Starting phenix.real_space_refine on Sat Sep 12 23:54:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oeo_20032/09_2026/6oeo_20032.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oeo_20032/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6oeo_20032/09_2026/6oeo_20032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oeo_20032/09_2026/6oeo_20032.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oeo_20032/09_2026/6oeo_20032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oeo_20032/09_2026/6oeo_20032.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6oeo_20032/09_2026/6oeo_20032.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oeo_20032/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.25, per 1000 atoms: 0.27 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: 2.12 Conformation dependent library (CDL) restraints added in 937.3 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: 2.60 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: 5.20 Time building geometry restraints manager: 2.73 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 1.20e-02 6.94e+03 2.03e+01 bond pdb=" C3' DC I 43 " pdb=" C2' DC I 43 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DG G 2 " pdb=" C2' DG G 2 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DT F 12 " pdb=" C2' DT F 12 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA J 41 " pdb=" C2' DA J 41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 ... (remaining 20355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 27562 2.09 - 4.18: 819 4.18 - 6.28: 48 6.28 - 8.37: 7 8.37 - 10.46: 3 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=" O4' DA J 18 " pdb=" C4' DA J 18 " pdb=" C3' DA J 18 " ideal model delta sigma weight residual 106.00 102.58 3.42 6.00e-01 2.78e+00 3.26e+01 angle pdb=" O4' DT J 14 " pdb=" C4' DT J 14 " pdb=" C3' DT J 14 " ideal model delta sigma weight residual 106.00 103.00 3.00 6.00e-01 2.78e+00 2.49e+01 angle pdb=" O5' DA I 20 " pdb=" C5' DA I 20 " pdb=" C4' DA I 20 " ideal model delta sigma weight residual 109.40 113.32 -3.92 8.00e-01 1.56e+00 2.40e+01 angle pdb=" C2' DC I 19 " pdb=" C1' DC I 19 " pdb=" N1 DC I 19 " ideal model delta sigma weight residual 114.30 121.03 -6.73 1.40e+00 5.10e-01 2.31e+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 - 0.097: 2953 0.097 - 0.195: 194 0.195 - 0.292: 5 0.292 - 0.390: 0 0.390 - 0.487: 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 -2.73 -2.24 -0.49 2.00e-01 2.50e+01 5.93e+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 -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' DG F 28 " pdb=" C4' DG F 28 " pdb=" O3' DG F 28 " pdb=" C2' DG F 28 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (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: 2.080 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 27.420 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.006 0.068 20368 Z= 0.411 Angle : 0.827 30.909 28443 Z= 0.592 Chirality : 0.050 0.487 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/Z covalent geometry : bond 0.00590 / 0.41 (20360) covalent geometry : angle 0.79061 / 0.59 (28439) hydrogen bonds : bond 0.09105 / 6.11 ( 928) hydrogen bonds : angle 5.73506 / 4.05 ( 2475) metal coordination : bond 0.03424 / 1.49 ( 8) metal coordination : angle 20.47592 / 10.35 ( 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 : 0.667 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: 0.8632 (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: 0.1612 time to fit residues: 37.5411 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 : 0.627 ------------------------------------------------------------------------------- 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: 40.0000 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: 30.0000 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... 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 990 HIS ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.100617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067463 restraints weight = 60383.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069137 restraints weight = 32323.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.070188 restraints weight = 22683.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.070735 restraints weight = 18692.