Starting phenix.real_space_refine on Thu Mar 5 04:58:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oeo_20032/03_2026/6oeo_20032.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeo_20032/03_2026/6oeo_20032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oeo_20032/03_2026/6oeo_20032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeo_20032/03_2026/6oeo_20032.map" model { file = "/net/cci-nas-00/data/ceres_data/6oeo_20032/03_2026/6oeo_20032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeo_20032/03_2026/6oeo_20032.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 2 6.06 5 P 204 5.49 5 S 108 5.16 5 C 11687 2.51 5 N 3450 2.21 5 O 4061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19516 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4818 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 608, 4815 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 Conformer: "B" Number of residues, atoms: 608, 4815 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 582} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 41 bond proxies already assigned to first conformer: 4912 Chain: "B" Number of atoms: 2673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2673 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 4863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4863 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 590} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2674 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 938 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1154 Classifications: {'DNA': 57} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1171 Classifications: {'DNA': 57} Link IDs: {'rna3p': 56} Chain: "N" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 283 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 5, 'TYR:plan': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2547 SG CYS A 727 86.774 49.596 96.475 1.00 81.65 S ATOM 2568 SG CYS A 730 89.334 47.558 97.645 1.00 85.67 S ATOM 10071 SG CYS C 727 28.937 105.793 98.885 1.00 63.74 S ATOM 10092 SG CYS C 730 26.645 107.873 100.371 1.00 63.96 S Time building chain proxies: 5.08, per 1000 atoms: 0.26 Number of scatterers: 19516 At special positions: 0 Unit cell: (117.7, 159.43, 163.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 Ca 4 19.99 S 108 16.00 P 204 15.00 O 4061 8.00 N 3450 7.00 C 11687 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: 1.62 Conformation dependent library (CDL) restraints added in 968.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 937 " pdb="ZN ZN A1103 " - pdb=" NE2 HIS A 942 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 730 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 727 " pdb=" ZN C1103 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 937 " pdb="ZN ZN C1103 " - pdb=" NE2 HIS C 942 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 730 " pdb="ZN ZN C1103 " - pdb=" SG CYS C 727 " Number of angles added : 4 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3686 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 19 sheets defined 37.6% alpha, 21.2% beta 96 base pairs and 151 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 401 through 408 Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 426 through 442 removed outlier: 4.185A pdb=" N ARG A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 removed outlier: 3.765A pdb=" N ALA A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.602A pdb=" N CYS A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.656A pdb=" N ALA A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.845A pdb=" N SER A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET A 570 " --> pdb=" O ALA A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 581 removed outlier: 3.698A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (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 removed outlier: 3.674A pdb=" N VAL A 712 " --> pdb=" O ASP A 708 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU A 716 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 749 through 763 removed outlier: 3.658A pdb=" N ASN A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 776 removed outlier: 4.167A pdb=" N ASP A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 813 removed outlier: 3.975A pdb=" N GLY A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 841 Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 859 through 870 Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.973A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 904 through 923 removed outlier: 4.682A pdb=" N SER A 910 " --> pdb=" O LEU A 906 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE A 911 " --> pdb=" O CYS A 907 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N PHE A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 942 removed outlier: 4.049A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 removed outlier: 4.337A pdb=" N GLU A 948 " --> pdb=" O PRO A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 973 removed outlier: 3.663A pdb=" N ASN A 965 " --> pdb=" O ASN A 961 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS A 966 " --> pdb=" O GLN A 962 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 967 " --> pdb=" O SER A 963 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 968 " --> pdb=" O GLY A 964 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 969 " --> pdb=" O ASN A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 995 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 3.538A pdb=" N MET A1003 " --> pdb=" O LEU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.859A pdb=" N LEU B 14 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 Processing helix chain 'C' and resid 402 through 423 removed outlier: 