Starting phenix.real_space_refine on Fri Jul 3 21:41:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpu_61715/07_2026/9jpu_61715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpu_61715/07_2026/9jpu_61715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jpu_61715/07_2026/9jpu_61715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpu_61715/07_2026/9jpu_61715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jpu_61715/07_2026/9jpu_61715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpu_61715/07_2026/9jpu_61715.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.024 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 4 6.06 5 P 56 5.49 5 S 111 5.16 5 C 9927 2.51 5 N 2773 2.21 5 O 3090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15963 Number of models: 1 Model: "" Number of chains: 13 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: 2716 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 344, 2687 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 344, 2687 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 324} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2722 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: 2694 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 345, 2684 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 345, 2684 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 325} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 2740 Chain: "F" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 309 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "L" 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: "M" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 286 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "E" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 554 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2074 SG CYS A 727 90.686 67.793 61.373 1.00 70.05 S ATOM 2095 SG CYS A 730 94.123 67.746 63.139 1.00 72.39 S ATOM 9201 SG CYS C 727 23.676 72.197 60.932 1.00 71.58 S ATOM 9222 SG CYS C 730 20.178 72.169 62.567 1.00 71.00 S ATOM 15481 SG CYS E 419 74.789 76.840 76.562 1.00126.49 S ATOM 15507 SG CYS E 423 74.834 77.160 73.532 1.00110.73 S ATOM 15790 SG CYS E 458 76.036 74.838 75.819 1.00141.77 S ATOM 15697 SG CYS E 446 70.331 79.745 87.200 1.00161.67 S ATOM 15920 SG CYS E 478 74.270 80.176 84.930 1.00164.88 S Residues with excluded nonbonded symmetry interactions: 5 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 Time building chain proxies: 5.15, per 1000 atoms: 0.32 Number of scatterers: 15963 At special positions: 0 Unit cell: (115.54, 140.98, 102.82, 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 4 29.99 Ca 2 19.99 S 111 16.00 P 56 15.00 O 3090 8.00 N 2773 7.00 C 9927 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: 1.35 Conformation dependent library (CDL) restraints added in 959.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" ND1 HIS E 455 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 423 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 419 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 458 " pdb=" ZN E 602 " pdb="ZN ZN E 602 " - pdb=" ND1 HIS E 481 " pdb="ZN ZN E 602 " - pdb=" NE2 HIS E 452 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 478 " pdb="ZN ZN E 602 " - pdb=" SG CYS E 446 " Number of angles added : 9 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3480 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 21 sheets defined 34.6% alpha, 21.7% beta 28 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 477 through 493 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 558 through 581 removed outlier: 5.004A pdb=" N GLU A 572 " --> pdb=" O MET A 568 " (cutoff:3.500A) removed outlier: 5.373A 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 708 through 716 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 763 Processing helix chain 'A' and resid 768 through 776 Processing helix chain 'A' and resid 792 through 812 Processing helix chain 'A' and resid 824 through 841 removed outlier: 3.806A pdb=" N GLN A 830 " --> pdb=" O ARG A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 867 removed outlier: 3.682A pdb=" N VAL A 863 " --> pdb=" O THR A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 872 through 890 removed outlier: 3.768A pdb=" N HIS A 876 " --> pdb=" O SER A 872 " (cutoff:3.500A) 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 897 through 902 Processing helix chain 'A' and resid 902 through 908 Processing helix chain 'A' and resid 909 through 923 Processing helix chain 'A' and resid 933 through 942 Processing helix chain 'A' and resid 943 through 951 Processing helix chain 'A' and resid 958 through 975 removed outlier: 3.657A pdb=" N LYS A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1004 removed outlier: 4.089A pdb=" N PHE A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.638A pdb=" N TRP B 172 " --> pdb=" O THR B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.534A pdb=" N HIS B 313 " --> pdb=" O SER B 309 " (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 507 Processing helix chain 'C' and resid 508 through 510 No H-bonds generated for 'chain 