Starting phenix.real_space_refine on Thu Sep 18 11:30:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpu_61715/09_2025/9jpu_61715.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpu_61715/09_2025/9jpu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jpu_61715/09_2025/9jpu_61715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpu_61715/09_2025/9jpu_61715.map" model { file = "/net/cci-nas-00/data/ceres_data/9jpu_61715/09_2025/9jpu_61715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpu_61715/09_2025/9jpu_61715.cif" } 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-2.0-5805/lib/python3.9/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: 4.84, per 1000 atoms: 0.30 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: 1.14 Conformation dependent library (CDL) restraints added in 736.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.31 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: 3.06 Time building geometry restraints manager: 1.47 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=" C VAL C 943 " pdb=" N PRO C 944 " ideal model delta sigma weight residual 1.337 1.355 -0.018 1.06e-02 8.90e+03 2.95e+00 bond pdb=" N GLY D 158 " pdb=" CA GLY D 158 " ideal model delta sigma weight residual 1.458 1.448 0.010 9.20e-03 1.18e+04 1.10e+00 bond pdb=" CG PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.75e-01 bond pdb=" C3' DG G 41 " pdb=" C2' DG G 41 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.60e-01 bond pdb=" O4' DG F 30 " pdb=" C1' DG F 30 " ideal model delta sigma weight residual 1.414 1.396 0.018 2.00e-02 2.50e+03 8.36e-01 ... (remaining 16446 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 22330 2.32 - 4.64: 158 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=" C ASN C 740 " pdb=" N LEU C 741 " pdb=" CA LEU C 741 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" N PRO C 944 " pdb=" CA PRO C 944 " pdb=" C PRO C 944 " ideal model delta sigma weight residual 114.27 109.90 4.37 1.35e+00 5.49e-01 1.05e+01 angle pdb=" C VAL C 943 " pdb=" N PRO C 944 " pdb=" CD PRO C 944 " ideal model delta sigma weight residual 125.00 136.59 -11.59 4.10e+00 5.95e-02 7.99e+00 ... (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: 1899 0.042 - 0.083: 379 0.083 - 0.125: 159 0.125 - 0.167: 7 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=" CA ILE D 331 " pdb=" N ILE D 331 " pdb=" C ILE D 331 " pdb=" CB ILE D 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE D 109 " pdb=" N ILE D 109 " pdb=" C ILE D 109 " pdb=" CB ILE D 109 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-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: 1.030 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 17.560 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 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 : 0.002 0.074 16467 Z= 0.115 Angle : 0.704 50.094 22505 Z= 0.294 Chirality : 0.040 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 aren 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 covalent geometry : bond 0.00233 (16451) covalent geometry : angle 0.48346 (22496) hydrogen bonds : bond 0.06081 ( 686) hydrogen bonds : angle 4.59109 ( 1890) metal coordination : bond 0.02500 ( 16) metal coordination : angle 25.59370 ( 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 : 0.536 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: 0.1182 time to fit residues: 67.6851 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 : 0.729 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 495 GLN A 515 HIS A 609 HIS A 633 HIS A 739 GLN C 495 GLN C 515 HIS ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 54 HIS D 101 ASN D 278 GLN E 457 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.058601 restraints weight = 127016.271| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 6.52 r_work: 0.2500 rms_B_bonded: 6.35 restraints_weight: 2.0000 r_work (final): 0.2500 ------------------------------------------------------------------------------- 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 = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16467 Z= 0.129 Angle : 0.572 8.402 22505 Z= 0.295 Chirality : 0.041 0.166 2445 Planarity : 0.004 0.068 2703 Dihedral : 15.598 59.996 2666 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.95 % Rotamer: Outliers : 1.78 % Allowed : 12.92 % Favored : 85.30 % 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 aren not related in a simple way. whole: 0.88 (0.20), residues: 1851 helix: 1.98 (0.23), residues: 573 sheet: 1.21 (0.28), residues: 377 loop : -0.63 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 39 TYR 0.019 0.001 TYR C 805 PHE 0.016 0.001 PHE B 31 TRP 0.010 0.001 TRP E 416 HIS 0.005 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00296 (16451) covalent geometry : angle 0.56837 (22496) hydrogen bonds : bond 0.03321 ( 686) hydrogen bonds : angle 4.22703 ( 1890) metal coordination : bond 0.01347 ( 16) metal coordination : angle 3.45256 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 213 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 602 MET cc_start: 0.8834 (mtp) cc_final: 0.8615 (mtp) REVERT: A 627 MET cc_start: 0.9101 (mmm) cc_final: 0.8718 (mmm) REVERT: A 858 MET cc_start: 0.9236 (mmm) cc_final: 0.8913 (mmm) REVERT: B 91 TYR cc_start: 0.8459 (m-80) cc_final: 0.7678 (m-80) REVERT: B 285 MET cc_start: 0.8653 (mmm) cc_final: 0.8024 (mmm) REVERT: B 302 MET cc_start: 0.7760 (ptp) cc_final: 0.7519 (ptp) REVERT: C 627 MET cc_start: 0.8764 (tpp) cc_final: 0.8495 (tpp) REVERT: C 803 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8325 (tp30) REVERT: C 804 PHE cc_start: 0.8672 (m-80) cc_final: 0.8466 (m-10) REVERT: C 848 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8178 (ttt180) REVERT: C 959 GLU cc_start: 0.9477 (mm-30) cc_final: 0.8848 (mm-30) REVERT: D 39 ARG cc_start: 0.8889 (tpp-160) cc_final: 0.8637 (tpt170) REVERT: D 152 MET cc_start: 0.8845 (mtp) cc_final: 0.8430 (ttm) REVERT: E 443 MET cc_start: 0.6913 (mtp) cc_final: 0.5519 (mmm) REVERT: E 445 TYR cc_start: 0.8073 (t80) cc_final: 0.7691 (t80) outliers start: 29 outliers final: 16 residues processed: 233 average time/residue: 0.1111 time to fit residues: 39.9758 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 : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 12 ILE 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 C residue 862 THR Chi-restraints excluded: chain D residue 52 GLN Chi-restraints excluded: chain D residue 101 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 143 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 975 ASN B 313 HIS ** C 609 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN D 54 HIS D 101 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.055316 restraints weight = 119026.855| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 6.27 r_work: 0.2468 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16467 Z= 0.157 Angle : 0.548 8.730 22505 Z= 0.284 Chirality : 0.040 0.149 2445 Planarity : 0.004 0.045 2703 Dihedral : 15.635 59.802 2663 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.27 % Allowed : 13.35 % Favored : 84.38 % 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 aren not related in a simple way. whole: 0.97 (0.20), residues: 1851 helix: 2.05 (0.23), residues: 570 sheet: 1.19 (0.28), residues: 387 loop : -0.54 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 39 TYR 0.017 0.001 TYR C 805 PHE 0.020 0.001 PHE A 916 TRP 0.010 0.001 TRP C 760 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00359 (16451) covalent geometry : angle 0.54211 (22496) hydrogen bonds : bond 0.03281 ( 686) hydrogen bonds : angle 4.17548 ( 1890) metal coordination : bond 0.01773 ( 16) metal coordination : angle 3.94500 ( 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 221 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 627 MET cc_start: 0.9154 (mmm) cc_final: 0.8700 (mmm) REVERT: A 661 ASP cc_start: 0.8252 (t0) cc_final: 0.7956 (t70) REVERT: A 858 MET cc_start: 0.9278 (mmm) cc_final: 0.9073 (mmm) REVERT: B 22 MET cc_start: 0.9461 (mtm) cc_final: 0.9255 (mtm) REVERT: B 91 TYR cc_start: 0.8546 (m-80) cc_final: 0.7769 (m-80) REVERT: B 285 MET cc_start: 0.8745 (mmm) cc_final: 0.8024 (mmm) REVERT: B 302 MET cc_start: 0.7965 (ptp) cc_final: 0.7731 (ptp) REVERT: B 334 ASP cc_start: 0.8686 (m-30) cc_final: 0.8469 (m-30) REVERT: C 547 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8530 (mp0) REVERT: C 627 MET cc_start: 0.8865 (tpp) cc_final: 0.8568 (tpp) REVERT: C 666 GLU cc_start: 0.9067 (mp0) cc_final: 0.8699 (pm20) REVERT: C 959 GLU cc_start: 0.9472 (mm-30) cc_final: 0.8788 (mm-30) REVERT: D 5 MET cc_start: 0.8087 (mtm) cc_final: 0.7448 (mtm) REVERT: D 152 MET cc_start: 0.8947 (mtp) cc_final: 0.8273 (ttt) REVERT: E 443 MET cc_start: 0.7217 (mtp) cc_final: 0.6661 (mtt) REVERT: E 445 TYR cc_start: 0.8110 (t80) cc_final: 0.7590 (t80) outliers start: 37 outliers final: 25 residues processed: 214 average time/residue: 0.1062 time to fit residues: 35.2461 Evaluate side-chains 199 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 ILE 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 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 593 VAL Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 0.0030 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 0.1980 chunk 153 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 181 HIS C 609 HIS C 975 ASN ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.076310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.057389 restraints weight = 104045.775| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 6.05 r_work: 0.2624 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16467 Z= 0.102 Angle : 0.532 9.610 22505 Z= 0.273 Chirality : 0.040 0.156 2445 Planarity : 0.003 0.038 2703 Dihedral : 15.441 59.912 2663 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.59 % Allowed : 14.76 % Favored : 83.65 % 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 aren not related in a simple way. whole: 1.00 (0.20), residues: 1851 helix: 2.05 (0.22), residues: 570 sheet: 1.18 (0.27), residues: 394 loop : -0.51 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 773 TYR 0.015 0.001 TYR C 805 PHE 0.017 0.001 PHE B 31 TRP 0.015 0.001 TRP C 760 HIS 0.007 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00227 (16451) covalent geometry : angle 0.52927 (22496) hydrogen bonds : bond 0.02993 ( 686) hydrogen bonds : angle 4.08916 ( 1890) metal coordination : bond 0.00866 ( 16) metal coordination : angle 2.84503 ( 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 236 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 MET cc_start: 0.8702 (mtp) cc_final: 0.8483 (ttt) REVERT: A 627 MET cc_start: 0.9174 (mmm) cc_final: 0.8807 (mmm) REVERT: A 661 ASP cc_start: 0.8337 (t0) cc_final: 0.7958 (t70) REVERT: B 285 MET cc_start: 0.8808 (mmm) cc_final: 0.8046 (mmm) REVERT: B 302 MET cc_start: 0.8084 (ptp) cc_final: 0.7842 (ptp) REVERT: B 334 ASP cc_start: 0.8609 (m-30) cc_final: 0.8403 (m-30) REVERT: C 627 MET cc_start: 0.8933 (tpp) cc_final: 0.8664 (tpp) REVERT: C 666 GLU cc_start: 0.9103 (mp0) cc_final: 0.8679 (pm20) REVERT: C 669 THR cc_start: 0.9434 (t) cc_final: 0.9100 (p) REVERT: C 742 VAL cc_start: 0.9136 (t) cc_final: 0.8920 (p) REVERT: C 959 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8628 (mm-30) REVERT: D 5 MET cc_start: 0.8083 (mtm) cc_final: 0.7465 (mtm) REVERT: D 152 MET cc_start: 0.9023 (mtp) cc_final: 0.8750 (ttm) REVERT: D 285 MET cc_start: 0.9068 (mmm) cc_final: 0.8848 (mmp) REVERT: E 437 GLU cc_start: 0.8089 (mp0) cc_final: 0.7790 (mp0) REVERT: E 443 MET cc_start: 0.7113 (mtp) cc_final: 0.6229 (mtt) REVERT: E 445 TYR cc_start: 0.8022 (t80) cc_final: 0.7546 (t80) REVERT: E 459 MET cc_start: 0.8491 (mmm) cc_final: 0.7914 (mmm) outliers start: 26 outliers final: 16 residues processed: 231 average time/residue: 0.1080 time to fit residues: 39.0999 Evaluate side-chains 200 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 45 VAL 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 887 LEU Chi-restraints excluded: chain E residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 77 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 43 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 860 GLN B 313 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.073837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.055213 restraints weight = 108822.516| |-----------------------------------------------------------------------------| r_work (start): 0.2700 rms_B_bonded: 6.05 r_work: 0.2488 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16467 Z= 0.155 Angle : 0.555 9.253 22505 Z= 0.284 Chirality : 0.041 0.242 2445 Planarity : 0.003 0.045 2703 Dihedral : 15.585 59.752 2662 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.96 % Allowed : 14.82 % Favored : 83.22 % 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 aren not related in a simple way. whole: 1.17 (0.21), residues: 1851 helix: 2.28 (0.23), residues: 557 sheet: 1.20 (0.28), residues: 385 loop : -0.37 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 972 TYR 0.015 0.001 TYR C 805 PHE 0.014 0.001 PHE A 916 TRP 0.010 0.001 TRP E 416 HIS 0.006 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00352 (16451) covalent geometry : angle 0.55065 (22496) hydrogen bonds : bond 0.03370 ( 686) hydrogen bonds : angle 4.10366 ( 1890) metal coordination : bond 0.01819 ( 16) metal coordination : angle 3.44216 ( 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 214 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8371 (t0) cc_final: 0.7972 (t70) REVERT: A 826 ARG cc_start: 0.9501 (tpt-90) cc_final: 0.9179 (ttt180) REVERT: A 841 MET cc_start: 0.9288 (mmt) cc_final: 0.9076 (mmt) REVERT: B 285 MET cc_start: 0.8768 (mmm) cc_final: 0.7940 (mmm) REVERT: C 547 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8626 (mp0) REVERT: C 627 MET cc_start: 0.8903 (tpp) cc_final: 0.8583 (tpp) REVERT: C 666 GLU cc_start: 0.9063 (mp0) cc_final: 0.8645 (pm20) REVERT: C 669 THR cc_start: 0.9392 (t) cc_final: 0.9007 (p) REVERT: C 959 GLU cc_start: 0.9377 (mm-30) cc_final: 0.8410 (mm-30) REVERT: D 5 MET cc_start: 0.8190 (mtm) cc_final: 0.7604 (mtm) REVERT: D 152 MET cc_start: 0.8978 (mtp) cc_final: 0.8577 (ttm) REVERT: D 285 MET cc_start: 0.9094 (mmm) cc_final: 0.8853 (mmp) REVERT: D 294 ASP cc_start: 0.9002 (m-30) cc_final: 0.8607 (p0) REVERT: E 418 THR cc_start: 0.8843 (p) cc_final: 0.8167 (t) REVERT: E 437 GLU cc_start: 0.8338 (mp0) cc_final: 0.8056 (mp0) REVERT: E 443 MET cc_start: 0.7179 (mtp) cc_final: 0.6454 (mtt) outliers start: 32 outliers final: 24 residues processed: 203 average time/residue: 0.1099 time to fit residues: 35.2495 Evaluate side-chains 199 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 45 VAL 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 563 LEU Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 350 CYS Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 428 ASN Chi-restraints excluded: chain E residue 468 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 8 optimal weight: 0.0980 chunk 158 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3149 r_free = 0.3149 target = 0.075626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.056172 restraints weight = 119773.852| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 6.54 r_work: 0.2507 rms_B_bonded: 6.40 restraints_weight: 2.0000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2511 r_free = 0.2511 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16467 Z= 0.109 Angle : 0.545 10.728 22505 Z= 0.277 Chirality : 0.040 0.232 2445 Planarity : 0.003 0.035 2703 Dihedral : 15.426 59.856 2662 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.02 % Allowed : 14.76 % Favored : 83.22 % 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 aren not related in a simple way. whole: 1.15 (0.21), residues: 1851 helix: 2.16 (0.22), residues: 564 sheet: 1.14 (0.27), residues: 396 loop : -0.31 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.019 0.001 TYR E 445 PHE 0.018 0.001 PHE B 31 TRP 0.011 0.001 TRP E 416 HIS 0.005 