4.920A pdb=" N GLU C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 441 Processing helix chain 'C' and resid 444 through 455 removed outlier: 3.763A pdb=" N ALA C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 478 through 493 Processing helix chain 'C' and resid 500 through 508 removed outlier: 4.216A pdb=" N ALA C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 569 Processing helix chain 'C' and resid 570 through 581 Processing helix chain 'C' and resid 664 through 682 Proline residue: C 674 - end of helix Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'C' and resid 733 through 740 removed outlier: 3.711A pdb=" N SER C 738 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 Processing helix chain 'C' and resid 768 through 777 Processing helix chain 'C' and resid 792 through 814 Processing helix chain 'C' and resid 824 through 842 Processing helix chain 'C' and resid 850 through 858 Processing helix chain 'C' and resid 859 through 868 removed outlier: 4.047A pdb=" N GLU C 868 " --> pdb=" O ASP C 864 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 895 Proline residue: C 891 - end of helix Processing helix chain 'C' and resid 902 through 923 removed outlier: 3.503A pdb=" N LEU C 906 " --> pdb=" O CYS C 902 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE C 911 " --> pdb=" O CYS C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 942 removed outlier: 3.781A pdb=" N HIS C 937 " --> pdb=" O THR C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 953 through 957 removed outlier: 3.685A pdb=" N ALA C 957 " --> pdb=" O GLY C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 963 removed outlier: 3.645A pdb=" N SER C 963 " --> pdb=" O GLU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 975 removed outlier: 4.381A pdb=" N LEU C 967 " --> pdb=" O SER C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 984 through 995 Processing helix chain 'C' and resid 999 through 1004 removed outlier: 4.375A pdb=" N MET C1003 " --> pdb=" O LEU C 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 15 removed outlier: 3.997A pdb=" N LEU D 14 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 334 through 338 Processing helix chain 'N' and resid 102 through 117 Proline residue: N 111 - end of helix removed outlier: 3.893A pdb=" N HIS N 117 " --> pdb=" O ILE N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 135 Processing helix chain 'N' and resid 141 through 155 removed outlier: 3.728A pdb=" N GLU N 145 " --> pdb=" O LYS N 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520 removed outlier: 7.058A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR A 707 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE A 624 " --> pdb=" O PRO A 654 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520 removed outlier: 7.058A pdb=" N CYS A 599 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N TYR A 707 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU A 632 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 628 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS A 596 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VAL A 626 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 598 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE A 624 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET A 627 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLU A 642 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 629 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 removed outlier: 3.584A pdb=" N VAL B 6 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE B 345 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 318 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24 removed outlier: 4.980A pdb=" N VAL B 28 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP B 49 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131 removed outlier: 6.368A pdb=" N VAL B 130 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N SER B 194 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 267 removed outlier: 5.535A pdb=" N GLN B 265 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 272 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 277 through 279 Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.731A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE C 624 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 518 through 520 removed outlier: 6.731A pdb=" N PHE C 591 " --> pdb=" O LYS C 699 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE C 701 " --> pdb=" O PHE C 591 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL C 593 " --> pdb=" O ILE C 701 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ARG C 703 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 595 " --> pdb=" O ARG C 703 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR C 592 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 629 " --> pdb=" O THR C 592 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL C 594 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 600 " --> pdb=" O ARG C 621 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG C 621 " --> pdb=" O ASP C 600 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N MET C 627 " --> pdb=" O GLU C 642 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU C 642 " --> pdb=" O MET C 627 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE C 629 " --> pdb=" O VAL C 640 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.690A pdb=" N VAL D 6 " --> pdb=" O PHE D 345 " (cutoff:3.500A) removed outlier: 4.517A 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: 5.385A pdb=" N VAL D 28 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 58 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP D 49 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 