'C' and resid 508 through 510' Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 removed outlier: 3.612A pdb=" N GLN C 581 " --> pdb=" O GLY C 577 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 684 Proline residue: C 674 - end of helix removed outlier: 4.122A pdb=" N SER C 684 " --> pdb=" O GLU C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 733 through 741 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: 3.574A pdb=" N GLY C 813 " --> pdb=" O GLN C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.728A pdb=" N ARG C 838 " --> pdb=" O ASP C 834 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS C 839 " --> pdb=" O LYS C 835 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG C 840 " --> pdb=" O HIS C 836 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET C 841 " --> pdb=" O LEU C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 removed outlier: 3.784A pdb=" N VAL C 863 " --> pdb=" O THR C 859 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 removed outlier: 3.898A pdb=" N HIS C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 878 " --> pdb=" O GLU C 874 " (cutoff:3.500A) Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 897 through 902 Processing helix chain 'C' and resid 902 through 908 removed outlier: 3.534A pdb=" N GLN C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 923 Processing helix chain 'C' and resid 933 through 942 Processing helix chain 'C' and resid 942 through 950 removed outlier: 3.846A pdb=" N ILE C 946 " --> pdb=" O HIS C 942 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE C 947 " --> pdb=" O VAL C 943 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU C 948 " --> pdb=" O PRO C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 975 removed outlier: 3.875A pdb=" N LYS C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 995 Processing helix chain 'C' and resid 996 through 1004 removed outlier: 4.124A pdb=" N PHE C1002 " --> pdb=" O TYR C 998 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C1004 " --> pdb=" O GLN C1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 Processing helix chain 'D' and resid 168 through 172 removed outlier: 3.910A pdb=" N TRP D 172 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.642A pdb=" N HIS D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 460 Processing helix chain 'E' and resid 462 through 470 Processing sheet with id=AA1, first strand: chain 'A' and resid 517 through 520 Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.703A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 536 removed outlier: 6.703A pdb=" N PHE A 622 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A 657 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 620 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 594 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 629 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N THR A 592 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE A 701 " --> pdb=" O PHE A 591 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 593 " --> pdb=" O ILE A 701 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ARG A 703 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 595 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.662A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.544A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 58 " --> pdb=" O AHIS B 47 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 80 removed outlier: 5.759A pdb=" N TYR B 108 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS B 127 " --> pdb=" O TYR B 108 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N MET B 110 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR B 125 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL B 112 " --> pdb=" O ARG B 123 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG B 123 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS B 114 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.132A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.931A pdb=" N LEU B 233 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 262 through 267 removed outlier: 4.142A pdb=" N THR B 266 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.068A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 620 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU C 657 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE C 622 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 518 through 519 removed outlier: 6.068A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE C 631 " --> pdb=" O PRO C 590 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.294A pdb=" N PHE D 345 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 20 through 24 removed outlier: 4.721A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 61 through 62 removed outlier: 7.057A pdb=" N ILE D 61 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N CYS D 124 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 107 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 130 through 131 removed outlier: 6.232A pdb=" N VAL D 130 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SER D 194 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 4.050A pdb=" N LEU D 233 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 262 through 264 Processing sheet with id=AC2, first strand: chain 'D' and resid 277 through 279 removed outlier: 3.602A pdb=" N LEU D 279 " --> pdb=" O GLN D 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 443 through 446 640 hydrogen bonds defined for protein. 