Starting phenix.real_space_refine on Thu Aug 6 15:31:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2026/7yrg_34055.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 290 5.49 5 S 51 5.16 5 C 9376 2.51 5 N 3024 2.21 5 O 3634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16377 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 790 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 841 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 836 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 2056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 2082 Chain: "L" Number of atoms: 1921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1916 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 240, 1916 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 1942 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13798 SG CYS K 275 34.989 21.023 55.188 1.00 81.78 S ATOM 14142 SG CYS K 319 32.495 18.444 53.871 1.00 86.30 S ATOM 14157 SG CYS K 321 36.070 17.784 53.089 1.00 93.19 S ATOM 14182 SG CYS K 324 34.891 17.744 56.692 1.00 91.94 S ATOM 15719 SG CYS L 275 79.466 77.873 56.063 1.00 81.78 S ATOM 16063 SG CYS L 319 81.952 80.476 54.778 1.00 86.30 S ATOM 16078 SG CYS L 321 78.374 81.144 54.021 1.00 93.19 S ATOM 16103 SG CYS L 324 79.567 81.128 57.619 1.00 91.94 S Time building chain proxies: 4.15, per 1000 atoms: 0.25 Number of scatterers: 16377 At special positions: 0 Unit cell: (116, 101, 114, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 51 16.00 P 290 15.00 O 3634 8.00 N 3024 7.00 C 9376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS K 279 " - pdb=" SG CYS K 305 " distance=2.03 Simple disulfide: pdb=" SG CYS L 279 " - pdb=" SG CYS L 305 " distance=2.03 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 487.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 275 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 324 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 319 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 321 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 275 " Number of angles added : 12 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 55.7% alpha, 6.5% beta 136 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.677A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.534A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.613A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 47 through 77 removed outlier: 3.593A pdb=" N VAL C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 75 " --> pdb=" O ASN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.776A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.534A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.613A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 76 removed outlier: 3.595A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 removed outlier: 3.579A pdb=" N ASP G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.700A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.561A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 123 Processing helix chain 'K' and resid 73 through 94 removed outlier: 4.146A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix Processing helix chain 'K' and resid 134 through 148 removed outlier: 3.876A pdb=" N LYS K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 160 through 167 removed outlier: 3.668A pdb=" N ARG K 164 " --> pdb=" O GLY K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.546A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG K 187 " --> pdb=" O PHE K 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 243 Processing helix chain 'K' and resid 266 through 271 removed outlier: 3.587A pdb=" N ILE K 271 " --> pdb=" O ALA K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 326 Processing helix chain 'K' and resid 354 through 363 Processing helix chain 'L' and resid 73 through 94 removed outlier: 4.145A pdb=" N ASP L 90 " --> pdb=" O SER L 86 " (cutoff:3.500A) Proline residue: L 91 - end of helix Processing helix chain 'L' and resid 134 through 135 No H-bonds generated for 'chain 'L' and resid 134 through 135' Processing helix chain 'L' and resid 137 through 137 No H-bonds generated for 'chain 'L' and resid 137 through 137' Processing helix chain 'L' and resid 138 through 148 removed outlier: 3.876A pdb=" N LYS L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 187 removed outlier: 3.546A pdb=" N TYR L 185 " --> pdb=" O HIS L 181 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG L 187 " --> pdb=" O PHE L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 235 through 243 Processing helix chain 'L' and resid 266 through 271 removed outlier: 3.586A pdb=" N ILE L 271 " --> pdb=" O ALA L 268 " (cutoff:3.500A) Processing helix chain 