80 removed outlier: 7.009A pdb=" N THR D 121 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LYS D 115 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB9, first strand: chain 'D' and resid 207 through 212 removed outlier: 4.421A 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 267 removed outlier: 4.030A pdb=" N ILE D 262 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 1997 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 239 hydrogen bonds 478 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 151 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4740 1.33 - 1.45: 5074 1.45 - 1.57: 9977 1.57 - 1.69: 405 1.69 - 1.82: 164 Bond restraints: 20360 Sorted by residual: bond pdb=" O3' DC J 19 " pdb=" P DA J 20 " ideal model delta sigma weight residual 1.607 1.553 0.054 1.50e-02 4.44e+03 1.30e+01 bond pdb=" N ASN A 850 " pdb=" CA ASN A 850 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.16e+00 bond pdb=" N ASP C 600 " pdb=" CA ASP C 600 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.24e-02 6.50e+03 6.33e+00 bond pdb=" N ARG C 713 " pdb=" CA ARG C 713 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.33e-02 5.65e+03 5.89e+00 bond pdb=" N ARG A 848 " pdb=" CA ARG A 848 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.50e+00 ... (remaining 20355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 27782 2.09 - 4.18: 607 4.18 - 6.28: 40 6.28 - 8.37: 9 8.37 - 10.46: 1 Bond angle restraints: 28439 Sorted by residual: angle pdb=" N ILE A 953 " pdb=" CA ILE A 953 " pdb=" C ILE A 953 " ideal model delta sigma weight residual 113.71 107.34 6.37 9.50e-01 1.11e+00 4.50e+01 angle pdb=" C4' DC I 19 " pdb=" C3' DC I 19 " pdb=" O3' DC I 19 " ideal model delta sigma weight residual 110.00 101.69 8.31 1.50e+00 4.44e-01 3.07e+01 angle pdb=" C4' DA J 18 " pdb=" C3' DA J 18 " pdb=" O3' DA J 18 " ideal model delta sigma weight residual 110.00 118.30 -8.30 1.50e+00 4.44e-01 3.06e+01 angle pdb=" C4' DT F 29 " pdb=" C3' DT F 29 " pdb=" O3' DT F 29 " ideal model delta sigma weight residual 110.00 118.11 -8.11 1.50e+00 4.44e-01 2.92e+01 angle pdb=" C2' DC I 19 " pdb=" C1' DC I 19 " pdb=" N1 DC I 19 " ideal model delta sigma weight residual 113.50 121.03 -7.53 1.50e+00 4.44e-01 2.52e+01 ... (remaining 28434 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 10720 35.68 - 71.35: 951 71.35 - 107.03: 14 107.03 - 142.70: 0 142.70 - 178.38: 9 Dihedral angle restraints: 11694 sinusoidal: 5976 harmonic: 5718 Sorted by residual: dihedral pdb=" CA ARG D 212 " pdb=" C ARG D 212 " pdb=" N ASN D 213 " pdb=" CA ASN D 213 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ARG B 212 " pdb=" C ARG B 212 " pdb=" N ASN B 213 " pdb=" CA ASN B 213 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PHE B 46 " pdb=" C PHE B 46 " pdb=" N HIS B 47 " pdb=" CA HIS B 47 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 11691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2910 0.083 - 0.167: 234 0.167 - 0.250: 8 0.250 - 0.333: 0 0.333 - 0.416: 1 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C3' DT F 29 " pdb=" C4' DT F 29 " pdb=" O3' DT F 29 " pdb=" C2' DT F 29 " both_signs ideal model delta sigma weight residual False -2.66 -2.24 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C3' DG F 30 " pdb=" C4' DG F 30 " pdb=" O3' DG F 30 " pdb=" C2' DG F 30 " both_signs ideal model delta sigma weight residual False -2.66 -2.87 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C3' DC I 17 " pdb=" C4' DC I 17 " pdb=" O3' DC I 17 " pdb=" C2' DC I 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.20e-01 ... (remaining 3150 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 212 " -0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C ARG B 212 " 0.047 2.00e-02 2.50e+03 pdb=" O ARG B 212 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN B 213 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT G 40 " 0.035 2.00e-02 2.50e+03 1.50e-02 5.65e+00 pdb=" N1 DT G 40 " -0.019 2.00e-02 2.50e+03 pdb=" C2 DT G 40 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DT G 40 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT G 40 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT G 40 " 0.006 2.00e-02 2.50e+03 pdb=" O4 DT G 40 " 0.015 2.00e-02 2.50e+03 pdb=" C5 DT G 40 " -0.004 2.00e-02 2.50e+03 pdb=" C7 DT G 40 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT G 40 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 317 " 0.018 2.00e-02 2.50e+03 1.48e-02 5.48e+00 pdb=" CG TRP D 317 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 317 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 317 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 317 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 317 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 317 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 317 " 0.004 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 121 2.49 - 3.10: 14196 3.10 - 3.70: 31373 3.70 - 4.30: 43179 4.30 - 4.90: 67298 Nonbonded interactions: 156167 Sorted by model distance: nonbonded pdb=" OD1 ASP C 600 " pdb="CA CA C1101 " model vdw 1.892 2.510 nonbonded pdb=" OD2 ASP C 600 " pdb="CA CA C1102 " model vdw 1.916 2.510 nonbonded pdb=" OD1 ASP A 600 " pdb="CA CA A1101 " model vdw 1.936 2.510 nonbonded pdb=" OE1 GLN C 962 " pdb="CA CA C1102 " model vdw 1.977 2.510 nonbonded pdb=" OP1 DC I 17 " pdb="CA CA A1102 " model vdw 1.993 2.510 ... (remaining 156162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 401 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 427 or (resid 428 through 429 \ and (name N or name CA or name C or name O or name CB )) or resid 430 or resid 4 \ 32 through 451 or (resid 452 through 453 and (name N or name CA or name C or nam \ e O or name CB )) or resid 454 through 