1758 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 132 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4834 1.34 - 1.45: 2831 1.45 - 1.57: 8509 1.57 - 1.69: 110 1.69 - 1.81: 167 Bond restraints: 16451 Sorted by residual: 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 1.19e+01 bond pdb=" C3' DG F 30 " pdb=" C2' DG F 30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC F 24 " pdb=" C2' DC F 24 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.58e+00 bond pdb=" C3' DT F 27 " pdb=" C2' DT F 27 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.18e+00 bond pdb=" C3' DT G 28 " pdb=" C2' DT G 28 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.07e+00 ... (remaining 16446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 22289 2.32 - 4.64: 199 4.64 - 6.95: 6 6.95 - 9.27: 0 9.27 - 11.59: 2 Bond angle restraints: 22496 Sorted by residual: angle pdb=" C VAL C 943 " pdb=" N PRO C 944 " pdb=" CA PRO C 944 " ideal model delta sigma weight residual 120.04 113.43 6.61 1.08e+00 8.57e-01 3.74e+01 angle pdb=" N VAL C 943 " pdb=" CA VAL C 943 " pdb=" C VAL C 943 " ideal model delta sigma weight residual 108.88 120.38 -11.50 2.16e+00 2.14e-01 2.83e+01 angle pdb=" O4' DT G 40 " pdb=" C4' DT G 40 " pdb=" C3' DT G 40 " ideal model delta sigma weight residual 106.00 102.89 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" N3 DT M 22 " pdb=" C4 DT M 22 " pdb=" O4 DT M 22 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT F 27 " pdb=" C4 DT F 27 " pdb=" O4 DT F 27 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 22491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 8941 17.42 - 34.83: 527 34.83 - 52.25: 218 52.25 - 69.67: 54 69.67 - 87.09: 2 Dihedral angle restraints: 9742 sinusoidal: 4335 harmonic: 5407 Sorted by residual: dihedral pdb=" CA ALA D 338 " pdb=" C ALA D 338 " pdb=" N MET D 339 " pdb=" CA MET D 339 " ideal model delta harmonic sigma weight residual -180.00 -164.15 -15.85 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA PHE A 557 " pdb=" C PHE A 557 " pdb=" N ARG A 558 " pdb=" CA ARG A 558 " ideal model delta harmonic sigma weight residual 180.00 164.29 15.71 0 5.00e+00 4.00e-02 9.87e+00 dihedral pdb=" CA ARG A 679 " pdb=" CB ARG A 679 " pdb=" CG ARG A 679 " pdb=" CD ARG A 679 " ideal model delta sinusoidal sigma weight residual -60.00 -119.33 59.33 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 9739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1839 0.042 - 0.083: 415 0.083 - 0.125: 180 0.125 - 0.167: 10 0.167 - 0.208: 1 Chirality restraints: 2445 Sorted by residual: chirality pdb=" CA VAL C 943 " pdb=" N VAL C 943 " pdb=" C VAL C 943 " pdb=" CB VAL C 943 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' DC G 35 " pdb=" C4' DC G 35 " pdb=" O3' DC G 35 " pdb=" C2' DC G 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" C3' DT M 22 " pdb=" C4' DT M 22 " pdb=" O3' DT M 22 " pdb=" C2' DT M 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 ... (remaining 2442 not shown) Planarity restraints: 2703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 179 " -0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 180 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 179 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.44e+00 pdb=" N PRO D 180 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 180 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 180 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 420 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO E 421 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 421 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 421 " 0.021 5.00e-02 4.00e+02 ... (remaining 2700 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1153 2.74 - 3.28: 15144 3.28 - 3.82: 26190 3.82 - 4.36: 30934 4.36 - 4.90: 53385 Nonbonded interactions: 126806 Sorted by model distance: nonbonded pdb=" OD2 ASP A 661 " pdb=" OG SER A 663 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR C 805 " pdb=" OD1 ASP C 834 " model vdw 2.225 3.040 nonbonded pdb=" OG SER C 895 " pdb=" OE1 GLU C 901 " model vdw 2.268 3.040 nonbonded pdb=" O ILE C 470 " pdb=" OG1 THR C 474 " model vdw 2.270 3.040 nonbonded pdb=" O ASP D 310 " pdb=" OG SER D 314 " model vdw 2.271 3.040 ... (remaining 126801 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 80 or (resid 81 through 8 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 89 through 1 \ 17 or (resid 118 and (name N or name CA or name C or name O or name CB )) or res \ id 119 through 236 or resid 238 through 267 or resid 269 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)) } 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: 1.870 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: 0.050 Process input model: 19.160 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 : 0.003 0.074 16467 Z= 0.224 Angle : 0.729 50.094 22505 Z= 0.376 Chirality : 0.042 0.208 2445 Planarity : 0.003 0.039 2703 Dihedral : 13.321 87.085 6262 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 1.84 % Allowed : 5.14 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.83 (0.20), residues: 1851 helix: 2.02 (0.23), residues: 556 sheet: 1.06 (0.28), residues: 379 loop : -0.60 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 756 TYR 0.016 0.001 TYR C 805 PHE 0.016 0.001 PHE D 48 TRP 0.013 0.001 TRP C 893 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.22 (16451) covalent geometry : angle 0.51889 / 0.36 (22496) hydrogen bonds : bond 0.06081 / 4.45 ( 686) hydrogen bonds : angle 4.59109 / 3.21 ( 1890) metal coordination : bond 0.02500 / 1.68 ( 16) metal coordination : angle 25.59370 / 14.19 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 357 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 TYR cc_start: 0.7398 (m-80) cc_final: 0.7197 (m-80) REVERT: C 663 SER cc_start: 0.8696 (m) cc_final: 0.8494 (p) REVERT: E 418 THR cc_start: 0.7711 (p) cc_final: 0.6961 (p) REVERT: E 443 MET cc_start: 0.4556 (mtp) cc_final: 0.4102 (mtt) outliers start: 30 outliers final: 8 residues processed: 379 average time/residue: 0.1023 time to fit residues: 58.8623 Evaluate side-chains 217 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain D residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 GLN A 515 HIS A 609 HIS A 633 HIS A 739 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 GLN ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 278 GLN E 457 GLN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.076181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.056902 restraints weight = 123888.693| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 6.51 r_work: 0.2594 rms_B_bonded: 6.36 restraints_weight: 2.0000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2508 r_free = 0.2508 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16467 Z= 0.137 Angle : 0.614 12.792 22505 Z= 0.316 Chirality : 0.042 0.199 2445 Planarity : 0.005 0.120 2703 Dihedral : 15.773 59.951 2666 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.71 % Allowed : 13.10 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.82 (0.20), residues: 1851 helix: 1.97 (0.23), residues: 572 sheet: 1.14 (0.28), residues: 376 loop : -0.67 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 39 TYR 0.018 0.001 TYR C 805 PHE 0.016 0.001 PHE B 31 TRP 0.010 0.001 TRP E 430 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16451) covalent geometry : angle 0.60003 / 0.32 (22496) hydrogen bonds : bond 0.03560 / 2.55 ( 686) hydrogen bonds : angle 4.28320 / 3.03 ( 1890) metal coordination : bond 0.02078 / 1.51 ( 16) metal coordination : angle 6.48711 / 3.38 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 ASP cc_start: 0.8456 (t0) cc_final: 0.8036 (t0) REVERT: A 627 MET cc_start: 0.9209 (mmm) cc_final: 0.8846 (mmm) REVERT: A 858 MET cc_start: 0.9320 (mmm) cc_final: 0.8930 (mmm) REVERT: B 285 MET cc_start: 0.8723 (mmm) cc_final: 0.8290 (mmm) REVERT: C 643 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8791 (tp30) REVERT: C 666 GLU cc_start: 0.9004 (mp0) cc_final: 0.8682 (mp0) REVERT: C 804 PHE cc_start: 0.8871 (m-80) cc_final: 0.8587 (m-10) REVERT: C 848 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8343 (ttt90) REVERT: C 959 GLU cc_start: 0.9416 (mm-30) cc_final: 0.8834 (mm-30) REVERT: D 152 MET cc_start: 0.9157 (mtp) cc_final: 0.8510 (tpp) REVERT: D 302 MET cc_start: 0.9386 (ttm) cc_final: 0.9094 (ttp) REVERT: E 443 MET cc_start: 0.6876 (mtp) cc_final: 0.5319 (mmm) REVERT: E 445 TYR cc_start: 0.7982 (t80) cc_final: 0.7612 (t80) REVERT: E 459 MET cc_start: 0.8826 (mmp) cc_final: 0.8468 (mmm) outliers start: 28 outliers final: 14 residues processed: 232 average time/residue: 0.1065 time to fit residues: 37.6639 Evaluate side-chains 194 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 985 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 164 optimal weight: 0.1980 chunk 178 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 23 optimal weight: 8.9990 chunk 143 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 ASN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.057442 restraints weight = 121704.495| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 6.43 r_work: 0.2514 rms_B_bonded: 6.38 restraints_weight: 2.0000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2518 r_free = 0.2518 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16467 Z= 0.111 Angle : 0.559 10.659 22505 Z= 0.291 Chirality : 0.041 0.173 2445 Planarity : 0.004 0.059 2703 Dihedral : 15.754 59.972 2663 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.84 % Allowed : 13.29 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.87 (0.20), residues: 1851 helix: 1.97 (0.23), residues: 572 sheet: 1.19 (0.28), residues: 378 loop : -0.63 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 39 TYR 0.017 0.001 TYR C 805 PHE 0.016 0.001 PHE D 48 TRP 0.014 0.001 TRP C 760 HIS 0.005 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (16451) covalent geometry : angle 