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071128 restraints weight = 16932.978| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20368 Z= 0.166 Angle : 0.710 9.760 28443 Z= 0.390 Chirality : 0.048 0.325 3153 Planarity : 0.005 0.056 2952 Dihedral : 25.683 179.175 4401 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 1.04 % Allowed : 10.04 % Favored : 88.92 % 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: -2.88 (0.18), residues: 1955 helix: -0.93 (0.19), residues: 688 sheet: -1.67 (0.27), residues: 373 loop : -2.82 (0.18), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 713 TYR 0.017 0.001 TYR A 816 PHE 0.023 0.001 PHE A 971 TRP 0.019 0.001 TRP D 317 HIS 0.006 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (20360) covalent geometry : angle 0.70836 / 0.39 (28439) hydrogen bonds : bond 0.04979 / 3.31 ( 928) hydrogen bonds : angle 4.87984 / 3.42 ( 2475) metal coordination : bond 0.01165 / 0.59 ( 8) metal coordination : angle 3.82560 / 2.00 ( 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 142 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 568 MET cc_start: 0.8395 (ttm) cc_final: 0.8065 (ttm) REVERT: A 649 GLU cc_start: 0.8076 (pp20) cc_final: 0.7499 (pp20) REVERT: A 691 MET cc_start: 0.9090 (tpp) cc_final: 0.8776 (tpp) REVERT: A 883 MET cc_start: 0.8163 (tpp) cc_final: 0.7794 (tpt) REVERT: A 984 MET cc_start: 0.8454 (mmt) cc_final: 0.8221 (mmt) REVERT: B 135 GLU cc_start: 0.8581 (pt0) cc_final: 0.8338 (pm20) REVERT: B 152 MET cc_start: 0.8850 (mmt) cc_final: 0.8429 (mmm) REVERT: B 270 GLU cc_start: 0.8834 (tt0) cc_final: 0.8597 (tm-30) REVERT: C 401 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7846 (tpt170) REVERT: C 418 PHE cc_start: 0.8343 (t80) cc_final: 0.8034 (t80) REVERT: C 847 MET cc_start: 0.7991 (mpp) cc_final: 0.7772 (mpp) REVERT: D 339 MET cc_start: 0.6856 (mmm) cc_final: 0.5238 (pmm) REVERT: D 349 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7017 (ttp-170) outliers start: 17 outliers final: 7 residues processed: 135 average time/residue: 0.1329 time to fit residues: 29.2183 Evaluate side-chains 118 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 CYS 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 812 ILE Chi-restraints excluded: chain C residue 863 VAL 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: 2.9990 chunk 92 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 206 optimal weight: 50.0000 chunk 114 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.099912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.067961 restraints weight = 80044.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.068392 restraints weight = 52304.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.068981 restraints weight = 33850.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069250 restraints weight = 28547.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.069417 restraints weight = 25603.388| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20368 Z= 0.196 Angle : 0.695 12.977 28443 Z= 0.381 Chirality : 0.047 0.353 3153 Planarity : 0.004 0.059 2952 Dihedral : 25.638 180.000 4401 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.24 % Rotamer: Outliers : 1.10 % Allowed : 12.49 % Favored : 86.41 % 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: -2.26 (0.18), residues: 1955 helix: -0.34 (0.20), residues: 689 sheet: -1.30 (0.27), residues: 363 loop : -2.54 (0.19), residues: 903 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 0.024 0.002 PHE A 804 TRP 0.017 0.001 TRP D 317 HIS 0.005 0.001 HIS A 937 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (20360) covalent geometry : angle 0.69352 / 0.38 (28439) hydrogen bonds : bond 0.04914 / 3.30 ( 928) hydrogen bonds : angle 4.70384 / 3.29 ( 2475) metal coordination : bond 0.01327 / 0.65 ( 8) metal coordination : angle 3.80224 / 1.96 ( 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 141 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 568 MET cc_start: 0.8507 (ttm) cc_final: 0.8302 (ttm) REVERT: A 649 GLU cc_start: 0.8126 (pp20) cc_final: 0.7580 (pp20) REVERT: A 883 MET cc_start: 0.8195 (tpp) cc_final: 0.7782 (tpt) REVERT: B 135 GLU cc_start: 0.8629 (pt0) cc_final: 0.8306 (pm20) REVERT: B 270 GLU cc_start: 0.9019 (tt0) cc_final: 0.8625 (tm-30) REVERT: C 401 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.7849 (tpt90) REVERT: C 418 PHE cc_start: 0.8175 (t80) cc_final: 0.7873 (t80) REVERT: C 691 MET cc_start: 0.8592 (tpp) cc_final: 0.8364 (ttm) REVERT: D 339 MET cc_start: 0.6934 (mmm) cc_final: 0.5255 (pmm) REVERT: D 349 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7301 (ttp-170) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.1326 time to fit residues: 29.2727 Evaluate side-chains 125 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 812 ILE Chi-restraints excluded: chain C residue 866 VAL 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: 4.9990 chunk 71 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 66 optimal weight: 0.0170 overall best weight: 2.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 89 HIS ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.100443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.067890 restraints weight = 65311.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069990 restraints weight = 34824.