455 or (resid 456 and (name N or name CA \ or name C or name O or name CB )) or resid 457 or (resid 458 and (name N or name \ CA or name C or name O or name CB )) or resid 459 through 879 or (resid 880 and \ (name N or name CA or name C or name O or name CB )) or resid 881 through 1103) \ ) selection = (chain 'C' and (resid 401 through 430 or resid 432 through 843 or (resid 844 and \ (name N or name CA or name C or name O or name CB )) or resid 845 through 854 o \ r (resid 855 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 56 through 860 or (resid 861 and (name N or name CA or name C or name O or name \ CB )) or resid 862 through 867 or (resid 868 and (name N or name CA or name C or \ name O or name CB )) or resid 869 through 1103)) } ncs_group { reference = (chain 'B' and (resid 1 through 334 or (resid 335 through 338 and (name N or nam \ e CA or name C or name O or name CB )) or resid 339 through 351)) selection = (chain 'D' and (resid 1 through 116 or (resid 117 and (name N or name CA or name \ C or name O or name CB )) or resid 118 through 339 or (resid 340 through 342 an \ d (name N or name CA or name C or name O or name CB )) or resid 343 through 351) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 23.370 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.005 0.068 20368 Z= 0.247 Angle : 0.761 30.909 28443 Z= 0.427 Chirality : 0.045 0.416 3153 Planarity : 0.004 0.050 2952 Dihedral : 21.769 178.376 8008 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.19 % Favored : 91.66 % Rotamer: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.16), residues: 1955 helix: -2.29 (0.16), residues: 674 sheet: -2.01 (0.26), residues: 362 loop : -3.54 (0.16), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 977 TYR 0.026 0.002 TYR D 91 PHE 0.016 0.002 PHE A 916 TRP 0.039 0.002 TRP D 317 HIS 0.006 0.001 HIS D 222 Details of bonding type rmsd covalent geometry : bond 0.00531 (20360) covalent geometry : angle 0.72091 (28439) hydrogen bonds : bond 0.09105 ( 928) hydrogen bonds : angle 5.73506 ( 2475) metal coordination : bond 0.03424 ( 8) metal coordination : angle 20.47592 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7919 (pp20) cc_final: 0.7396 (pp20) REVERT: A 691 MET cc_start: 0.9095 (tpp) cc_final: 0.8807 (tpp) REVERT: A 883 MET cc_start: 0.8208 (tpp) cc_final: 0.7806 (tpt) REVERT: B 270 GLU cc_start: 0.8881 (tt0) cc_final: 0.8633 (tm-30) REVERT: C 401 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.8001 (tpt90) REVERT: C 418 PHE cc_start: 0.8094 (t80) cc_final: 0.7817 (t80) REVERT: C 847 MET cc_start: 0.8042 (mpp) cc_final: 0.7758 (mpp) REVERT: C 883 MET cc_start: 0.9245 (tpp) cc_final: 0.8788 (tpp) REVERT: D 339 MET cc_start: 0.7062 (mmm) cc_final: 0.5300 (pmm) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.1342 time to fit residues: 31.0434 Evaluate side-chains 108 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 GLN A 515 HIS A 750 HIS A 850 ASN ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN A 990 HIS B 4 GLN B 23 ASN B 33 GLN B 53 ASN C 395 HIS C 414 GLN C 581 GLN C 820 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.100721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.067778 restraints weight = 61041.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.069380 restraints weight = 33575.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.070380 restraints weight = 23956.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070872 restraints weight = 19881.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.071271 restraints weight = 18134.575| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20368 Z= 0.166 Angle : 0.662 9.810 28443 Z= 0.360 Chirality : 0.042 0.193 3153 Planarity : 0.004 0.056 2952 Dihedral : 25.463 178.488 4401 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.45 % Favored : 93.50 % Rotamer: Outliers : 0.98 % Allowed : 10.41 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.18), residues: 1955 helix: -0.83 (0.19), residues: 689 sheet: -1.53 (0.27), residues: 355 loop : -2.77 (0.18), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 713 TYR 0.016 0.001 TYR C 928 PHE 0.025 0.001 PHE A 804 TRP 0.018 0.001 TRP D 317 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00371 (20360) covalent geometry : angle 0.66074 (28439) hydrogen bonds : bond 0.04234 ( 928) hydrogen bonds : angle 4.74084 ( 2475) metal coordination : bond 0.00843 ( 8) metal coordination : angle 3.94147 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.8043 (pp20) cc_final: 0.7515 (pp20) REVERT: A 883 MET cc_start: 0.8165 (tpp) cc_final: 0.7793 (tpt) REVERT: A 984 MET cc_start: 0.8385 (mmt) cc_final: 0.8179 (mmt) REVERT: B 135 GLU cc_start: 0.8602 (pt0) cc_final: 0.8316 (pm20) REVERT: B 270 GLU cc_start: 0.8890 (tt0) cc_final: 0.8611 (tm-30) REVERT: C 401 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.7834 (tpt90) REVERT: C 418 PHE cc_start: 0.8379 (t80) cc_final: 0.8074 (t80) REVERT: C 841 MET cc_start: 0.8312 (tpp) cc_final: 0.8028 (tpp) REVERT: C 889 MET cc_start: 0.8894 (mtm) cc_final: 0.8642 (mtm) REVERT: D 339 MET cc_start: 0.6932 (mmm) cc_final: 0.5264 (pmm) REVERT: D 349 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7208 (ttp-170) outliers start: 16 outliers final: 6 residues processed: 137 average time/residue: 0.1144 time to fit residues: 25.2738 Evaluate side-chains 119 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 150 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 206 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 89 HIS C 498 GLN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 965 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.099872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.067685 restraints weight = 79667.