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00244 (16451) covalent geometry : angle 0.54189 (22496) hydrogen bonds : bond 0.03071 ( 686) hydrogen bonds : angle 4.07007 ( 1890) metal coordination : bond 0.00920 ( 16) metal coordination : angle 2.99431 ( 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 220 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8352 (t0) cc_final: 0.7925 (t70) REVERT: A 826 ARG cc_start: 0.9479 (tpt-90) cc_final: 0.9154 (ttt180) REVERT: B 285 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7824 (mmm) REVERT: B 313 HIS cc_start: 0.9176 (m-70) cc_final: 0.8549 (m-70) REVERT: C 627 MET cc_start: 0.8790 (tpp) cc_final: 0.8507 (tpp) REVERT: C 666 GLU cc_start: 0.9083 (mp0) cc_final: 0.8647 (pm20) REVERT: C 669 THR cc_start: 0.9428 (t) cc_final: 0.9053 (p) REVERT: C 742 VAL cc_start: 0.9056 (t) cc_final: 0.8831 (p) REVERT: C 959 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 5 MET cc_start: 0.8211 (mtm) cc_final: 0.7693 (mtm) REVERT: D 14 LEU cc_start: 0.9026 (mt) cc_final: 0.8797 (mt) REVERT: D 152 MET cc_start: 0.8959 (mtp) cc_final: 0.8587 (ttm) REVERT: D 285 MET cc_start: 0.9056 (mmm) cc_final: 0.8809 (mmp) REVERT: D 294 ASP cc_start: 0.9019 (m-30) cc_final: 0.8647 (p0) REVERT: E 418 THR cc_start: 0.8746 (p) cc_final: 0.8033 (t) REVERT: E 437 GLU cc_start: 0.8336 (mp0) cc_final: 0.7518 (pm20) REVERT: E 443 MET cc_start: 0.7241 (mtp) cc_final: 0.6593 (mtt) REVERT: E 445 TYR cc_start: 0.8520 (t80) cc_final: 0.7730 (t80) outliers start: 33 outliers final: 24 residues processed: 211 average time/residue: 0.1045 time to fit residues: 34.7924 Evaluate side-chains 202 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 THR 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 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 595 VAL Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 468 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 31 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3123 r_free = 0.3123 target = 0.074352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.055700 restraints weight = 110104.809| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 6.08 r_work: 0.2503 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16467 Z= 0.132 Angle : 0.552 11.560 22505 Z= 0.281 Chirality : 0.041 0.259 2445 Planarity : 0.003 0.034 2703 Dihedral : 15.470 59.993 2662 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.14 % Allowed : 15.00 % Favored : 82.85 % 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 aren not related in a simple way. whole: 1.21 (0.21), residues: 1851 helix: 2.32 (0.23), residues: 557 sheet: 1.06 (0.28), residues: 375 loop : -0.24 (0.22), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.017 0.001 TYR E 445 PHE 0.028 0.001 PHE B 345 TRP 0.011 0.001 TRP E 416 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00300 (16451) covalent geometry : angle 0.54977 (22496) hydrogen bonds : bond 0.03208 ( 686) hydrogen bonds : angle 4.07370 ( 1890) metal coordination : bond 0.01395 ( 16) metal coordination : angle 2.77597 ( 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 215 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 ASP cc_start: 0.8362 (t0) cc_final: 0.8113 (t70) REVERT: A 826 ARG cc_start: 0.9466 (tpt-90) cc_final: 0.9187 (ttt180) REVERT: A 984 MET cc_start: 0.8587 (mmm) cc_final: 0.8007 (mmm) REVERT: B 166 GLN cc_start: 0.9419 (tt0) cc_final: 0.9089 (mp-120) REVERT: B 285 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.7969 (mmm) REVERT: B 313 HIS cc_start: 0.9166 (m90) cc_final: 0.8430 (m90) REVERT: C 547 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8486 (mp0) REVERT: C 627 MET cc_start: 0.8869 (tpp) cc_final: 0.8565 (tpp) REVERT: C 666 GLU cc_start: 0.9071 (mp0) cc_final: 0.8615 (pm20) REVERT: C 669 THR cc_start: 0.9447 (t) cc_final: 0.9082 (p) REVERT: C 959 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8275 (mm-30) REVERT: D 5 MET cc_start: 0.8218 (mtm) cc_final: 0.7695 (mtm) REVERT: D 14 LEU cc_start: 0.9035 (mt) cc_final: 0.8799 (mt) REVERT: D 152 MET cc_start: 0.9003 (mtp) cc_final: 0.8628 (ttm) REVERT: D 285 MET cc_start: 0.9041 (mmm) cc_final: 0.8801 (mmp) REVERT: D 294 ASP cc_start: 0.9019 (m-30) cc_final: 0.8663 (p0) REVERT: E 418 THR cc_start: 0.8743 (p) cc_final: 0.8127 (t) REVERT: E 437 GLU cc_start: 0.8419 (mp0) cc_final: 0.7519 (pm20) REVERT: E 445 TYR cc_start: 0.8468 (t80) cc_final: 0.7603 (t80) REVERT: E 462 GLU cc_start: 0.8615 (pm20) cc_final: 0.8338 (pm20) outliers start: 35 outliers final: 28 residues processed: 205 average time/residue: 0.1106 time to fit residues: 35.4512 Evaluate side-chains 201 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 77 THR 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 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 862 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 428 ASN Chi-restraints excluded: chain E residue 468 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 124 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 29 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 HIS A 965 ASN ** 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 = 0.3185 r_free = 0.3185 target = 0.074605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.056086 restraints weight = 113294.743| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 6.04 r_work: 0.2477 rms_B_bonded: 5.98 restraints_weight: 2.0000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2482 r_free = 0.2482 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16467 Z= 0.166 Angle : 0.571 10.791 22505 Z= 0.291 Chirality : 0.041 0.266 2445 Planarity : 0.003 0.036 2703 Dihedral : 15.554 59.827 2662 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.90 % Allowed : 15.43 % Favored : 82.67 % 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 aren not related in a simple way. whole: 1.15 (0.20), residues: 1851 helix: 2.27 (0.23), residues: 564 sheet: 1.17 (0.29), residues: 361 loop : -0.34 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 159 TYR 0.017 0.001 TYR E 445 PHE 0.020 0.001 PHE B 31 TRP 0.009 0.001 TRP E 453 HIS 0.004 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00378 (16451) covalent geometry : angle 0.56807 (22496) hydrogen bonds : bond 0.03391 ( 686) hydrogen bonds : angle 4.15315 ( 1890) metal coordination : bond 0.01863 ( 16) metal coordination : angle 2.97932 ( 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 206 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9465 (tpt-90) cc_final: 0.9188 (ttt180) REVERT: A 841 MET cc_start: 0.9207 (mmt) cc_final: 0.8826 (mmt) REVERT: A 984 MET cc_start: 0.8664 (mmm) cc_final: 0.8039 (mmm) REVERT: B 285 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7952 (mmm) REVERT: B 302 MET cc_start: 0.8046 (ptp) cc_final: 0.7791 (mpp) REVERT: B 313 HIS cc_start: 0.9217 (m90) cc_final: 0.8939 (m90) REVERT: C 547 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8513 (mp0) REVERT: C 627 MET cc_start: 0.8961 (tpp) cc_final: 0.8635 (tpp) REVERT: C 666 GLU cc_start: 0.9061 (mp0) cc_final: 0.8593 (pm20) REVERT: C 669 THR cc_start: 0.9480 (t) cc_final: 0.9043 (p) REVERT: C 849 MET cc_start: 0.8434 (ttm) cc_final: 0.8215 (ttt) REVERT: C 959 GLU cc_start: 0.9289 (mm-30) cc_final: 0.8195 (mm-30) REVERT: D 5 MET cc_start: 0.8264 (mtm) cc_final: 0.7773 (mtm) REVERT: D 152 MET cc_start: 0.9011 (mtp) cc_final: 0.8576 (ttm) REVERT: D 285 MET cc_start: 0.9014 (mmm) cc_final: 0.8728 (mmp) REVERT: D 294 ASP cc_start: 0.8977 (m-30) cc_final: 0.8607 (p0) REVERT: E 418 THR cc_start: 0.8831 (p) cc_final: 0.8270 (t) REVERT: E 437 GLU cc_start: 0.8285 (mp0) cc_final: 0.7953 (mp0) outliers start: 31 outliers final: 28 residues processed: 198 average time/residue: 0.0984 time to fit residues: 30.8528 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 : 0.487 ------------------------------------------------------------------------------- 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 638 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 45 VAL 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 B