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.069606 restraints weight = 22090.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069873 restraints weight = 24040.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.069961 restraints weight = 21242.060| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20368 Z= 0.171 Angle : 0.673 11.231 28443 Z= 0.369 Chirality : 0.046 0.348 3153 Planarity : 0.004 0.053 2952 Dihedral : 25.587 179.926 4401 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.60 % Favored : 93.35 % Rotamer: Outliers : 2.08 % Allowed : 13.47 % Favored : 84.45 % 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: -1.86 (0.19), residues: 1955 helix: 0.01 (0.20), residues: 685 sheet: -1.04 (0.28), residues: 367 loop : -2.34 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 713 TYR 0.015 0.001 TYR C 928 PHE 0.026 0.001 PHE A 804 TRP 0.016 0.001 TRP D 317 HIS 0.005 0.001 HIS A 818 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (20360) covalent geometry : angle 0.67267 / 0.37 (28439) hydrogen bonds : bond 0.04605 / 3.06 ( 928) hydrogen bonds : angle 4.56050 / 3.19 ( 2475) metal coordination : bond 0.01175 / 0.57 ( 8) metal coordination : angle 2.74333 / 1.41 ( 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 158 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7987 (pp20) cc_final: 0.7507 (pp20) REVERT: A 883 MET cc_start: 0.8321 (tpp) cc_final: 0.7891 (tpt) REVERT: B 5 MET cc_start: 0.8529 (tpp) cc_final: 0.7950 (tpp) REVERT: B 135 GLU cc_start: 0.8590 (pt0) cc_final: 0.8276 (pm20) REVERT: B 270 GLU cc_start: 0.9049 (tt0) cc_final: 0.8584 (tm-30) REVERT: C 401 ARG cc_start: 0.8366 (mmm-85) cc_final: 0.7825 (tpt90) REVERT: C 418 PHE cc_start: 0.8233 (t80) cc_final: 0.7905 (t80) REVERT: D 47 HIS cc_start: 0.8696 (OUTLIER) cc_final: 0.7968 (t-90) REVERT: D 299 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8689 (mm) REVERT: D 339 MET cc_start: 0.6812 (mmm) cc_final: 0.5199 (pmm) REVERT: D 349 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7225 (ttp-170) outliers start: 34 outliers final: 19 residues processed: 148 average time/residue: 0.1190 time to fit residues: 29.0278 Evaluate side-chains 138 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 812 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 484 MET 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 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 47 HIS Chi-restraints excluded: chain D residue 289 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 50 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 chunk 175 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.100524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068266 restraints weight = 77628.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069662 restraints weight = 41143.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069849 restraints weight = 26697.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070071 restraints weight = 25414.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070165 restraints weight = 22780.272| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20368 Z= 0.167 Angle : 0.665 11.923 28443 Z= 0.363 Chirality : 0.046 0.342 3153 Planarity : 0.004 0.057 2952 Dihedral : 25.514 179.772 4401 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 2.33 % Allowed : 14.27 % Favored : 83.40 % 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: -1.63 (0.19), residues: 1955 helix: 0.17 (0.20), residues: 686 sheet: -0.81 (0.28), residues: 367 loop : -2.23 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 894 TYR 0.015 0.001 TYR C 928 PHE 0.026 0.001 PHE A 804 TRP 0.015 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (20360) covalent geometry : angle 0.66398 / 0.36 (28439) hydrogen bonds : bond 0.04540 / 3.02 ( 928) hydrogen bonds : angle 4.47658 / 3.13 ( 2475) metal coordination : bond 0.01114 / 0.54 ( 8) metal coordination : angle 2.98395 / 1.51 ( 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 162 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.8004 (pp20) cc_final: 0.7528 (pp20) REVERT: A 883 MET cc_start: 0.8306 (tpp) cc_final: 0.7742 (tpt) REVERT: A 984 MET cc_start: 0.8455 (mmt) cc_final: 0.8221 (mmt) REVERT: B 135 GLU cc_start: 0.8586 (pt0) cc_final: 0.8286 (pm20) REVERT: B 270 GLU cc_start: 0.9042 (tt0) cc_final: 0.8587 (tm-30) REVERT: C 401 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7805 (tpt90) REVERT: C 418 PHE cc_start: 0.8206 (t80) cc_final: 0.7884 (t80) REVERT: C 602 MET cc_start: 0.8688 (ttp) cc_final: 0.8420 (mtt) REVERT: D 47 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: D 299 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8635 (mm) REVERT: D 302 MET cc_start: 0.7151 (mmm) cc_final: 0.6867 (mmm) REVERT: D 339 MET cc_start: 0.6772 (mmm) cc_final: 0.5186 (pmm) REVERT: D 349 