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068529 restraints weight = 46620.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.068945 restraints weight = 30244.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.069240 restraints weight = 26417.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069339 restraints weight = 23992.852| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20368 Z= 0.199 Angle : 0.659 12.168 28443 Z= 0.357 Chirality : 0.042 0.193 3153 Planarity : 0.004 0.051 2952 Dihedral : 25.395 179.654 4401 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 1.59 % Allowed : 12.19 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.18), residues: 1955 helix: -0.23 (0.20), residues: 687 sheet: -1.24 (0.27), residues: 367 loop : -2.46 (0.19), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 713 TYR 0.016 0.001 TYR C 928 PHE 0.029 0.002 PHE A 804 TRP 0.019 0.001 TRP D 317 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00449 (20360) covalent geometry : angle 0.65771 (28439) hydrogen bonds : bond 0.04384 ( 928) hydrogen bonds : angle 4.58353 ( 2475) metal coordination : bond 0.01091 ( 8) metal coordination : angle 3.76526 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 127 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7997 (pp20) cc_final: 0.7623 (pp20) REVERT: A 883 MET cc_start: 0.8198 (tpp) cc_final: 0.7642 (tpt) REVERT: B 135 GLU cc_start: 0.8601 (pt0) cc_final: 0.8378 (pm20) REVERT: B 270 GLU cc_start: 0.9021 (tt0) cc_final: 0.8582 (tm-30) REVERT: C 401 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.7796 (tpt90) REVERT: C 418 PHE cc_start: 0.8103 (t80) cc_final: 0.7834 (t80) REVERT: C 739 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: D 339 MET cc_start: 0.6778 (mmm) cc_final: 0.5189 (pmm) REVERT: D 349 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7365 (ttp-170) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 0.1059 time to fit residues: 24.8410 Evaluate side-chains 132 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 177 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 115 optimal weight: 0.0980 chunk 76 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 ASN ** D 173 ASN ** 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 = 0.3838 r_free = 0.3838 target = 0.102057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.069963 restraints weight = 66294.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071069 restraints weight = 41681.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.071106 restraints weight = 28489.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.071274 restraints weight = 26209.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071402 restraints weight = 24615.812| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20368 Z= 0.137 Angle : 0.621 11.816 28443 Z= 0.335 Chirality : 0.040 0.193 3153 Planarity : 0.004 0.046 2952 Dihedral : 25.212 179.126 4401 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.12 % Favored : 94.83 % Rotamer: Outliers : 1.90 % Allowed : 13.29 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.19), residues: 1955 helix: 0.21 (0.20), residues: 689 sheet: -0.62 (0.29), residues: 346 loop : -2.30 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 894 TYR 0.014 0.001 TYR C 481 PHE 0.027 0.001 PHE A 804 TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00303 (20360) covalent geometry : angle 0.62089 (28439) hydrogen bonds : bond 0.03722 ( 928) hydrogen bonds : angle 4.34042 ( 2475) metal coordination : bond 0.00538 ( 8) metal coordination : angle 2.21471 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7938 (pp20) cc_final: 0.7575 (pp20) REVERT: A 834 ASP cc_start: 0.7830 (t0) cc_final: 0.7624 (t70) REVERT: A 883 MET cc_start: 0.8288 (tpp) cc_final: 0.7839 (tpt) REVERT: A 973 LYS cc_start: 0.9014 (tppt) cc_final: 0.8429 (tppt) REVERT: A 984 MET cc_start: 0.8224 (mmt) cc_final: 0.8003 (mmt) REVERT: B 5 MET cc_start: 0.8616 (tpp) cc_final: 0.8166 (tpp) REVERT: B 135 GLU cc_start: 0.8581 (pt0) cc_final: 0.8321 (pm20) REVERT: B 270 GLU cc_start: 0.9098 (tt0) cc_final: 0.8549 (tm-30) REVERT: C 401 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7716 (tpt90) REVERT: C 418 PHE cc_start: 0.8124 (t80) cc_final: 0.7840 (t80) REVERT: C 739 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8677 (mp10) REVERT: D 299 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8590 (mm) REVERT: D 339 MET cc_start: 0.6780 (mmm) cc_final: 0.5299 (pmm) REVERT: D 349 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7410 (ttp-170) outliers start: 31 outliers final: 13 residues processed: 154 average time/residue: 0.1172 time to fit residues: 29.2605 Evaluate side-chains 140 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 837 LEU Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS ** D 173 ASN ** 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 = 0.3814 r_free = 0.3814 target = 0.100650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.068553 restraints weight = 76739.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.069667 restraints weight = 42755.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070127 restraints weight = 27207.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.070327 restraints weight = 24672.