'L' and resid 321 through 326 Processing helix chain 'L' and resid 354 through 363 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.001A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.736A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 104 removed outlier: 7.077A pdb=" N THR C 103 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.950A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 45 through 46 removed outlier: 7.413A pdb=" N ARG G 45 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AB1, first strand: chain 'K' and resid 195 through 199 Processing sheet with id=AB2, first strand: chain 'K' and resid 261 through 265 removed outlier: 3.552A pdb=" N ASP K 222 " --> pdb=" O ALA K 293 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL K 291 " --> pdb=" O ILE K 224 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N LEU K 226 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 12.158A pdb=" N ALA K 289 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS K 292 " --> pdb=" O LYS K 280 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS K 280 " --> pdb=" O LYS K 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 272 through 273 removed outlier: 6.242A pdb=" N ASN K 272 " --> pdb=" O CYS K 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'L' and resid 195 through 199 Processing sheet with id=AB5, first strand: chain 'L' and resid 261 through 265 removed outlier: 3.552A pdb=" N ASP L 222 " --> pdb=" O ALA L 293 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL L 291 " --> pdb=" O ILE L 224 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N LEU L 226 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 12.158A pdb=" N ALA L 289 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS L 292 " --> pdb=" O LYS L 280 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS L 280 " --> pdb=" O LYS L 292 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 272 through 273 removed outlier: 6.241A pdb=" N ASN L 272 " --> pdb=" O CYS L 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 530 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 3.37 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1981 1.29 - 1.42: 5694 1.42 - 1.55: 8914 1.55 - 1.68: 594 1.68 - 1.81: 79 Bond restraints: 17262 Sorted by residual: bond pdb=" N ARG K 357 " pdb=" CA ARG K 357 " ideal model delta sigma weight residual 1.459 1.344 0.115 1.23e-02 6.61e+03 8.71e+01 bond pdb=" N ARG L 357 " pdb=" CA ARG L 357 " ideal model delta sigma weight residual 1.459 1.345 0.115 1.23e-02 6.61e+03 8.67e+01 bond pdb=" CA LYS L 362 " pdb=" C LYS L 362 " ideal model delta sigma weight residual 1.524 1.639 -0.115 1.27e-02 6.20e+03 8.19e+01 bond pdb=" CA LYS K 362 " pdb=" C LYS K 362 " ideal model delta sigma weight residual 1.524 1.638 -0.115 1.27e-02 6.20e+03 8.14e+01 bond pdb=" CA LEU L 358 " pdb=" C LEU L 358 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.35e-02 5.49e+03 6.05e+01 ... (remaining 17257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 23773 2.33 - 4.66: 627 4.66 - 6.99: 72 6.99 - 9.32: 28 9.32 - 11.65: 4 Bond angle restraints: 24504 Sorted by residual: angle pdb=" C LEU L 361 " pdb=" N LYS L 362 " pdb=" CA LYS L 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" C LEU K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" N LYS L 356 " pdb=" CA LYS L 356 " pdb=" C LYS L 356 " ideal model delta sigma weight residual 111.14 118.03 -6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N LYS K 356 " pdb=" CA LYS K 356 " pdb=" C LYS K 356 " ideal model delta sigma weight residual 111.14 118.01 -6.87 1.08e+00 8.57e-01 4.05e+01 angle pdb=" N GLY F 9 " pdb=" CA GLY F 9 " pdb=" C GLY F 9 " ideal model delta sigma weight residual 112.49 119.26 -6.77 1.21e+00 6.83e-01 3.13e+01 ... (remaining 24499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 8031 31.24 - 62.49: 1669 62.49 - 93.73: 62 93.73 - 124.98: 1 124.98 - 156.22: 4 Dihedral angle restraints: 9767 sinusoidal: 5989 harmonic: 3778 Sorted by residual: dihedral pdb=" CB CYS K 279 " pdb=" SG CYS K 279 " pdb=" SG CYS K 305 " pdb=" CB CYS K 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.86 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS L 279 " pdb=" SG CYS L 279 " pdb=" SG CYS L 305 " pdb=" CB CYS L 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.84 50.84 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" C ECX F 20 " pdb=" N ECX F 20 " pdb=" CA ECX F 20 " pdb=" CB ECX F 20 " ideal model delta harmonic sigma weight residual -122.60 -108.05 -14.55 0 2.50e+00 1.60e-01 3.39e+01 ... (remaining 9764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2606 0.103 - 0.207: 120 0.207 - 0.310: 4 0.310 - 0.414: 2 0.414 - 0.517: 4 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CB