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7345 (ttp-170) outliers start: 38 outliers final: 23 residues processed: 153 average time/residue: 0.1290 time to fit residues: 32.2315 Evaluate side-chains 141 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 812 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 C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR 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 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 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 289 LEU 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: 0.9990 chunk 91 optimal weight: 5.9990 chunk 190 optimal weight: 40.0000 chunk 166 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 193 optimal weight: 50.0000 chunk 171 optimal weight: 6.9990 chunk 9 optimal weight: 0.0770 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 ASN ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.100878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.068799 restraints weight = 62747.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.069820 restraints weight = 40761.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.069943 restraints weight = 27736.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.070060 restraints weight = 25808.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070172 restraints weight = 24424.656| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20368 Z= 0.164 Angle : 0.660 12.446 28443 Z= 0.360 Chirality : 0.045 0.337 3153 Planarity : 0.004 0.057 2952 Dihedral : 25.455 179.423 4401 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.09 % Favored : 93.86 % Rotamer: Outliers : 2.45 % Allowed : 14.51 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.19), residues: 1955 helix: 0.29 (0.21), residues: 686 sheet: -0.55 (0.29), residues: 356 loop : -2.18 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 894 TYR 0.014 0.001 TYR C 928 PHE 0.025 0.001 PHE A 804 TRP 0.015 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (20360) covalent geometry : angle 0.65970 / 0.36 (28439) hydrogen bonds : bond 0.04433 / 2.94 ( 928) hydrogen bonds : angle 4.42002 / 3.08 ( 2475) metal coordination : bond 0.01104 / 0.54 ( 8) metal coordination : angle 2.33652 / 1.20 ( 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 161 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 649 GLU cc_start: 0.8004 (pp20) cc_final: 0.7495 (pp20) REVERT: A 883 MET cc_start: 0.8274 (tpp) cc_final: 0.7730 (tpt) REVERT: A 984 MET cc_start: 0.8353 (mmt) cc_final: 0.8128 (mmt) REVERT: B 5 MET cc_start: 0.8514 (tpp) cc_final: 0.8044 (tpp) REVERT: B 135 GLU cc_start: 0.8604 (pt0) cc_final: 0.8269 (pm20) REVERT: B 266 THR cc_start: 0.8091 (OUTLIER) cc_final: 0.6848 (t) REVERT: B 270 GLU cc_start: 0.9119 (tt0) cc_final: 0.8603 (tm-30) REVERT: B 292 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8176 (tp) REVERT: C 401 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7811 (tpt90) REVERT: C 418 PHE cc_start: 0.8139 (t80) cc_final: 0.7847 (t80) REVERT: C 494 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7593 (mtt-85) REVERT: C 602 MET cc_start: 0.8719 (ttp) cc_final: 0.8384 (mtt) REVERT: C 841 MET cc_start: 0.8554 (tpp) cc_final: 0.8343 (mtt) REVERT: D 47 HIS cc_start: 0.8730 (OUTLIER) cc_final: 0.7982 (t-90) REVERT: D 339 MET cc_start: 0.6775 (mmm) cc_final: 0.5184 (pmm) REVERT: D 349 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7401 (ttp-170) outliers start: 40 outliers final: 23 residues processed: 152 average time/residue: 0.1364 time to fit residues: 33.6154 Evaluate side-chains 148 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 812 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 266 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 477 SER Chi-restraints excluded: chain C residue 494 ARG 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 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 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: 5.9990 chunk 175 optimal weight: 0.0020 chunk 74 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 136 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 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** D 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.101432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068162 restraints weight = 61213.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.069856 restraints weight = 32041.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070916 restraints weight = 22259.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.071557 restraints weight = 18249.