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070442 restraints weight = 22585.462| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20368 Z= 0.181 Angle : 0.643 11.219 28443 Z= 0.345 Chirality : 0.041 0.186 3153 Planarity : 0.004 0.046 2952 Dihedral : 25.152 179.435 4401 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.22 % Rotamer: Outliers : 1.78 % Allowed : 14.82 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.19), residues: 1955 helix: 0.31 (0.20), residues: 689 sheet: -0.57 (0.30), residues: 324 loop : -2.17 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 894 TYR 0.013 0.001 TYR C 928 PHE 0.026 0.001 PHE A 804 TRP 0.016 0.001 TRP D 317 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00410 (20360) covalent geometry : angle 0.64210 (28439) hydrogen bonds : bond 0.04086 ( 928) hydrogen bonds : angle 4.36566 ( 2475) metal coordination : bond 0.01175 ( 8) metal coordination : angle 2.49406 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7939 (pp20) cc_final: 0.7542 (pp20) REVERT: A 883 MET cc_start: 0.8276 (tpp) cc_final: 0.7782 (tpt) REVERT: A 973 LYS cc_start: 0.9008 (tppt) cc_final: 0.8463 (tppt) REVERT: B 5 MET cc_start: 0.8658 (tpp) cc_final: 0.8157 (tpp) REVERT: B 135 GLU cc_start: 0.8569 (pt0) cc_final: 0.8334 (pm20) REVERT: B 270 GLU cc_start: 0.8999 (tt0) cc_final: 0.8552 (tm-30) REVERT: B 292 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8158 (tp) REVERT: C 401 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7660 (tpt90) REVERT: C 418 PHE cc_start: 0.7978 (t80) cc_final: 0.7725 (t80) REVERT: C 739 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8670 (mp10) REVERT: D 47 HIS cc_start: 0.8681 (OUTLIER) cc_final: 0.8040 (t-90) REVERT: D 280 GLU cc_start: 0.7799 (pm20) cc_final: 0.7498 (pm20) REVERT: D 299 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8612 (mm) REVERT: D 339 MET cc_start: 0.6780 (mmm) cc_final: 0.5262 (pmm) REVERT: D 349 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7357 (ttp-170) outliers start: 29 outliers final: 17 residues processed: 149 average time/residue: 0.1168 time to fit residues: 27.9700 Evaluate side-chains 142 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 299 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 46 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 9 optimal weight: 0.2980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.100256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.067151 restraints weight = 62666.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.068821 restraints weight = 33004.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.069874 restraints weight = 23016.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.070480 restraints weight = 18873.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070803 restraints weight = 16994.403| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20368 Z= 0.200 Angle : 0.662 13.203 28443 Z= 0.352 Chirality : 0.041 0.190 3153 Planarity : 0.004 0.046 2952 Dihedral : 25.138 178.935 4401 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.39 % Allowed : 15.00 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.19), residues: 1955 helix: 0.32 (0.21), residues: 691 sheet: -0.56 (0.30), residues: 336 loop : -2.10 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 894 TYR 0.015 0.001 TYR C 481 PHE 0.019 0.001 PHE A 804 TRP 0.019 0.001 TRP D 317 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00453 (20360) covalent geometry : angle 0.66099 (28439) hydrogen bonds : bond 0.04159 ( 928) hydrogen bonds : angle 4.39148 ( 2475) metal coordination : bond 0.01331 ( 8) metal coordination : angle 2.73211 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7890 (pp20) cc_final: 0.7486 (pp20) REVERT: A 883 MET cc_start: 0.8097 (tpp) cc_final: 0.7624 (tpt) REVERT: A 973 LYS cc_start: 0.8851 (tppt) cc_final: 0.8363 (tppt) REVERT: B 135 GLU cc_start: 0.8568 (pt0) cc_final: 0.8301 (pm20) REVERT: B 152 MET cc_start: 0.8674 (mmp) cc_final: 0.7942 (mmp) REVERT: B 242 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8040 (pp) REVERT: B 270 GLU cc_start: 0.8909 (tt0) cc_final: 0.8542 (tm-30) REVERT: B 292 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8157 (tp) REVERT: C 401 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.7723 (tpt90) REVERT: C 739 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8643 (mp10) REVERT: D 47 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8044 (t-90) REVERT: D 339 MET cc_start: 0.6742 (mmm) cc_final: 0.5280 (pmm) REVERT: D 349 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7169 (ttp-170) outliers start: 39 outliers final: 22 residues processed: 157 average time/residue: 0.1234 time to fit residues: 31.4556 Evaluate side-chains 143 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 11 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 147 optimal weight: 0.0000 chunk 138 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** 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 = 0.3812 r_free = 0.3812 target = 0.100528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.067619 restraints weight = 59692.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069188 restraints weight = 33159.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070174 restraints weight = 23739.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070601 restraints weight = 19817.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071016 restraints weight = 18158.318| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20368 Z= 0.189 Angle : 0.673 15.271 28443 Z= 0.354 Chirality : 0.041 0.203 3153 Planarity : 0.004 0.047 2952 Dihedral : 25.097 178.719 4401 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 2.45 % Allowed : 15.55 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.19), residues: 1955 helix: 0.36 (0.21), residues: 688 sheet: -0.52 (0.30), residues: 341 loop : -2.02 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 894 TYR 0.018 0.001 TYR C 481 PHE 0.025 0.001 PHE A 804 TRP 0.019 0.001 TRP D 317 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00429 (20360) covalent geometry : angle 0.67239 (28439) hydrogen bonds : bond 0.04113 ( 928) hydrogen bonds : angle 4.35884 ( 2475) metal coordination : bond 0.01224 ( 8) metal coordination : angle 2.49700 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7907 (pp20) cc_final: 0.7453 (pp20) REVERT: A 883 MET cc_start: 0.8196 (tpp) cc_final: 0.7790 (tpt) REVERT: A 973 LYS cc_start: 0.8819 (tppt) cc_final: 0.8353 (tppt) REVERT: B 5 MET cc_start: 0.8583 (tpp) cc_final: 0.8187 (tpp) REVERT: B 135 GLU cc_start: 0.8569 (pt0) cc_final: 0.8257 (pm20) REVERT: B 242 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8049 (pp) REVERT: B 266 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.6936 (t) REVERT: B 270 GLU cc_start: 0.8954 (tt0) cc_final: 0.8589 (tm-30) REVERT: B 292 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8126 (tp) REVERT: C 401 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7767 (tpt90) REVERT: C 418 PHE cc_start: 0.8242 (t80) cc_final: 0.7917 (t80) REVERT: C 739 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8656 (mp10) REVERT: D 47 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.8039 (t-90) REVERT: D 214 ASP cc_start: 0.7944 (m-30) cc_final: 0.7742 (m-30) REVERT: D 339 MET cc_start: 0.6613 (mmm) cc_final: 0.5128 (pmm) REVERT: D 349 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.7179 (ttp-170) outliers start: 40 outliers final: 25 residues processed: 157 average time/residue: 0.1191 time to fit residues: 30.2715 Evaluate side-chains 154 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 866 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 176 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 740 ASN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.102188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.070076 restraints weight = 83037.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071210 restraints weight = 44210.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.071802 restraints weight = 27465.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071999 restraints weight = 24244.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.072146 restraints weight = 21918.403| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20368 Z= 0.140 Angle : 0.646 13.239 28443 Z= 0.339 Chirality : 0.040 0.221 3153 Planarity : 0.004 0.048 2952 Dihedral : 24.950 179.068 4401 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 2.02 % Allowed : 16.41 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1955 helix: 0.55 (0.21), residues: 690 sheet: -0.14 (0.31), residues: 312 loop : -1.96 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 894 TYR 0.016 0.001 TYR C 481 PHE 0.027 0.001 PHE A 804 TRP 0.014 0.001 TRP D 317 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00312 (20360) covalent geometry : angle 0.64562 (28439) hydrogen bonds : bond 0.03603 ( 928) hydrogen bonds : angle 4.17299 ( 2475) metal coordination : bond 0.00534 ( 8) metal coordination : angle 2.13414 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 141 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7831 (pp20) cc_final: 0.7432 (pp20) REVERT: A 883 MET cc_start: 0.8313 (tpp) cc_final: 0.7912 (tpt) REVERT: B 5 MET cc_start: 0.8598 (tpp) cc_final: 0.8182 (tpp) REVERT: B 135 GLU cc_start: 0.8525 (pt0) cc_final: 0.8287 (pm20) REVERT: B 242 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8064 (pp) REVERT: B 266 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.6821 (t) REVERT: B 270 GLU cc_start: 0.9029 (tt0) cc_final: 0.8587 (tm-30) REVERT: C 401 ARG cc_start: 0.8257 (mmm-85) cc_final: 0.7692 (tpt90) REVERT: C 739 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8619 (mp10) REVERT: D 47 HIS cc_start: 0.8703 (OUTLIER) cc_final: 0.8170 (t-90) REVERT: D 264 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 280 GLU cc_start: 0.7835 (pm20) cc_final: 0.7580 (pm20) REVERT: D 339 MET cc_start: 0.6705 (mmm) cc_final: 0.4980 (pmm) REVERT: D 349 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7120 (ttp-170) outliers start: 33 outliers final: 18 residues processed: 167 average time/residue: 0.1204 time to fit residues: 32.4071 Evaluate side-chains 148 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 437 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 206 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.101064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068054 restraints weight = 63808.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.069718 restraints weight = 34289.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.070752 restraints weight = 24074.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.071258 restraints weight = 19858.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071631 restraints weight = 17993.402| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20368 Z= 0.180 Angle : 0.682 16.800 28443 Z= 0.355 Chirality : 0.041 0.202 3153 Planarity : 0.004 0.048 2952 Dihedral : 24.952 178.472 4401 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.02 % Allowed : 16.72 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.19), residues: 1955 helix: 0.59 (0.21), residues: 689 sheet: -0.26 (0.30), residues: 328 loop : -1.92 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 894 TYR 0.014 0.001 TYR C 481 PHE 0.026 0.001 PHE A 804 TRP 0.021 0.001 TRP C 760 HIS 0.004 0.001 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00411 (20360) covalent geometry : angle 0.68184 (28439) hydrogen bonds : bond 0.03971 ( 928) hydrogen bonds : angle 4.22590 ( 2475) metal coordination : bond 0.01224 ( 8) metal coordination : angle 2.14615 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.504 Fit side-chains REVERT: A 649 GLU cc_start: 0.7832 (pp20) cc_final: 0.7401 (pp20) REVERT: A 883 MET cc_start: 0.8269 (tpp) cc_final: 0.7859 (tpt) REVERT: A 973 LYS cc_start: 0.8616 (tppt) cc_final: 0.8026 (tptt) REVERT: B 5 MET cc_start: 0.8638 (tpp) cc_final: 0.8202 (tpp) REVERT: B 135 GLU cc_start: 0.8576 (pt0) cc_final: 0.8273 (pm20) REVERT: B 152 MET cc_start: 0.8607 (mmp) cc_final: 0.8375 (mmp) REVERT: B 242 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8022 (pp) REVERT: B 266 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.6924 (t) REVERT: B 270 GLU cc_start: 0.8965 (tt0) cc_final: 0.8633 (tm-30) REVERT: C 401 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.7690 (tpt90) REVERT: C 739 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8652 (mp10) REVERT: C 894 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8442 (mmm-85) REVERT: D 47 HIS cc_start: 0.8716 (OUTLIER) cc_final: 0.8041 (t-90) REVERT: D 214 ASP cc_start: 0.7893 (t70) cc_final: 0.7131 (t70) REVERT: D 264 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8424 (p) REVERT: D 339 MET cc_start: 0.6661 (mmm) cc_final: 0.5060 (pmm) REVERT: D 349 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7069 (ttp-170) outliers start: 33 outliers final: 21 residues processed: 150 average time/residue: 0.1192 time to fit residues: 28.9504 Evaluate side-chains 146 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 726 ILE Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 110 optimal weight: 0.7980 chunk 67 optimal weight: 0.0070 chunk 80 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.101969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070034 restraints weight = 64133.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071510 restraints weight = 34515.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.071853 restraints weight = 23489.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071971 restraints weight = 23679.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071984 restraints weight = 21163.429| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20368 Z= 0.148 Angle : 0.672 15.975 28443 Z= 0.349 Chirality : 0.040 0.204 3153 Planarity : 0.004 0.049 2952 Dihedral : 24.889 178.738 4401 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 1.78 % Allowed : 17.15 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.19), residues: 1955 helix: 0.64 (0.21), residues: 685 sheet: -0.22 (0.30), residues: 328 loop : -1.84 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 894 TYR 0.020 0.001 TYR C 481 PHE 0.027 0.001 PHE A 804 TRP 0.016 0.001 TRP D 317 HIS 0.006 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00336 (20360) covalent geometry : angle 0.67110 (28439) hydrogen bonds : bond 0.03698 ( 928) hydrogen bonds : angle 4.14705 ( 2475) metal coordination : bond 0.00705 ( 8) metal coordination : angle 2.07403 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.663 Fit side-chains REVERT: A 649 GLU cc_start: 0.7812 (pp20) cc_final: 0.7476 (pp20) REVERT: A 883 MET cc_start: 0.8254 (tpp) cc_final: 0.7792 (tpt) REVERT: A 973 LYS cc_start: 0.8774 (tppt) cc_final: 0.8248 (tptt) REVERT: B 5 MET cc_start: 0.8628 (tpp) cc_final: 0.8187 (tpp) REVERT: B 135 GLU cc_start: 0.8547 (pt0) cc_final: 0.8277 (pm20) REVERT: B 152 MET cc_start: 0.8683 (mmp) cc_final: 0.8446 (mmp) REVERT: B 242 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8073 (pp) REVERT: B 266 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.6813 (t) REVERT: B 270 GLU cc_start: 0.9072 (tt0) cc_final: 0.8617 (tm-30) REVERT: C 401 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7721 (tpt90) REVERT: C 739 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8646 (mp10) REVERT: C 894 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8426 (mmm-85) REVERT: D 47 HIS cc_start: 0.8726 (OUTLIER) cc_final: 0.8167 (t-90) REVERT: D 214 ASP cc_start: 0.7879 (t70) cc_final: 0.7105 (t70) REVERT: D 264 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8364 (p) REVERT: D 339 MET cc_start: 0.6485 (mmm) cc_final: 0.5102 (pmm) REVERT: D 349 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7141 (ttp-170) outliers start: 29 outliers final: 20 residues processed: 148 average time/residue: 0.1225 time to fit residues: 29.8224 Evaluate side-chains 149 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 739 GLN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 769 VAL Chi-restraints excluded: chain C residue 863 VAL Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 47 HIS Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 27 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.102133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.070205 restraints weight = 78649.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071215 restraints weight = 44607.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.071832 restraints weight = 27951.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.071993 restraints weight = 24799.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072182 restraints weight = 22431.144| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20368 Z= 0.149 Angle : 0.670 16.236 28443 Z= 0.348 Chirality : 0.040 0.199 3153 Planarity : 0.004 0.048 2952 Dihedral : 24.825 178.600 4401 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 1.78 % Allowed : 17.21 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.19), residues: 1955 helix: 0.66 (0.21), residues: 692 sheet: -0.14 (0.31), residues: 320 loop : -1.84 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 894 TYR 0.019 0.001 TYR C 481 PHE 0.026 0.001 PHE A 804 TRP 0.017 0.001 TRP D 317 HIS 0.004 0.001 HIS A 818 Details of bonding type rmsd covalent geometry : bond 0.00339 (20360) covalent geometry : angle 0.66929 (28439) hydrogen bonds : bond 0.03697 ( 928) hydrogen bonds : angle 4.11551 ( 2475) metal coordination : bond 0.00830 ( 8) metal coordination : angle 1.98740 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.62 seconds wall clock time: 56 minutes 53.55 seconds (3413.55 seconds total)