Starting phenix.real_space_refine on Thu Aug 6 17:16:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpu_61715/08_2026/9jpu_61715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpu_61715/08_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_61715/08_2026/9jpu_61715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpu_61715/08_2026/9jpu_61715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jpu_61715/08_2026/9jpu_61715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpu_61715/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 4.15, per 1000 atoms: 0.26 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: 1.29 Conformation dependent library (CDL) restraints added in 788.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 727 " pdb=" ZN C1102 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1102 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 727 " pdb="ZN ZN C1102 " - pdb=" SG CYS C 730 " 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: 1.72 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: 3.01 Time building geometry restraints manager: 1.65 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: 1.680 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.090 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.360 ------------------------------------------------------------------------------- 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= 0.377 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 0.51981 / 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 : 0.441 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: 0.1115 time to fit residues: 63.8545 Evaluate side-chains 216 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 = 0.076244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.056938 restraints weight = 123765.151| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 6.54 r_work: 0.2600 rms_B_bonded: 6.30 restraints_weight: 2.0000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16467 Z= 0.137 Angle : 0.618 11.957 22505 Z= 0.318 Chirality : 0.042 0.176 2445 Planarity : 0.005 0.121 2703 Dihedral : 15.783 59.809 2666 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 1.59 % Allowed : 13.23 % 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: 1.96 (0.23), residues: 572 sheet: 1.14 (0.28), residues: 376 loop : -0.68 (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 0.017 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 0.00297 / 0.14 (16451) covalent geometry : angle 0.60553 / 0.32 (22496) hydrogen bonds : bond 0.03586 / 2.57 ( 686) hydrogen bonds : angle 4.28581 / 3.03 ( 1890) metal coordination : bond 0.02009 / 1.46 ( 16) metal coordination : angle 6.23225 / 3.18 ( 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 241 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8974 (mtp) cc_final: 0.8680 (mtm) REVERT: A 627 MET cc_start: 0.9227 (mmm) cc_final: 0.8871 (mmm) REVERT: A 858 MET cc_start: 0.9322 (mmm) cc_final: 0.8941 (mmm) REVERT: B 285 MET cc_start: 0.8718 (mmm) cc_final: 0.8290 (mmm) REVERT: C 643 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8782 (tp30) REVERT: C 666 GLU cc_start: 0.9003 (mp0) cc_final: 0.8679 (mp0) REVERT: C 804 PHE cc_start: 0.8851 (m-80) cc_final: 0.8572 (m-10) REVERT: C 848 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8317 (ttt90) REVERT: D 39 ARG cc_start: 0.8919 (tpp-160) cc_final: 0.8602 (tpp-160) REVERT: D 152 MET cc_start: 0.9146 (mtp) cc_final: 0.8454 (tpp) REVERT: D 302 MET cc_start: 0.9386 (ttm) cc_final: 0.9092 (ttp) REVERT: E 443 MET cc_start: 0.6876 (mtp) cc_final: 0.5328 (mmm) REVERT: E 445 TYR cc_start: 0.7991 (t80) cc_final: 0.7621 (t80) REVERT: E 459 MET cc_start: 0.8834 (mmp) cc_final: 0.8476 (mmm) outliers start: 26 outliers final: 14 residues processed: 232 average time/residue: 0.1066 time to fit residues: 38.2110 Evaluate side-chains 191 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 164 optimal weight: 0.0980 chunk 178 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 chunk 26 optimal weight: 0.0040 chunk 23 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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** ** E 481 HIS ** 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 = 0.3224 r_free = 0.3224 target = 0.077991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.059060 restraints weight = 122683.423| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 6.39 r_work: 0.2511 rms_B_bonded: 6.29 restraints_weight: 