 59109.339| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.51 r_work: 0.3062 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17482 Z= 0.129 Angle : 0.539 10.701 24182 Z= 0.299 Chirality : 0.042 0.167 2641 Planarity : 0.004 0.043 2672 Dihedral : 21.232 78.617 3316 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 1.85 % Allowed : 13.09 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1787 helix: 1.51 (0.22), residues: 568 sheet: 0.67 (0.30), residues: 313 loop : -1.01 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 148 TYR 0.016 0.001 TYR A 757 PHE 0.028 0.001 PHE A 911 TRP 0.022 0.001 TRP D 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (17474) covalent geometry : angle 0.53686 / 0.30 (24178) hydrogen bonds : bond 0.03507 / 2.27 ( 768) hydrogen bonds : angle 4.10623 / 2.91 ( 2129) metal coordination : bond 0.00808 / 0.59 ( 8) metal coordination : angle 4.16474 / 1.96 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.590 Fit side-chains REVERT: A 520 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7759 (mt0) REVERT: A 602 MET cc_start: 0.8695 (mtp) cc_final: 0.8475 (mtp) REVERT: A 939 THR cc_start: 0.9088 (m) cc_final: 0.8806 (p) REVERT: B 339 MET cc_start: 0.6247 (mtt) cc_final: 0.5906 (mtp) REVERT: C 649 GLU cc_start: 0.8101 (pm20) cc_final: 0.7880 (pm20) REVERT: C 889 MET cc_start: 0.8515 (mtp) cc_final: 0.8196 (mtt) REVERT: C 968 PHE cc_start: 0.8884 (t80) cc_final: 0.8648 (t80) REVERT: D 285 MET cc_start: 0.8312 (mmm) cc_final: 0.8100 (mmm) outliers start: 26 outliers final: 22 residues processed: 176 average time/residue: 0.1426 time to fit residues: 37.9492 Evaluate side-chains 172 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 ASN Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 961 ASN Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 326 THR Chi-restraints excluded: chain D residue 329 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 473 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 961 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104833 restraints weight = 65390.061| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.67 r_work: 0.3050 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17482 Z= 0.141 Angle : 0.544 10.798 24182 Z= 0.301 Chirality : 0.042 0.168 2641 Planarity : 0.004 0.057 2672 Dihedral : 21.215 78.879 3316 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 2.04 % Allowed : 12.96 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1787 helix: 1.53 (0.22), residues: 568 sheet: 0.77 (0.30), residues: 308 loop : -1.00 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.028 0.001 PHE A 911 TRP 0.021 0.002 TRP B 317 HIS 0.004 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (17474) covalent geometry : angle 0.54075 / 0.30 (24178) hydrogen bonds : bond 0.03557 / 2.31 ( 768) hydrogen bonds : angle 4.10231 / 2.91 ( 2129) metal coordination : bond 0.00858 / 0.63 ( 8) metal coordination : angle 4.32627 / 2.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.600 Fit side-chains REVERT: A 520 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: A 602 MET cc_start: 0.8704 (mtp) cc_final: 0.8483 (mtp) REVERT: A 939 THR cc_start: 0.9105 (m) cc_final: 0.8810 (p) REVERT: B 51 LYS cc_start: 0.7663 (ptpp) cc_final: 0.7337 (mtpp) REVERT: B 55 LEU cc_start: 0.9136 (tp) cc_final: 0.8879 (tp) REVERT: B 339 MET cc_start: 0.6360 (mtt) cc_final: 0.6031 (mtp) REVERT: C 649 GLU cc_start: 0.8102 (pm20) cc_final: 0.7879 (pm20) REVERT: C 889 MET cc_start: 0.8544 (mtp) cc_final: 0.8203 (mtt) REVERT: D 285 MET cc_start: 0.8320 (mmm) cc_final: 0.8111 (mmm) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.1456 time to fit residues: 39.2995 Evaluate side-chains 175 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 571 GLU Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 598 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103182 restraints weight = 55845.119| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.36 r_work: 0.3022 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3031 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17482 Z= 0.193 Angle : 0.592 10.218 24182 Z= 0.324 Chirality : 0.045 0.197 2641 Planarity : 0.005 0.055 2672 Dihedral : 21.295 79.056 3316 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.18 % Favored : 95.77 % Rotamer: Outliers : 1.72 % Allowed : 13.35 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1787 helix: 1.40 (0.22), residues: 568 sheet: 0.73 (0.30), residues: 313 loop : -1.07 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 148 TYR 0.017 0.002 TYR A 805 PHE 0.027 0.002 PHE A 911 TRP 0.027 0.002 TRP B 317 HIS 0.005 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (17474) covalent geometry : angle 0.58832 / 0.32 (24178) hydrogen bonds : bond 0.04137 / 2.70 ( 768) hydrogen bonds : angle 4.21024 / 2.98 ( 2129) metal coordination : bond 0.01040 / 0.76 ( 8) metal coordination : angle 5.16898 / 2.47 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.600 Fit side-chains REVERT: A 602 MET cc_start: 0.8706 (mtp) cc_final: 0.8484 (mtp) REVERT: A 939 THR cc_start: 0.9136 (m) cc_final: 0.8786 (p) REVERT: B 51 LYS cc_start: 0.7757 (ptpp) cc_final: 0.7487 (mtpp) REVERT: B 55 LEU cc_start: 0.9153 (tp) cc_final: 0.8886 (tp) REVERT: B 339 MET cc_start: 0.6374 (mtt) cc_final: 0.6065 (mtp) REVERT: C 649 GLU cc_start: 0.8174 (pm20) cc_final: 0.7955 (pm20) REVERT: C 889 MET cc_start: 0.8561 (mtp) cc_final: 0.8223 (mtt) outliers start: 24 outliers final: 23 residues processed: 173 average time/residue: 0.1423 time to fit residues: 37.3278 Evaluate side-chains 177 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 GLN Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 553 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 715 VAL Chi-restraints excluded: chain C residue 733 THR Chi-restraints excluded: chain C residue 973 LYS Chi-restraints excluded: chain C residue 995 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 298 GLU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 335 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 961 ASN ** 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 = 0.3616 r_free = 0.3616 target = 0.131978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.104658 restraints weight = 50094.959| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.45 r_work: 0.3075 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17482 Z= 0.137 Angle : 0.548 11.181 24182 Z= 0.302 Chirality : 0.043 0.165 2641 Planarity : 0.004 0.054 2672 Dihedral : 21.238 80.257 3316 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.60 % Allowed : 13.35 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1787 helix: 1.52 (0.22), residues: 569 sheet: 0.83 (0.30), residues: 308 loop : -0.95 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 529 TYR 0.016 0.001 TYR A 757 PHE 0.028 0.001 PHE A 911 TRP 0.023 0.002 TRP D 317 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (17474) covalent geometry : angle 0.54552 / 0.30 (24178) hydrogen bonds : bond 0.03558 / 2.31 ( 768) hydrogen bonds : angle 4.11988 / 2.92 ( 2129) metal coordination : bond 0.00781 / 0.58 ( 8) metal coordination : angle 4.24253 / 2.03 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4047.54 seconds wall clock time: 70 minutes 14.20 seconds (4214.20 seconds total)