0.55648 / 0.29 (22496) hydrogen bonds : bond 0.03334 / 2.38 ( 686) hydrogen bonds : angle 4.19656 / 2.97 ( 1890) metal coordination : bond 0.01048 / 0.79 ( 16) metal coordination : angle 2.93223 / 1.52 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 ASP cc_start: 0.8290 (t0) cc_final: 0.7690 (t0) REVERT: A 602 MET cc_start: 0.9391 (mtm) cc_final: 0.9053 (mtp) REVERT: A 627 MET cc_start: 0.9138 (mmm) cc_final: 0.8721 (mmm) REVERT: B 39 ARG cc_start: 0.8829 (ttp-170) cc_final: 0.8589 (ttp-170) REVERT: B 285 MET cc_start: 0.8573 (mmm) cc_final: 0.8002 (mmm) REVERT: C 627 MET cc_start: 0.8865 (tpp) cc_final: 0.8598 (tpp) REVERT: C 643 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8742 (tp30) REVERT: C 666 GLU cc_start: 0.9012 (mp0) cc_final: 0.8797 (mp0) REVERT: C 804 PHE cc_start: 0.8718 (m-80) cc_final: 0.8499 (m-10) REVERT: C 959 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8687 (mm-30) REVERT: D 5 MET cc_start: 0.7931 (mtm) cc_final: 0.7322 (mtm) REVERT: D 39 ARG cc_start: 0.8904 (tpp-160) cc_final: 0.8631 (tpp-160) REVERT: D 152 MET cc_start: 0.8888 (mtp) cc_final: 0.8489 (ttm) REVERT: D 302 MET cc_start: 0.9399 (ttm) cc_final: 0.9145 (ttp) REVERT: E 418 THR cc_start: 0.8851 (m) cc_final: 0.8446 (p) REVERT: E 443 MET cc_start: 0.6981 (mtp) cc_final: 0.6370 (mtt) REVERT: E 445 TYR cc_start: 0.8040 (t80) cc_final: 0.7657 (t80) outliers start: 30 outliers final: 16 residues processed: 223 average time/residue: 0.1190 time to fit residues: 41.9383 Evaluate side-chains 196 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 63 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 153 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.7698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 181 HIS B 313 HIS C 609 HIS ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.077896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058967 restraints weight = 108583.198| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 6.11 r_work: 0.2523 rms_B_bonded: 6.11 restraints_weight: 2.0000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16467 Z= 0.115 Angle : 0.550 9.744 22505 Z= 0.286 Chirality : 0.041 0.228 2445 Planarity : 0.004 0.051 2703 Dihedral : 15.776 59.963 2663 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.33 % Allowed : 13.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.92 (0.20), residues: 1851 helix: 1.99 (0.22), residues: 568 sheet: 1.20 (0.28), residues: 387 loop : -0.57 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 39 TYR 0.015 0.001 TYR C 805 PHE 0.018 0.001 PHE B 31 TRP 0.012 0.001 TRP C 760 HIS 0.007 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (16451) covalent geometry : angle 0.54769 / 0.29 (22496) hydrogen bonds : bond 0.03400 / 2.42 ( 686) hydrogen bonds : angle 4.16384 / 2.95 ( 1890) metal coordination : bond 0.01091 / 0.80 ( 16) metal coordination : angle 2.48254 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.9069 (mmm) cc_final: 0.8607 (mmm) REVERT: B 22 MET cc_start: 0.9262 (mtm) cc_final: 0.9002 (mtm) REVERT: B 31 PHE cc_start: 0.8930 (t80) cc_final: 0.8684 (t80) REVERT: B 285 MET cc_start: 0.8586 (mmm) cc_final: 0.7930 (mmm) REVERT: B 334 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8440 (m-30) REVERT: C 627 MET cc_start: 0.8792 (tpp) cc_final: 0.8437 (tpp) REVERT: C 666 GLU cc_start: 0.9034 (mp0) cc_final: 0.8771 (mp0) REVERT: C 669 THR cc_start: 0.9391 (t) cc_final: 0.9015 (p) REVERT: C 959 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8569 (mm-30) REVERT: D 39 ARG cc_start: 0.8976 (tpp-160) cc_final: 0.8204 (tpp-160) REVERT: D 152 MET cc_start: 0.8851 (mtp) cc_final: 0.8456 (ttm) REVERT: E 418 THR cc_start: 0.8948 (m) cc_final: 0.8550 (p) REVERT: E 443 MET cc_start: 0.7088 (mtp) cc_final: 0.6569 (mtt) REVERT: E 459 MET cc_start: 0.8411 (mmm) cc_final: 0.7958 (mmm) outliers start: 38 outliers final: 29 residues processed: 219 average time/residue: 0.1189 time to fit residues: 41.0672 Evaluate side-chains 210 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 287 CYS Chi-restraints excluded: chain B residue 334 ASP Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 776 VAL Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 0.4980 chunk 174 optimal weight: 0.1980 chunk 155 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.077798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.058866 restraints weight = 114304.860| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 6.19 r_work: 0.2518 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2523 r_free = 0.2523 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16467 Z= 0.113 Angle : 0.549 10.581 22505 Z= 0.285 Chirality : 0.041 0.206 2445 Planarity : 0.003 0.040 2703 Dihedral : 15.763 59.974 2663 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.96 % Allowed : 14.21 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.95 (0.20), residues: 1851 helix: 2.01 (0.22), residues: 568 sheet: 1.18 (0.28), residues: 387 loop : -0.54 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.014 0.001 TYR C 805 PHE 0.019 0.001 PHE D 345 TRP 0.009 0.001 TRP E 416 HIS 0.007 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16451) covalent