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.071748 restraints weight = 16427.585| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 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 = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20368 Z= 0.141 Angle : 0.653 12.406 28443 Z= 0.353 Chirality : 0.045 0.326 3153 Planarity : 0.004 0.055 2952 Dihedral : 25.377 179.467 4401 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.47 % Rotamer: Outliers : 2.27 % Allowed : 15.19 % Favored : 82.55 % 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: -1.29 (0.19), residues: 1955 helix: 0.42 (0.21), residues: 686 sheet: -0.41 (0.29), residues: 356 loop : -2.08 (0.20), residues: 913 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 0.027 0.001 PHE A 804 TRP 0.014 0.001 TRP D 317 HIS 0.005 0.001 HIS A 795 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (20360) covalent geometry : angle 0.65202 / 0.35 (28439) hydrogen bonds : bond 0.04210 / 2.78 ( 928) hydrogen bonds : angle 4.32744 / 3.01 ( 2475) metal coordination : bond 0.00765 / 0.38 ( 8) metal coordination : angle 2.31174 / 1.18 ( 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: 37 poor density : 127 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7920 (pp20) cc_final: 0.7455 (pp20) REVERT: A 883 MET cc_start: 0.8246 (tpp) cc_final: 0.7714 (tpt) REVERT: B 5 MET cc_start: 0.8542 (tpp) cc_final: 0.8082 (tpp) REVERT: B 135 GLU cc_start: 0.8540 (pt0) cc_final: 0.8241 (pm20) REVERT: B 270 GLU cc_start: 0.8902 (tt0) cc_final: 0.8528 (tm-30) REVERT: B 292 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8134 (tp) REVERT: C 401 ARG cc_start: 0.8315 (mmm-85) cc_final: 0.7803 (tpt90) REVERT: C 418 PHE cc_start: 0.8297 (t80) cc_final: 0.7981 (t80) REVERT: C 494 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7567 (mtt-85) REVERT: C 602 MET cc_start: 0.8645 (ttp) cc_final: 0.8367 (mtt) REVERT: D 47 HIS cc_start: 0.8679 (OUTLIER) cc_final: 0.8002 (t-90) REVERT: D 264 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8436 (p) REVERT: D 339 MET cc_start: 0.6620 (mmm) cc_final: 0.5174 (pmm) REVERT: D 349 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7193 (ttp-170) outliers start: 37 outliers final: 20 residues processed: 154 average time/residue: 0.1312 time to fit residues: 32.6474 Evaluate side-chains 138 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL 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 C residue 866 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 133 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 THR 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: 3.9990 chunk 119 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.0030 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 313 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.102038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070076 restraints weight = 89276.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.071043 restraints weight = 48781.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.071773 restraints weight = 30171.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072021 restraints weight = 26163.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.072117 restraints weight = 22829.976| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 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 = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20368 Z= 0.134 Angle : 0.658 13.731 28443 Z= 0.353 Chirality : 0.044 0.314 3153 Planarity : 0.004 0.052 2952 Dihedral : 25.292 179.358 4401 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 2.02 % Allowed : 16.04 % Favored : 81.94 % 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: -1.20 (0.19), residues: 1955 helix: 0.44 (0.21), residues: 688 sheet: -0.35 (0.29), residues: 356 loop : -1.98 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 894 TYR 0.014 0.001 TYR D 108 PHE 0.025 0.001 PHE A 804 TRP 0.013 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (20360) covalent geometry : angle 0.65764 / 0.35 (28439) hydrogen bonds : bond 0.04113 / 2.73 ( 928) hydrogen bonds : angle 4.27385 / 2.97 ( 2475) metal coordination : bond 0.00652 / 0.34 ( 8) metal coordination : angle 2.00739 / 1.02 ( 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 156 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7930 (pp20) cc_final: 0.7477 (pp20) REVERT: A 883 MET cc_start: 0.8239 (tpp) cc_final: 0.7696 (tpt) REVERT: B 5 MET cc_start: 0.8571 (tpp) cc_final: 0.8101 (tpp) REVERT: B 135 GLU cc_start: 0.8532 (pt0) cc_final: 0.8327 (pm20) REVERT: B 242 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8206 (pp) REVERT: B 266 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.6824 (t) REVERT: B 270 GLU cc_start: 0.9042 (tt0) cc_final: 0.8576 (tm-30) REVERT: B 292 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8142 (tp) REVERT: C 401 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7765 (tpt90) REVERT: C 418 PHE cc_start: 0.8076 (t80) cc_final: 0.7796 (t80) REVERT: C 494 