2.0000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16467 Z= 0.111 Angle : 0.558 9.666 22505 Z= 0.291 Chirality : 0.041 0.167 2445 Planarity : 0.004 0.061 2703 Dihedral : 15.773 59.994 2663 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: 0.86 (0.20), residues: 1851 helix: 1.96 (0.23), residues: 573 sheet: 1.17 (0.28), residues: 378 loop : -0.62 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 39 TYR 0.017 0.001 TYR C 805 PHE 0.016 0.001 PHE D 48 TRP 0.012 0.001 TRP C 760 HIS 0.005 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (16451) covalent geometry : angle 0.55459 / 0.29 (22496) hydrogen bonds : bond 0.03206 / 2.26 ( 686) hydrogen bonds : angle 4.19675 / 2.97 ( 1890) metal coordination : bond 0.01106 / 0.83 ( 16) metal coordination : angle 3.15848 / 1.66 ( 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 223 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.9098 (mmm) cc_final: 0.8658 (mmm) REVERT: A 858 MET cc_start: 0.9272 (mmm) cc_final: 0.9069 (mmm) REVERT: B 39 ARG cc_start: 0.8789 (ttp-170) cc_final: 0.8572 (ttp-170) REVERT: B 285 MET cc_start: 0.8542 (mmm) cc_final: 0.7965 (mmm) REVERT: C 627 MET cc_start: 0.8857 (tpp) cc_final: 0.8557 (tpp) REVERT: C 643 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8729 (tp30) REVERT: C 666 GLU cc_start: 0.9011 (mp0) cc_final: 0.8798 (mp0) REVERT: C 804 PHE cc_start: 0.8707 (m-80) cc_final: 0.8490 (m-10) REVERT: D 5 MET cc_start: 0.7986 (mtm) cc_final: 0.7378 (mtm) REVERT: D 39 ARG cc_start: 0.8863 (tpp-160) cc_final: 0.8526 (tpp-160) REVERT: D 152 MET cc_start: 0.8955 (mtp) cc_final: 0.8536 (ttm) REVERT: D 302 MET cc_start: 0.9397 (ttm) cc_final: 0.9147 (ttp) REVERT: E 418 THR cc_start: 0.8844 (m) cc_final: 0.8431 (p) REVERT: E 443 MET cc_start: 0.7015 (mtp) cc_final: 0.6471 (mtt) REVERT: E 445 TYR cc_start: 0.8059 (t80) cc_final: 0.7676 (t80) REVERT: E 459 MET cc_start: 0.8624 (mmp) cc_final: 0.8104 (mmm) outliers start: 30 outliers final: 16 residues processed: 217 average time/residue: 0.0986 time to fit residues: 33.7943 Evaluate side-chains 194 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 478 CYS 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 436 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 153 optimal weight: 0.0040 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.076913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.058182 restraints weight = 107770.732| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 6.03 r_work: 0.2595 rms_B_bonded: 6.00 restraints_weight: 2.0000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2514 r_free = 0.2514 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 = 0.2514 r_free = 0.2514 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16467 Z= 0.139 Angle : 0.560 9.767 22505 Z= 0.290 Chirality : 0.041 0.250 2445 Planarity : 0.004 0.059 2703 Dihedral : 15.839 59.969 2663 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.33 % Allowed : 13.53 % Favored : 84.14 % 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 (0.23), residues: 568 sheet: 1.16 (0.28), residues: 379 loop : -0.53 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 39 TYR 0.016 0.001 TYR C 805 PHE 0.017 0.001 PHE B 31 TRP 0.009 0.001 TRP C 760 HIS 0.008 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16451) covalent geometry : angle 0.55699 / 0.29 (22496) hydrogen bonds : bond 0.03397 / 2.41 ( 686) hydrogen bonds : angle 4.18091 / 2.96 ( 1890) metal coordination : bond 0.01396 / 0.99 ( 16) metal coordination : angle 2.78190 / 1.38 ( 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 223 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.9235 (mmm) cc_final: 0.8814 (mmm) REVERT: A 841 MET cc_start: 0.9338 (mmt) cc_final: 0.8917 (mmt) REVERT: B 285 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: C 627 MET cc_start: 0.9093 (tpp) cc_final: 0.8778 (tpp) REVERT: C 666 GLU cc_start: 0.9098 (mp0) cc_final: 0.8842 (mp0) REVERT: C 669 THR cc_start: 0.9470 (t) cc_final: 0.9104 (p) REVERT: D 152 MET cc_start: 0.9088 (mtp) cc_final: 0.8741 (ttm) REVERT: E 418 THR cc_start: 0.8844 (m) cc_final: 0.8446 (p) REVERT: E 443 MET cc_start: 0.6889 (mtp) cc_final: 0.6248 (mtt) outliers start: 38 outliers final: 28 residues processed: 210 average time/residue: 0.1031 time to fit residues: 34.2740 Evaluate side-chains 200 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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 776 VAL Chi-restraints excluded: chain C residue 