VAL F 21 " pdb=" CA VAL F 21 " pdb=" CG1 VAL F 21 " pdb=" CG2 VAL F 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 2733 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 362 " 0.025 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS K 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS K 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS K 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 362 " 0.025 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C LYS L 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS L 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS L 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 21 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C VAL F 21 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL F 21 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU F 22 " 0.022 2.00e-02 2.50e+03 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.81: 11 1.81 - 2.58: 237 2.58 - 3.35: 19887 3.35 - 4.13: 45935 4.13 - 4.90: 74331 Nonbonded interactions: 140401 Sorted by model distance: nonbonded pdb=" OE2 GLU E 73 " pdb=" CG ARG F 23 " model vdw 1.035 3.440 nonbonded pdb=" O LEU C 117 " pdb=" NZ LYS F 44 " model vdw 1.189 3.120 nonbonded pdb=" OD1 ASP E 77 " pdb=" O LEU F 10 " model vdw 1.254 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 1.434 3.040 nonbonded pdb=" O SER E 57 " pdb=" NH2 ARG F 40 " model vdw 1.578 3.120 ... (remaining 140396 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' selection = (chain 'E' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 118)) selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 62 through 135 or resid 137 through 152 or resid 171 throu \ gh 200 or resid 202 through 402)) selection = (chain 'L' and (resid 62 through 151 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 200 or resid 202 through 402)) } 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: 0.520 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.020 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 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 : 0.009 0.346 17275 Z= 0.729 Angle : 0.924 11.650 24520 Z= 0.716 Chirality : 0.053 0.517 2736 Planarity : 0.006 0.073 2102 Dihedral : 25.617 156.219 7331 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.11 % Allowed : 1.20 % Favored : 97.69 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.22), residues: 1277 helix: 0.28 (0.19), residues: 704 sheet: -1.44 (0.48), residues: 80 loop : -2.33 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 357 TYR 0.012 0.001 TYR G 60 PHE 0.013 0.002 PHE K 154 TRP 0.007 0.001 TRP K 264 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.61 (17262) covalent geometry : angle 0.91744 / 0.72 (24504) SS BOND : bond 0.00284 / 0.14 ( 2) SS BOND : angle 0.83745 / 0.43 ( 4) hydrogen bonds : bond 0.12965 / 8.55 ( 858) hydrogen bonds : angle 5.59357 / 4.12 ( 2210) metal coordination : bond 0.01074 / 0.45 ( 8) metal coordination : angle 5.07934 / 2.46 ( 12) Misc. bond : bond 0.30713 / 15.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 451 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ILE cc_start: 0.8165 (mt) cc_final: 0.7965 (mt) REVERT: B 88 TYR cc_start: 0.6529 (m-80) cc_final: 0.6067 (m-10) REVERT: D 34 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7220 (mmtt) REVERT: D 95 GLN cc_start: 0.7758 (tt0) cc_final: 0.7460 (tt0) REVERT: E 54 TYR cc_start: 0.6552 (m-80) cc_final: 0.6340 (m-10) REVERT: H 39 ILE cc_start: 0.8380 (pt) cc_final: 0.7851 (tt) REVERT: H 54 ILE cc_start: 0.8631 (tt) cc_final: 0.8399 (tt) REVERT: K 173 MET cc_start: 0.4822 (mmp) cc_final: 0.2940 (ttp) REVERT: K 195 PHE cc_start: 0.6802 (p90) cc_final: 0.6591 (p90) REVERT: K 354 THR cc_start: 0.2864 (p) cc_final: 0.2062 (p) REVERT: L 72 MET cc_start: 0.3021 (pmm) cc_final: 0.2729 (ptt) outliers start: 8 outliers final: 0 residues processed: 456 average time/residue: 0.1696 time to fit residues: 106.7611 Evaluate side-chains 239 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS L 96 GLN L 149 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.146289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.115809 restraints weight = 46129.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.116885 restraints weight = 41187.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117152 restraints weight = 34314.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.117528 restraints weight = 30592.