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7528 (mtt-85) REVERT: C 602 MET cc_start: 0.8641 (ttp) cc_final: 0.8364 (mtt) REVERT: C 841 MET cc_start: 0.8657 (tpp) cc_final: 0.8427 (mtt) REVERT: D 47 HIS cc_start: 0.8654 (OUTLIER) cc_final: 0.8024 (t-90) REVERT: D 264 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8402 (p) REVERT: D 339 MET cc_start: 0.6773 (mmm) cc_final: 0.5287 (pmm) REVERT: D 349 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7380 (ttp-170) outliers start: 33 outliers final: 19 residues processed: 150 average time/residue: 0.1370 time to fit residues: 32.9374 Evaluate side-chains 148 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 887 LEU 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 292 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL 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 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: 0.8980 chunk 55 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 206 optimal weight: 50.0000 chunk 81 optimal weight: 7.9990 chunk 131 optimal weight: 0.0020 overall best weight: 2.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 GLN C 495 GLN ** C 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 HIS ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.098993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.066521 restraints weight = 63948.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068000 restraints weight = 36297.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068276 restraints weight = 23286.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068460 restraints weight = 23308.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.068458 restraints weight = 20941.685| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 0.050 20368 Z= 0.196 Angle : 0.697 13.839 28443 Z= 0.371 Chirality : 0.045 0.319 3153 Planarity : 0.004 0.053 2952 Dihedral : 25.297 178.560 4401 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 2.20 % Allowed : 16.23 % Favored : 81.57 % 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: -1.26 (0.19), residues: 1955 helix: 0.42 (0.21), residues: 686 sheet: -0.33 (0.31), residues: 324 loop : -2.02 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 894 TYR 0.014 0.001 TYR C 928 PHE 0.027 0.002 PHE A 804 TRP 0.019 0.001 TRP D 317 HIS 0.007 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (20360) covalent geometry : angle 0.69617 / 0.37 (28439) hydrogen bonds : bond 0.04525 / 3.02 ( 928) hydrogen bonds : angle 4.37271 / 3.05 ( 2475) metal coordination : bond 0.01559 / 0.72 ( 8) metal coordination : angle 2.23473 / 1.13 ( 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 155 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.675 Fit side-chains REVERT: A 649 GLU cc_start: 0.8028 (pp20) cc_final: 0.7518 (pp20) REVERT: A 883 MET cc_start: 0.8116 (tpp) cc_final: 0.7616 (tpt) REVERT: A 973 LYS cc_start: 0.8626 (tppt) cc_final: 0.7956 (tptt) REVERT: B 5 MET cc_start: 0.8649 (tpp) cc_final: 0.8140 (tpp) REVERT: B 135 GLU cc_start: 0.8656 (pt0) cc_final: 0.8252 (pm20) REVERT: B 266 THR cc_start: 0.8093 (OUTLIER) cc_final: 0.6800 (t) REVERT: B 270 GLU cc_start: 0.9151 (tt0) cc_final: 0.8590 (tm-30) REVERT: B 292 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8145 (tp) REVERT: C 401 ARG cc_start: 0.8322 (mmm-85) cc_final: 0.7797 (tpt90) REVERT: C 418 PHE cc_start: 0.8165 (t80) cc_final: 0.7874 (t80) REVERT: C 494 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7445 (mtt-85) REVERT: C 568 MET cc_start: 0.8723 (mtp) cc_final: 0.8519 (mtp) REVERT: C 602 MET cc_start: 0.8730 (ttp) cc_final: 0.8457 (mtt) REVERT: D 47 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.7951 (t-90) REVERT: D 214 ASP cc_start: 0.8192 (t0) cc_final: 0.7430 (t70) REVERT: D 264 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.8378 (p) REVERT: D 339 MET cc_start: 0.6700 (mmm) cc_final: 0.5194 (pmm) REVERT: D 349 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7410 (ttp-170) outliers start: 36 outliers final: 25 residues processed: 145 average time/residue: 0.1317 time to fit residues: 31.1046 Evaluate side-chains 146 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 834 ASP 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 292 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 494 ARG 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 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 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 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: 0.9980 chunk 80 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.099795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.067310 restraints weight = 64491.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.068928 restraints weight = 36384.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.069213 restraints weight = 22904.