803 GLU 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: 7.9990 chunk 174 optimal weight: 0.4980 chunk 155 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3210 r_free = 0.3210 target = 0.077173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058310 restraints weight = 114362.515| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 6.18 r_work: 0.2592 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.2592 ------------------------------------------------------------------------------- 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 = 0.25 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 = 0.25 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: 0.8406 moved from start: 0.2217 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= 0.123 Angle : 0.556 10.217 22505 Z= 0.288 Chirality : 0.041 0.202 2445 Planarity : 0.004 0.090 2703 Dihedral : 15.822 59.971 2663 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.20 % Allowed : 13.78 % Favored : 84.02 % 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: 0.98 (0.20), residues: 1851 helix: 2.09 (0.23), residues: 567 sheet: 1.16 (0.28), residues: 379 loop : -0.51 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 39 TYR 0.024 0.001 TYR E 445 PHE 0.021 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 0.00271 / 0.12 (16451) covalent geometry : angle 0.55387 / 0.29 (22496) hydrogen bonds : bond 0.03360 / 2.39 ( 686) hydrogen bonds : angle 4.16554 / 2.95 ( 1890) metal coordination : bond 0.01174 / 0.84 ( 16) metal coordination : angle 2.33709 / 1.14 ( 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: 36 poor density : 183 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8360 (t0) cc_final: 0.7922 (t70) REVERT: A 841 MET cc_start: 0.9348 (mmt) cc_final: 0.9011 (mmt) REVERT: B 285 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8209 (mmm) REVERT: C 547 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8583 (mp0) REVERT: C 627 MET cc_start: 0.9054 (tpp) cc_final: 0.8749 (tpp) REVERT: C 666 GLU cc_start: 0.9098 (mp0) cc_final: 0.8825 (mp0) REVERT: C 669 THR cc_start: 0.9496 (t) cc_final: 0.9105 (p) REVERT: D 152 MET cc_start: 0.9087 (mtp) cc_final: 0.8707 (ttm) REVERT: E 418 THR cc_start: 0.8873 (m) cc_final: 0.8469 (p) REVERT: E 437 GLU cc_start: 0.7940 (mp0) cc_final: 0.7686 (mp0) REVERT: E 443 MET cc_start: 0.7042 (mtp) cc_final: 0.6262 (mtt) REVERT: E 445 TYR cc_start: 0.8566 (t80) cc_final: 0.7759 (t80) outliers start: 36 outliers final: 29 residues processed: 205 average time/residue: 0.0944 time to fit residues: 30.3383 Evaluate side-chains 203 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 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 C residue 985 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 482 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 178 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 HIS ** 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 = 0.3207 r_free = 0.3207 target = 0.076855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.057939 restraints weight = 121373.059| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 6.32 r_work: 0.2586 rms_B_bonded: 6.20 restraints_weight: 2.0000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2504 r_free = 0.2504 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: 0.2504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16467 Z= 0.121 Angle : 0.555 9.679 22505 Z= 0.288 Chirality : 0.041 0.186 2445 Planarity : 0.003 0.065 2703 Dihedral : 15.799 59.780 2663 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.02 % Allowed : 14.08 % Favored : 83.89 % 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: 0.99 (0.20), residues: 1851 helix: 2.08 (0.22), residues: 567 sheet: 1.11 (0.28), residues: 388 loop : -0.49 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 39 TYR 0.019 0.001 TYR E 445 PHE 0.026 0.001 PHE B 345 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 0.00260 / 0.12 (16451) covalent geometry : angle 0.55322 / 0.29 (22496) hydrogen bonds : bond 0.03380 / 2.42 ( 686) hydrogen bonds : angle 4.12268 / 2.92 ( 1890) metal coordination : bond 0.01168 / 0.83 ( 16) metal coordination : angle 2.35172 / 1.09 ( 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: 33 poor density : 188 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8411 (t0) cc_final: 0.8165 (t70) REVERT: A 841 MET cc_start: 0.9331 (mmt) cc_final: 0.9013 (mmt) REVERT: B 285 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8178 (mmm) REVERT: C 547 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8811 (mp0) REVERT: C 627 MET cc_start: 0.9039 (tpp) cc_final: 0.8771 (tpp) REVERT: C 666 GLU cc_start: 0.9142 (mp0) cc_final: 0.8880 (mp0) REVERT: C 669 THR cc_start: 0.9497 (t) cc_final: 0.9124 (p) REVERT: D 5 MET cc_start: 0.8083 (mtm) cc_final: 0.7546 (mtm) REVERT: D 152 MET cc_start: 0.9067 (mtp) cc_final: 0.8675 (ttm) REVERT: E 437 GLU cc_start: 0.7979 (mp0) cc_final: 0.7674 (mp0) REVERT: E 443 MET cc_start: 0.7037 (mtp) cc_final: 0.6302 (mtt) REVERT: E 445 TYR cc_start: 0.8509 (t80) cc_final: 0.7619 (t80) outliers start: 33 outliers final: 21 residues processed: 209 average time/residue: 0.1014 time to fit residues: 32.8890 Evaluate side-chains 199 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 B residue 287 CYS 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 E residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 11 optimal weight: 0.0010 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 860 GLN 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 = 0.3220 r_free = 0.3220 target = 0.077467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.058571 restraints weight = 115767.424| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 6.23 r_work: 0.2600 rms_B_bonded: 6.21 restraints_weight: 2.0000 r_work (final): 0.2600 ------------------------------------------------------------------------------- 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 = 0.24 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 = 0.24 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: 0.8413 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16467 Z= 0.109 Angle : 0.553 9.446 22505 Z= 0.285 Chirality : 0.041 0.193 2445 Planarity : 0.003 0.043 2703 Dihedral : 15.756 59.637 2662 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.20 % Allowed : 14.39 % Favored : 83.40 % 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: 2.09 (0.22), residues: 568 sheet: 0.97 (0.27), residues: 381 loop : -0.42 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 826 TYR 0.016 0.001 TYR E 445 PHE 0.035 0.001 PHE B 345 TRP 0.010 0.001 TRP E 416 HIS 0.007 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (16451) covalent geometry : angle 0.55090 / 0.29 (22496) hydrogen bonds : bond 0.03330 / 2.38 ( 686) hydrogen bonds : angle 4.10110 / 2.91 ( 1890) metal coordination : bond 0.01062 / 0.78 ( 16) metal coordination : angle 2.39733 / 1.18 ( 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 228 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8459 (t0) cc_final: 0.8211 (t70) REVERT: A 841 MET cc_start: 0.9316 (mmt) cc_final: 0.9003 (mmt) REVERT: A 984 MET cc_start: 0.8570 (mmm) cc_final: 0.8010 (mmm) REVERT: B 22 MET cc_start: 0.9422 (mtm) cc_final: 0.9119 (mtm) REVERT: B 285 MET cc_start: 0.8900 (mmm) cc_final: 0.8192 (mmm) REVERT: C 627 MET cc_start: 0.9040 (tpp) cc_final: 0.8744 (tpp) REVERT: C 666 GLU cc_start: 0.9139 (mp0) cc_final: 0.8874 (mp0) REVERT: C 669 THR cc_start: 0.9503 (t) cc_final: 0.9129 (p) REVERT: D 5 MET cc_start: 0.8069 (mtm) cc_final: 0.7552 (mtm) REVERT: D 152 MET cc_start: 0.9049 (mtp) cc_final: 0.8720 (ttm) REVERT: E 418 THR cc_start: 0.8995 (m) cc_final: 0.8168 (t) REVERT: E 437 GLU cc_start: 0.8253 (mp0) cc_final: 0.7893 (mp0) REVERT: E 443 MET cc_start: 0.7087 (mtp) cc_final: 0.6376 (mtt) outliers start: 36 outliers final: 21 residues processed: 217 average time/residue: 0.0962 time to fit residues: 33.4110 Evaluate side-chains 203 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 887 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 SER 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 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 334 ASP Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 428 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.077318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.058448 restraints weight = 115857.598| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 6.23 r_work: 0.2601 rms_B_bonded: 6.17 restraints_weight: 2.0000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2520 r_free = 0.2520 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 = 0.2520 r_free = 0.2520 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: 0.2520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2576 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= 0.112 Angle : 0.567 9.721 22505 Z= 0.289 Chirality : 0.041 0.278 2445 Planarity : 0.003 0.037 2703 Dihedral : 15.748 59.715 2662 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.59 % Allowed : 15.43 % Favored : 82.98 % 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: 1.01 (0.20), residues: 1851 helix: 2.11 (0.22), residues: 568 sheet: 0.93 (0.27), residues: 384 loop : -0.37 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 826 TYR 0.015 0.001 TYR C 805 PHE 0.021 0.001 PHE B 31 TRP 0.012 0.001 TRP C 760 HIS 0.006 0.000 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (16451) covalent geometry : angle 0.56473 / 0.29 (22496) hydrogen bonds : bond 0.03328 / 2.38 ( 686) hydrogen bonds : angle 4.09424 / 2.90 ( 1890) metal coordination : bond 0.01322 / 0.95 ( 16) metal coordination : angle 2.56833 / 1.34 ( 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 208 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9501 (ttt180) cc_final: 0.9176 (ttt180) REVERT: A 841 MET cc_start: 0.9283 (mmt) cc_final: 0.8991 (mmt) REVERT: A 984 MET cc_start: 0.8512 (mmm) cc_final: 0.7847 (mmm) REVERT: B 285 MET cc_start: 0.8900 (mmm) cc_final: 0.8108 (mmm) REVERT: B 302 MET cc_start: 0.8262 (pmm) cc_final: 0.7905 (pmm) REVERT: C 627 MET cc_start: 0.9018 (tpp) cc_final: 0.8723 (tpp) REVERT: C 666 GLU cc_start: 0.9167 (mp0) cc_final: 0.8904 (mp0) REVERT: C 669 THR cc_start: 0.9499 (t) cc_final: 0.9124 (p) REVERT: D 5 MET cc_start: 0.8089 (mtm) cc_final: 0.7573 (mtm) REVERT: D 14 LEU cc_start: 0.9157 (mt) cc_final: 0.8950 (mt) REVERT: D 152 MET cc_start: 0.9036 (mtp) cc_final: 0.8709 (ttm) REVERT: E 418 THR cc_start: 0.8946 (m) cc_final: 0.8219 (t) REVERT: E 437 GLU cc_start: 0.8282 (mp0) cc_final: 0.7909 (mp0) REVERT: E 443 MET cc_start: 0.7122 (mtp) cc_final: 0.6466 (mtt) REVERT: E 445 TYR cc_start: 0.8494 (t80) cc_final: 0.7697 (t80) outliers start: 26 outliers final: 20 residues processed: 202 average time/residue: 0.1043 time to fit residues: 33.2751 Evaluate side-chains 199 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 79 SER 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 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 334 ASP Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 130 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 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: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 750 HIS A 965 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.054608 restraints weight = 97433.680| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 5.72 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16467 Z= 0.204 Angle : 0.617 10.801 22505 Z= 0.314 Chirality : 0.042 0.280 2445 Planarity : 0.004 0.042 2703 Dihedral : 15.949 59.864 2662 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.53 % Allowed : 15.68 % Favored : 82.79 % 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: 2.19 (0.23), residues: 560 sheet: 1.02 (0.28), residues: 370 loop : -0.38 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 826 TYR 0.017 0.001 TYR B 195 PHE 0.019 0.002 PHE C 916 TRP 0.013 0.001 TRP E 416 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (16451) covalent geometry : angle 0.61355 / 0.31 (22496) hydrogen bonds : bond 0.03849 / 2.70 ( 686) hydrogen bonds : angle 4.23886 / 3.02 ( 1890) metal coordination : bond 0.02494 / 1.75 ( 16) metal coordination : angle 3.26971 / 1.59 ( 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 197 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9531 (ttt180) cc_final: 0.9142 (ttt180) REVERT: A 841 MET cc_start: 0.8946 (mmt) cc_final: 0.8578 (mmt) REVERT: A 984 MET cc_start: 0.8308 (mmm) cc_final: 0.7553 (mmm) REVERT: B 152 MET cc_start: 0.7777 (mmm) cc_final: 0.7424 (mmm) REVERT: B 166 GLN cc_start: 0.9306 (tt0) cc_final: 0.9025 (mp-120) REVERT: B 285 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7869 (mmm) REVERT: C 627 MET cc_start: 0.8789 (tpp) cc_final: 0.8359 (tpp) REVERT: C 666 GLU cc_start: 0.8902 (mp0) cc_final: 0.8662 (mp0) REVERT: C 669 THR cc_start: 0.9444 (t) cc_final: 0.9002 (p) REVERT: D 5 MET cc_start: 0.7612 (mtm) cc_final: 0.7211 (mtm) REVERT: D 152 MET cc_start: 0.8968 (mtp) cc_final: 0.8538 (ttm) REVERT: E 418 THR cc_start: 0.9002 (m) cc_final: 0.8209 (t) REVERT: E 437 GLU cc_start: 0.8218 (mp0) cc_final: 0.7874 (mp0) REVERT: E 443 MET cc_start: 0.6924 (mtp) cc_final: 0.6384 (mtt) outliers start: 25 outliers final: 23 residues processed: 190 average time/residue: 0.1150 time to fit residues: 34.1682 Evaluate side-chains 190 