geometry : angle 0.54705 / 0.28 (22496) hydrogen bonds : bond 0.03326 / 2.38 ( 686) hydrogen bonds : angle 4.13548 / 2.93 ( 1890) metal coordination : bond 0.00991 / 0.71 ( 16) metal coordination : angle 2.11564 / 1.00 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.9074 (mmm) cc_final: 0.8591 (mmm) REVERT: A 661 ASP cc_start: 0.8087 (t0) cc_final: 0.7635 (t70) REVERT: A 849 MET cc_start: 0.9529 (mmm) cc_final: 0.8958 (tpt) REVERT: B 285 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7931 (mmm) REVERT: C 547 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8618 (mp0) REVERT: C 627 MET cc_start: 0.8794 (tpp) cc_final: 0.8442 (tpp) REVERT: C 666 GLU cc_start: 0.9052 (mp0) cc_final: 0.8786 (mp0) REVERT: C 669 THR cc_start: 0.9413 (t) cc_final: 0.9024 (p) REVERT: C 959 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8506 (mm-30) REVERT: D 39 ARG cc_start: 0.8807 (tpp-160) cc_final: 0.8469 (tpp-160) REVERT: D 152 MET cc_start: 0.8846 (mtp) cc_final: 0.8415 (ttm) REVERT: E 418 THR cc_start: 0.8879 (m) cc_final: 0.8247 (t) REVERT: E 437 GLU cc_start: 0.7869 (mp0) cc_final: 0.7656 (mp0) REVERT: E 443 MET cc_start: 0.7216 (mtp) cc_final: 0.6559 (mtt) REVERT: E 445 TYR cc_start: 0.8520 (t80) cc_final: 0.7793 (t80) REVERT: E 459 MET cc_start: 0.8432 (mmm) cc_final: 0.7999 (mmm) outliers start: 32 outliers final: 23 residues processed: 208 average time/residue: 0.1175 time to fit residues: 38.6724 Evaluate side-chains 207 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 91 TYR Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 593 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 35 optimal weight: 0.0070 chunk 178 optimal weight: 10.0000 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.056740 restraints weight = 120461.557| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 6.34 r_work: 0.2506 rms_B_bonded: 6.31 restraints_weight: 2.0000 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16467 Z= 0.117 Angle : 0.553 11.060 22505 Z= 0.286 Chirality : 0.041 0.196 2445 Planarity : 0.003 0.040 2703 Dihedral : 15.768 59.851 2663 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.96 % Allowed : 14.21 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.95 (0.20), residues: 1851 helix: 2.04 (0.22), residues: 569 sheet: 1.09 (0.28), residues: 379 loop : -0.49 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.014 0.001 TYR C 805 PHE 0.016 0.001 PHE A 916 TRP 0.010 0.001 TRP E 416 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (16451) covalent geometry : angle 0.55131 / 0.29 (22496) hydrogen bonds : bond 0.03345 / 2.39 ( 686) hydrogen bonds : angle 4.13972 / 2.94 ( 1890) metal coordination : bond 0.01103 / 0.78 ( 16) metal coordination : angle 2.21022 / 1.02 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8186 (t0) cc_final: 0.7928 (t70) REVERT: A 841 MET cc_start: 0.9286 (mmt) cc_final: 0.8859 (mmt) REVERT: B 22 MET cc_start: 0.9298 (mtm) cc_final: 0.9009 (mtm) REVERT: B 152 MET cc_start: 0.7663 (mmm) cc_final: 0.7335 (mmm) REVERT: B 166 GLN cc_start: 0.9397 (tt0) cc_final: 0.9087 (mp-120) REVERT: B 285 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7923 (mmm) REVERT: C 547 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8778 (mp0) REVERT: C 627 MET cc_start: 0.8854 (tpp) cc_final: 0.8511 (tpp) REVERT: C 666 GLU cc_start: 0.9079 (mp0) cc_final: 0.8823 (mp0) REVERT: C 669 THR cc_start: 0.9438 (t) cc_final: 0.9059 (p) REVERT: C 959 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8518 (mm-30) REVERT: D 5 MET cc_start: 0.7983 (mtm) cc_final: 0.7424 (mtm) REVERT: D 152 MET cc_start: 0.8894 (mtp) cc_final: 0.8460 (ttm) REVERT: E 418 THR cc_start: 0.8887 (m) cc_final: 0.8156 (t) REVERT: E 437 GLU cc_start: 0.7985 (mp0) cc_final: 0.7722 (mp0) REVERT: E 443 MET cc_start: 0.7213 (mtp) cc_final: 0.6558 (mtt) REVERT: E 445 TYR cc_start: 0.8464 (t80) cc_final: 0.7641 (t80) outliers start: 32 outliers final: 24 residues processed: 209 average time/residue: 0.1191 time to fit residues: 39.1196 Evaluate side-chains 203 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 436 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 173 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 GLN B 313 HIS ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.077461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.058600 restraints weight = 115753.044| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 6.20 r_work: 0.2515 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16467 Z= 0.112 Angle : 0.550 9.833 22505 Z= 0.284 Chirality : 0.041 0.202 2445 Planarity : 0.003 0.033 2703 Dihedral : 15.741 59.806 2662 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.65 % Allowed : 14.64 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.96 (0.20), residues: 1851 helix: 2.03 (0.22), residues: 570 sheet: 0.97 (0.28), residues: 380 loop : -0.41 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 713 TYR 0.014 0.001 TYR C 805 PHE 0.019 0.001 PHE B 31 TRP 0.011 0.001 TRP E 416 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (16451) covalent geometry : angle 0.54817 / 0.28 (22496) hydrogen bonds : bond 0.03291 / 2.35 ( 