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069394 restraints weight = 22905.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069384 restraints weight = 20579.353| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20368 Z= 0.150 Angle : 0.676 14.479 28443 Z= 0.360 Chirality : 0.044 0.316 3153 Planarity : 0.004 0.053 2952 Dihedral : 25.234 178.607 4401 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.53 % Favored : 94.42 % Rotamer: Outliers : 1.90 % Allowed : 16.84 % 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: -1.11 (0.19), residues: 1955 helix: 0.50 (0.21), residues: 684 sheet: -0.28 (0.31), residues: 324 loop : -1.87 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 894 TYR 0.017 0.001 TYR C 481 PHE 0.025 0.001 PHE A 804 TRP 0.017 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (20360) covalent geometry : angle 0.67521 / 0.36 (28439) hydrogen bonds : bond 0.04211 / 2.80 ( 928) hydrogen bonds : angle 4.30315 / 3.00 ( 2475) metal coordination : bond 0.00911 / 0.45 ( 8) metal coordination : angle 2.42299 / 1.24 ( 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 150 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7993 (pp20) cc_final: 0.7473 (pp20) REVERT: A 883 MET cc_start: 0.8049 (tpp) cc_final: 0.7536 (tpt) REVERT: A 973 LYS cc_start: 0.8717 (tppt) cc_final: 0.8103 (tptt) REVERT: A 984 MET cc_start: 0.8403 (mmt) cc_final: 0.8173 (mmt) REVERT: B 5 MET cc_start: 0.8641 (tpp) cc_final: 0.8136 (tpp) REVERT: B 135 GLU cc_start: 0.8594 (pt0) cc_final: 0.8245 (pm20) REVERT: B 242 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8183 (pp) REVERT: B 266 THR cc_start: 0.8066 (OUTLIER) cc_final: 0.6756 (t) REVERT: B 270 GLU cc_start: 0.9148 (tt0) cc_final: 0.8585 (tm-30) REVERT: B 292 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8114 (tp) REVERT: C 401 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7784 (tpt90) REVERT: C 418 PHE cc_start: 0.8171 (t80) cc_final: 0.7878 (t80) REVERT: C 494 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7415 (mtt-85) REVERT: C 602 MET cc_start: 0.8726 (ttp) cc_final: 0.8476 (mtt) REVERT: C 894 ARG cc_start: 0.8825 (mmm160) cc_final: 0.8450 (mmm-85) REVERT: D 47 HIS cc_start: 0.8741 (OUTLIER) cc_final: 0.7949 (t-90) REVERT: D 214 ASP cc_start: 0.8171 (t0) cc_final: 0.7452 (t70) REVERT: D 264 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8386 (p) REVERT: D 339 MET cc_start: 0.6613 (mmm) cc_final: 0.5114 (pmm) REVERT: D 349 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7333 (ttp-170) outliers start: 31 outliers final: 20 residues processed: 143 average time/residue: 0.1410 time to fit residues: 32.3494 Evaluate side-chains 144 residues out of total 1726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 887 LEU 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 292 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 494 ARG Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 726 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 27 optimal weight: 0.8980 chunk 191 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 94 optimal weight: 0.0870 chunk 91 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** D 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.100188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.067372 restraints weight = 79205.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.069629 restraints weight = 39135.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.069815 restraints weight = 22699.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.069875 restraints weight = 20954.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.069967 restraints weight = 19675.762| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2183 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= 0.139 Angle : 0.667 11.046 28443 Z= 0.355 Chirality : 0.044 0.306 3153 Planarity : 0.004 0.053 2952 Dihedral : 25.187 179.167 4401 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.32 % Favored : 94.63 % Rotamer: Outliers : 2.02 % Allowed : 16.84 % Favored : 81.14 % 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: -1.08 (0.19), residues: 1955 helix: 0.48 (0.21), residues: 686 sheet: -0.25 (0.30), residues: 328 loop : -1.84 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 894 TYR 0.015 0.001 TYR C 481 PHE 0.021 0.001 PHE A 804 TRP 0.015 0.001 TRP D 317 HIS 0.005 0.001 HIS A 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (20360) covalent geometry : angle 0.66640 / 0.36 (28439) hydrogen bonds : bond 0.04124 / 2.74 ( 928) hydrogen bonds : angle 4.25711 / 2.97 ( 2475) metal coordination : bond 0.00709 / 0.36 ( 8) metal coordination : angle 2.09085 / 1.06 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3434.30 seconds wall clock time: 60 minutes 4.89 seconds (3604.89 seconds total)