residue 285 MET Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 478 CYS Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 788 VAL Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 CYS 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: 0.9990 chunk 152 optimal weight: 0.9990 chunk 8 optimal weight: 0.0040 chunk 29 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 67 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.056471 restraints weight = 95849.302| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 5.62 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.294 16467 Z= 0.187 Angle : 0.774 59.144 22505 Z= 0.440 Chirality : 0.041 0.411 2445 Planarity : 0.003 0.034 2703 Dihedral : 15.557 59.882 2662 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % Favored : 82.42 % Cbeta Deviations : 0.06 % 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 aren not related in a simple way. whole: 1.16 (0.20), residues: 1851 helix: 2.30 (0.23), residues: 564 sheet: 1.12 (0.28), residues: 365 loop : -0.34 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 969 TYR 0.015 0.001 TYR C 805 PHE 0.013 0.001 PHE A 916 TRP 0.008 0.001 TRP E 453 HIS 0.003 0.001 HIS C 990 Details of bonding type rmsd covalent geometry : bond 0.00442 (16451) covalent geometry : angle 0.77163 (22496) hydrogen bonds : bond 0.03372 ( 686) hydrogen bonds : angle 4.15401 ( 1890) metal coordination : bond 0.01712 ( 16) metal coordination : angle 2.94579 ( 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 200 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9413 (tpt-90) cc_final: 0.9032 (ttt180) REVERT: A 841 MET cc_start: 0.8831 (mmt) cc_final: 0.8475 (mmt) REVERT: A 948 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 984 MET cc_start: 0.8305 (mmm) cc_final: 0.7623 (mmm) REVERT: B 285 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: B 302 MET cc_start: 0.8072 (ptp) cc_final: 0.7800 (mpp) REVERT: B 313 HIS cc_start: 0.8958 (m90) cc_final: 0.8636 (m90) REVERT: C 547 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8375 (mp0) REVERT: C 627 MET cc_start: 0.8727 (tpp) cc_final: 0.8358 (tpp) REVERT: C 666 GLU cc_start: 0.8861 (mp0) cc_final: 0.8419 (pm20) REVERT: C 669 THR cc_start: 0.9433 (t) cc_final: 0.8974 (p) REVERT: C 849 MET cc_start: 0.8145 (ttm) cc_final: 0.7891 (ttt) REVERT: C 959 GLU cc_start: 0.9152 (mm-30) cc_final: 0.7985 (mm-30) REVERT: D 5 MET cc_start: 0.7752 (mtm) cc_final: 0.7375 (mtm) REVERT: D 101 ASN cc_start: 0.9335 (OUTLIER) cc_final: 0.8227 (t0) REVERT: D 152 MET cc_start: 0.9006 (mtp) cc_final: 0.8562 (ttm) REVERT: D 285 MET cc_start: 0.8944 (mmm) cc_final: 0.8651 (mmp) REVERT: D 294 ASP cc_start: 0.8855 (m-30) cc_final: 0.8549 (p0) REVERT: E 418 THR cc_start: 0.8664 (p) cc_final: 0.8164 (t) REVERT: E 437 GLU cc_start: 0.8122 (mp0) cc_final: 0.7216 (pm20) outliers start: 29 outliers final: 25 residues processed: 191 average time/residue: 0.1148 time to fit residues: 34.3654 Evaluate side-chains 197 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 170 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 GLU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 45 VAL 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 788 VAL Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 CYS 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: 9.9990 chunk 5 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 106 optimal weight: 0.1980 chunk 163 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.056095 restraints weight = 124040.090| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 6.24 r_work: 0.2480 rms_B_bonded: 6.08 restraints_weight: 2.0000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2480 r_free = 0.2480 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 16467 Z= 0.163 Angle : 0.770 59.191 22505 Z= 0.421 Chirality : 0.041 0.244 2445 Planarity : 0.003 0.034 2703 Dihedral : 15.555 59.946 2662 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.78 % Allowed : 15.80 % 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 