686) hydrogen bonds : angle 4.11521 / 2.92 ( 1890) metal coordination : bond 0.00980 / 0.69 ( 16) metal coordination : angle 2.07598 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9494 (tpt-90) cc_final: 0.9038 (ttt180) REVERT: A 984 MET cc_start: 0.8558 (mmm) cc_final: 0.7990 (mmm) REVERT: B 152 MET cc_start: 0.7754 (mmm) cc_final: 0.7289 (mmm) REVERT: B 166 GLN cc_start: 0.9382 (tt0) cc_final: 0.9072 (mp-120) REVERT: B 285 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7886 (mmm) REVERT: C 627 MET cc_start: 0.8816 (tpp) cc_final: 0.8462 (tpp) REVERT: C 666 GLU cc_start: 0.9077 (mp0) cc_final: 0.8816 (mp0) REVERT: C 669 THR cc_start: 0.9426 (t) cc_final: 0.9044 (p) REVERT: C 959 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8523 (mm-30) REVERT: D 5 MET cc_start: 0.7983 (mtm) cc_final: 0.7417 (mtm) REVERT: D 152 MET cc_start: 0.8840 (mtp) cc_final: 0.8439 (ttm) REVERT: D 302 MET cc_start: 0.9466 (ttp) cc_final: 0.9243 (ttp) REVERT: E 418 THR cc_start: 0.8896 (m) cc_final: 0.7892 (t) REVERT: E 437 GLU cc_start: 0.8085 (mp0) cc_final: 0.7725 (mp0) REVERT: E 443 MET cc_start: 0.7405 (mtp) cc_final: 0.6895 (mtt) outliers start: 27 outliers final: 17 residues processed: 207 average time/residue: 0.1259 time to fit residues: 40.6899 Evaluate side-chains 202 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 79 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.0010 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.077835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.058932 restraints weight = 115701.553| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 6.23 r_work: 0.2614 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16467 Z= 0.109 Angle : 0.570 9.519 22505 Z= 0.293 Chirality : 0.041 0.274 2445 Planarity : 0.003 0.033 2703 Dihedral : 15.713 59.858 2662 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.53 % Allowed : 14.94 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 0.98 (0.20), residues: 1851 helix: 2.04 (0.22), residues: 568 sheet: 0.94 (0.28), residues: 383 loop : -0.36 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.023 0.001 TYR E 445 PHE 0.016 0.001 PHE C 916 TRP 0.012 0.001 TRP E 416 HIS 0.005 0.000 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (16451) covalent geometry : angle 0.56897 / 0.29 (22496) hydrogen bonds : bond 0.03260 / 2.33 ( 686) hydrogen bonds : angle 4.10408 / 2.91 ( 1890) metal coordination : bond 0.00882 / 0.62 ( 16) metal coordination : angle 1.79153 / 0.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9442 (tpt-90) cc_final: 0.8957 (ttt180) REVERT: A 984 MET cc_start: 0.8514 (mmm) cc_final: 0.7841 (mmm) REVERT: B 152 MET cc_start: 0.8073 (mmm) cc_final: 0.7653 (mmm) REVERT: B 166 GLN cc_start: 0.9415 (tt0) cc_final: 0.9120 (mp-120) REVERT: B 285 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8136 (mmm) REVERT: B 320 SER cc_start: 0.8111 (m) cc_final: 0.7803 (p) REVERT: C 627 MET cc_start: 0.9012 (tpp) cc_final: 0.8718 (tpp) REVERT: C 666 GLU cc_start: 0.9138 (mp0) cc_final: 0.8880 (mp0) REVERT: C 669 THR cc_start: 0.9482 (t) cc_final: 0.9146 (p) REVERT: C 959 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8559 (mm-30) REVERT: D 5 MET cc_start: 0.8069 (mtm) cc_final: 0.7522 (mtm) REVERT: D 152 MET cc_start: 0.9049 (mtp) cc_final: 0.8714 (ttm) REVERT: D 302 MET cc_start: 0.9470 (ttp) cc_final: 0.9258 (ttp) REVERT: E 418 THR cc_start: 0.8898 (m) cc_final: 0.7758 (t) REVERT: E 437 GLU cc_start: 0.8124 (mp0) cc_final: 0.7744 (mp0) REVERT: E 443 MET cc_start: 0.7168 (mtp) cc_final: 0.6483 (mtt) outliers start: 25 outliers final: 19 residues processed: 205 average time/residue: 0.1245 time to fit residues: 39.6451 Evaluate side-chains 202 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 428 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 8 optimal weight: 0.0010 chunk 29 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 185 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 overall best weight: 1.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.075677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.057047 restraints weight = 100063.032| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 5.78 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16467 Z= 0.171 Angle : 0.602 9.921 22505 Z= 0.307 Chirality : 0.042 0.287 2445 Planarity : 0.003 0.034 2703 Dihedral : 15.859 59.877 2662 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.53 % Allowed : 15.31 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 1.04 (0.20), residues: 1851 helix: 2.13 (0.23), residues: 567 sheet: 0.94 (0.28), residues: 379 loop : -0.33 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 970 TYR 0.016 0.001 TYR E 476 PHE 0.021 0.001 PHE B 31 TRP 0.012 0.001 TRP E 416 HIS 0.007 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16451) covalent geometry : angle 0.59966 / 0.31 (22496) hydrogen bonds : bond 0.03583 / 2.52 ( 686) hydrogen bonds : angle 4.18110 / 2.97 ( 1890) metal coordination : bond 0.01996 / 1.36 ( 16) metal coordination : angle 2.44539 / 1.