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 77 THR 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 754 LEU Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 334 ASP 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 171 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 176 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 975 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3208 r_free = 0.3208 target = 0.075859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.057016 restraints weight = 126960.847| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 6.34 r_work: 0.2490 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2743 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= 0.123 Angle : 0.589 11.157 22505 Z= 0.299 Chirality : 0.041 0.269 2445 Planarity : 0.003 0.033 2703 Dihedral : 15.818 59.978 2662 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.59 % Allowed : 15.80 % Favored : 82.61 % 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: 1.08 (0.20), residues: 1851 helix: 2.22 (0.22), residues: 561 sheet: 0.88 (0.28), residues: 375 loop : -0.30 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 826 TYR 0.016 0.001 TYR E 476 PHE 0.029 0.001 PHE B 345 TRP 0.014 0.001 TRP E 416 HIS 0.005 0.001 HIS A 990 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16451) covalent geometry : angle 0.58734 / 0.30 (22496) hydrogen bonds : bond 0.03448 / 2.46 ( 686) hydrogen bonds : angle 4.18943 / 2.97 ( 1890) metal coordination : bond 0.01311 / 0.95 ( 16) metal coordination : angle 2.51507 / 1.15 ( 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: 26 poor density : 176 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9503 (ttt180) cc_final: 0.9241 (ttt180) REVERT: A 841 MET cc_start: 0.9263 (mmt) cc_final: 0.8972 (mmt) REVERT: A 984 MET cc_start: 0.8534 (mmm) cc_final: 0.7859 (mmm) REVERT: B 152 MET cc_start: 0.8102 (mmm) cc_final: 0.7778 (mmm) REVERT: B 166 GLN cc_start: 0.9417 (tt0) cc_final: 0.9092 (mp-120) REVERT: B 285 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: C 627 MET cc_start: 0.8855 (tpp) cc_final: 0.8505 (tpp) REVERT: C 666 GLU cc_start: 0.9086 (mp0) cc_final: 0.8847 (mp0) REVERT: C 669 THR cc_start: 0.9469 (t) cc_final: 0.9068 (p) REVERT: C 849 MET cc_start: 0.8373 (ttm) cc_final: 0.8172 (ttt) REVERT: D 5 MET cc_start: 0.8135 (mtm) cc_final: 0.7613 (mtm) REVERT: D 152 MET cc_start: 0.8926 (mtp) cc_final: 0.8491 (ttm) REVERT: E 418 THR cc_start: 0.9007 (m) cc_final: 0.8227 (t) REVERT: E 437 GLU cc_start: 0.8387 (mp0) cc_final: 0.7964 (mp0) REVERT: E 443 MET cc_start: 0.7380 (mtp) cc_final: 0.6826 (mtt) outliers start: 26 outliers final: 20 residues processed: 195 average time/residue: 0.1128 time to fit residues: 34.6790 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 : 0.602 ------------------------------------------------------------------------------- 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 77 THR 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 803 GLU Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 334 ASP 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: 0.0670 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.076224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.057689 restraints weight = 110266.277| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 6.00 r_work: 0.2517 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 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 = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16467 Z= 0.118 Angle : 0.589 12.495 22505 Z= 0.298 Chirality : 0.041 0.262 2445 Planarity : 0.003 0.033 2703 Dihedral : 15.771 59.880 2662 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.47 % Allowed : 16.11 % Favored : 82.42 % 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: 1.07 (0.20), residues: 1851 helix: 2.23 (0.22), residues: 561 sheet: 0.92 (0.28), residues: 378 loop : -0.33 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 826 TYR 0.016 0.001 TYR E 476 PHE 0.029 0.001 PHE B 345 TRP 0.014 0.001 TRP E 416 HIS 0.006 0.001 HIS E 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (16451) covalent geometry : angle 0.58731 / 0.30 (22496) hydrogen bonds : bond 0.03394 / 2.41 ( 686) hydrogen bonds : angle 4.17030 / 2.96 ( 1890) metal coordination : bond 0.01127 / 0.83 ( 16) metal coordination : angle 2.08597 / 0.92 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3371.27 seconds wall clock time: 58 minutes 47.97 seconds (3527.97 seconds total)