aren not related in a simple way. whole: 1.15 (0.20), residues: 1851 helix: 2.28 (0.23), residues: 564 sheet: 1.12 (0.28), residues: 365 loop : -0.33 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 969 TYR 0.014 0.001 TYR C 805 PHE 0.015 0.001 PHE B 31 TRP 0.007 0.001 TRP E 453 HIS 0.003 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00384 (16451) covalent geometry : angle 0.76843 (22496) hydrogen bonds : bond 0.03380 ( 686) hydrogen bonds : angle 4.15740 ( 1890) metal coordination : bond 0.01614 ( 16) metal coordination : angle 2.91316 ( 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 199 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 826 ARG cc_start: 0.9464 (tpt-90) cc_final: 0.9184 (ttt180) REVERT: A 948 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9270 (tm-30) REVERT: A 984 MET cc_start: 0.8657 (mmm) cc_final: 0.8039 (mmm) REVERT: B 285 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.7944 (mmm) REVERT: B 302 MET cc_start: 0.7999 (ptp) cc_final: 0.7735 (mpp) REVERT: B 345 PHE cc_start: 0.9381 (m-10) cc_final: 0.9171 (m-10) REVERT: C 547 GLU cc_start: 0.9221 (mm-30) cc_final: 0.8505 (mp0) REVERT: C 627 MET cc_start: 0.8926 (tpp) cc_final: 0.8594 (tpp) REVERT: C 666 GLU cc_start: 0.9049 (mp0) cc_final: 0.8600 (pm20) REVERT: C 669 THR cc_start: 0.9473 (t) cc_final: 0.9058 (p) REVERT: C 849 MET cc_start: 0.8417 (ttm) cc_final: 0.8192 (ttt) REVERT: C 959 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8168 (mm-30) REVERT: D 5 MET cc_start: 0.8247 (mtm) cc_final: 0.7752 (mtm) REVERT: D 152 MET cc_start: 0.8985 (mtp) cc_final: 0.8546 (ttm) REVERT: D 285 MET cc_start: 0.9004 (mmm) cc_final: 0.8716 (mmp) REVERT: D 294 ASP cc_start: 0.8984 (m-30) cc_final: 0.8604 (p0) REVERT: E 418 THR cc_start: 0.8828 (p) cc_final: 0.8259 (t) REVERT: E 437 GLU cc_start: 0.8288 (mp0) cc_final: 0.7296 (pm20) outliers start: 29 outliers final: 27 residues processed: 190 average time/residue: 0.1093 time to fit residues: 32.7754 Evaluate side-chains 198 residues out of total 1634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 638 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain A residue 953 ILE Chi-restraints excluded: chain B residue 45 VAL 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 788 VAL Chi-restraints excluded: chain C residue 862 THR Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 887 LEU Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 CYS Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 468 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 54 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 72 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 HIS ** D 33 GLN ** 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 = 0.3186 r_free = 0.3186 target = 0.074693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.056422 restraints weight = 108946.798| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 5.91 r_work: 0.2490 rms_B_bonded: 5.87 restraints_weight: 2.0000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.203 16467 Z= 0.163 Angle : 0.770 59.191 22505 Z= 0.421 Chirality : 0.041 0.244 2445 Planarity : 0.003 0.034 2703 Dihedral : 15.555 59.946 2662 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.71 % Allowed : 15.86 % 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 aren not related in a simple way. whole: 1.15 (0.20), residues: 1851 helix: 2.28 (0.23), residues: 564 sheet: 1.12 (0.28), residues: 365 loop : -0.33 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 969 TYR 0.014 0.001 TYR C 805 PHE 0.015 0.001 PHE B 31 TRP 0.007 0.001 TRP E 453 HIS 0.003 0.001 HIS A 990 Details of bonding type rmsd covalent geometry : bond 0.00384 (16451) covalent geometry : angle 0.76843 (22496) hydrogen bonds : bond 0.03380 ( 686) hydrogen bonds : angle 4.15740 ( 1890) metal coordination : bond 0.01614 ( 16) metal coordination : angle 2.91316 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.86 seconds wall clock time: 62 minutes 40.53 seconds (3760.53 seconds total)