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9515 (tpt-90) cc_final: 0.8924 (ttt180) REVERT: A 984 MET cc_start: 0.8256 (mmm) cc_final: 0.7500 (mmm) REVERT: B 22 MET cc_start: 0.9120 (mtm) cc_final: 0.8748 (mtm) REVERT: B 152 MET cc_start: 0.7496 (mmm) cc_final: 0.7028 (mmm) REVERT: B 166 GLN cc_start: 0.9318 (tt0) cc_final: 0.9051 (mp-120) REVERT: B 285 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7819 (mmm) REVERT: C 627 MET cc_start: 0.8705 (tpp) cc_final: 0.8292 (tpp) REVERT: C 666 GLU cc_start: 0.8894 (mp0) cc_final: 0.8660 (mp0) REVERT: C 669 THR cc_start: 0.9411 (t) cc_final: 0.8979 (p) REVERT: C 959 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8399 (mm-30) REVERT: D 5 MET cc_start: 0.7533 (mtm) cc_final: 0.7064 (mtm) REVERT: D 152 MET cc_start: 0.8898 (mtp) cc_final: 0.8454 (ttm) REVERT: D 302 MET cc_start: 0.9356 (ttp) cc_final: 0.9099 (ttp) REVERT: E 418 THR cc_start: 0.8891 (m) cc_final: 0.7816 (t) REVERT: E 437 GLU cc_start: 0.8148 (mp0) cc_final: 0.7789 (mp0) REVERT: E 443 MET cc_start: 0.7053 (mtp) cc_final: 0.6567 (mtt) outliers start: 25 outliers final: 20 residues processed: 196 average time/residue: 0.1241 time to fit residues: 37.9011 Evaluate side-chains 194 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 428 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 171 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 176 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 128 optimal weight: 0.0970 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 ASN B 313 HIS ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.074588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.055400 restraints weight = 128450.733| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 6.43 r_work: 0.2477 rms_B_bonded: 6.33 restraints_weight: 2.0000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16467 Z= 0.135 Angle : 0.600 11.096 22505 Z= 0.303 Chirality : 0.041 0.264 2445 Planarity : 0.003 0.033 2703 Dihedral : 15.806 59.775 2662 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.35 % Allowed : 15.55 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 1.06 (0.20), residues: 1851 helix: 2.19 (0.23), residues: 562 sheet: 0.86 (0.27), residues: 384 loop : -0.29 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 848 TYR 0.016 0.001 TYR E 476 PHE 0.031 0.001 PHE B 345 TRP 0.013 0.001 TRP E 416 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (16451) covalent geometry : angle 0.59829 / 0.30 (22496) hydrogen bonds : bond 0.03427 / 2.44 ( 686) hydrogen bonds : angle 4.16330 / 2.95 ( 1890) metal coordination : bond 0.01394 / 0.98 ( 16) metal coordination : angle 2.22094 / 0.97 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9509 (tpt-90) cc_final: 0.9086 (ttt180) REVERT: A 841 MET cc_start: 0.9122 (mmt) cc_final: 0.8867 (mmt) REVERT: A 984 MET cc_start: 0.8555 (mmm) cc_final: 0.7893 (mmm) REVERT: B 22 MET cc_start: 0.9287 (mtm) cc_final: 0.8974 (mtm) REVERT: B 152 MET cc_start: 0.7969 (mmm) cc_final: 0.7571 (mmm) REVERT: B 166 GLN cc_start: 0.9423 (tt0) cc_final: 0.9099 (mp-120) REVERT: B 285 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7845 (mmm) REVERT: C 627 MET cc_start: 0.8860 (tpp) cc_final: 0.8504 (tpp) REVERT: C 666 GLU cc_start: 0.9085 (mp0) cc_final: 0.8846 (mp0) REVERT: C 669 THR cc_start: 0.9449 (t) cc_final: 0.9061 (p) REVERT: C 959 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8536 (mm-30) REVERT: D 5 MET cc_start: 0.8078 (mtm) cc_final: 0.7546 (mtm) REVERT: D 152 MET cc_start: 0.8903 (mtp) cc_final: 0.8472 (ttm) REVERT: E 418 THR cc_start: 0.8946 (m) cc_final: 0.7877 (t) REVERT: E 437 GLU cc_start: 0.8314 (mp0) cc_final: 0.7934 (mp0) REVERT: E 443 MET cc_start: 0.7525 (mtp) cc_final: 0.6965 (mtt) REVERT: E 462 GLU cc_start: 0.8449 (pm20) cc_final: 0.8231 (pm20) outliers start: 22 outliers final: 18 residues processed: 194 average time/residue: 0.1239 time to fit residues: 37.4988 Evaluate side-chains 196 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.056156 restraints weight = 109542.004| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 6.09 r_work: 0.2523 rms_B_bonded: 6.04 restraints_weight: 2.0000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2519 r_free = 0.2519 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16467 Z= 0.120 Angle : 0.592 12.134 22505 Z= 0.300 Chirality : 0.041 0.268 2445 Planarity : 0.003 0.033 2703 Dihedral : 15.756 59.794 2662 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.59 % Allowed : 15.37 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % 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: 1.09 (0.20), residues: 1851 helix: 2.20 (0.23), residues: 562 sheet: 0.88 (0.28), residues: 379 loop : -0.27 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 848 TYR 0.016 0.001 TYR E 476 PHE 0.027 0.001 PHE B 345 TRP 0.013 0.001 TRP E 416 HIS 0.011 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16451) covalent geometry : angle 0.59106 / 0.30 (22496) hydrogen bonds : bond 0.03367 / 2.39 ( 686) hydrogen bonds : angle 4.14519 / 2.93 ( 1890) metal coordination : bond 0.01105 / 0.78 ( 16) metal coordination : angle 1.99163 / 0.87 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3763.89 seconds wall clock time: 65 minutes 37.12 seconds (3937.12 seconds total)