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.117602 restraints weight = 28487.932| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17275 Z= 0.190 Angle : 0.831 10.159 24520 Z= 0.460 Chirality : 0.053 0.280 2736 Planarity : 0.007 0.117 2102 Dihedral : 29.169 150.986 4789 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.56 % Allowed : 3.42 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1277 helix: 0.51 (0.19), residues: 708 sheet: -1.26 (0.56), residues: 52 loop : -2.25 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 39 TYR 0.024 0.002 TYR F 72 PHE 0.023 0.003 PHE L 183 TRP 0.005 0.001 TRP K 264 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (17262) covalent geometry : angle 0.82307 / 0.46 (24504) SS BOND : bond 0.00054 / 0.03 ( 2) SS BOND : angle 1.50762 / 0.83 ( 4) hydrogen bonds : bond 0.06292 / 4.13 ( 858) hydrogen bonds : angle 4.43068 / 3.18 ( 2210) metal coordination : bond 0.00675 / 0.29 ( 8) metal coordination : angle 5.13559 / 2.48 ( 12) Misc. bond : bond 0.00574 / 0.28 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 301 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 LYS cc_start: 0.7615 (ptpt) cc_final: 0.7194 (mmtt) REVERT: E 129 ARG cc_start: 0.7463 (tmt-80) cc_final: 0.6919 (tpt170) REVERT: G 104 ILE cc_start: 0.8927 (mm) cc_final: 0.8725 (mm) REVERT: H 39 ILE cc_start: 0.8142 (pt) cc_final: 0.7832 (tp) REVERT: K 173 MET cc_start: 0.4267 (mmp) cc_final: 0.2348 (ttt) REVERT: K 273 HIS cc_start: 0.5800 (t70) cc_final: 0.5182 (t70) REVERT: K 283 SER cc_start: 0.4279 (t) cc_final: 0.3715 (p) REVERT: K 354 THR cc_start: 0.3591 (p) cc_final: 0.2836 (t) REVERT: L 89 LEU cc_start: 0.7600 (mp) cc_final: 0.7209 (mp) REVERT: L 100 MET cc_start: 0.6164 (mmm) cc_final: 0.5305 (tpp) REVERT: L 183 PHE cc_start: 0.6512 (m-80) cc_final: 0.6190 (m-80) outliers start: 2 outliers final: 1 residues processed: 302 average time/residue: 0.1361 time to fit residues: 60.6608 Evaluate side-chains 226 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 9.9990 chunk 104 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 100 optimal weight: 7.9990 chunk 23 optimal weight: 40.0000 chunk 29 optimal weight: 30.0000 chunk 50 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 overall best weight: 6.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.137605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.105644 restraints weight = 56376.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.105100 restraints weight = 49204.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105541 restraints weight = 39410.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105914 restraints weight = 34171.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106140 restraints weight = 32029.168| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 17275 Z= 0.332 Angle : 0.991 19.058 24520 Z= 0.543 Chirality : 0.058 0.451 2736 Planarity : 0.009 0.133 2102 Dihedral : 29.215 157.556 4789 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 1.11 % Allowed : 6.29 % Favored : 92.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.82 (0.21), residues: 1277 helix: -0.44 (0.18), residues: 719 sheet: -2.06 (0.66), residues: 38 loop : -2.20 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.002 ARG G 31 TYR 0.033 0.005 TYR A 99 PHE 0.033 0.004 PHE H 70 TRP 0.029 0.004 TRP L 264 HIS 0.019 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.33 (17262) covalent geometry : angle 0.98756 / 0.54 (24504) SS BOND : bond 0.00221 / 0.11 ( 2) SS BOND : angle 1.54476 / 0.84 ( 4) hydrogen bonds : bond 0.08004 / 5.30 ( 858) hydrogen bonds : angle 5.08599 / 3.69 ( 2210) metal coordination : bond 0.00754 / 0.35 ( 8) metal coordination : angle 3.59860 / 1.74 ( 12) Misc. bond : bond 0.02654 / 1.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 314 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7404 (t0) cc_final: 0.7198 (t0) REVERT: B 29 ILE cc_start: 0.8664 (mm) cc_final: 0.8179 (mm) REVERT: B 96 THR cc_start: 0.8560 (m) cc_final: 0.8299 (p) REVERT: D 34 LYS cc_start: 0.7955 (ptpt) cc_final: 0.7386 (mmtt) REVERT: D 120 LYS cc_start: 0.7443 (mttt) cc_final: 0.6767 (tptp) REVERT: E 50 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7693 (mt-10) REVERT: E 76 GLN cc_start: 0.8635 (tt0) cc_final: 0.8166 (tt0) REVERT: F 24 ASP cc_start: 0.8403 (p0) cc_final: 0.8201 (p0) REVERT: F 25 ASN cc_start: 0.8779 (m-40) cc_final: 0.8375 (m-40) REVERT: F 88 TYR cc_start: 0.8486 (m-10) cc_final: 0.8169 (m-10) REVERT: G 19 ARG cc_start: 0.8477 (ttp-170) cc_final: 0.8227 (ttp80) REVERT: G 22 ARG cc_start: 0.8264 (ttt180) cc_final: 0.8023 (mtp180) REVERT: G 53 TYR cc_start: 0.9159 (t80) cc_final: 0.8894 (t80) REVERT: K 173 MET cc_start: 0.4174 (mmp) cc_final: 0.2169 (ttp) REVERT: K 188 MET cc_start: 0.4837 (pmm) cc_final: 0.4427 (pmm) REVERT: K 307 TYR cc_start: 0.5615 (m-10) cc_final: 0.5396 (m-10) REVERT: L 100 MET cc_start: 0.6398 (mmm) cc_final: 0.5192 (tpp) REVERT: L 181 HIS cc_start: 0.5980 (t70) cc_final: 0.5006 (t70) REVERT: L 183 PHE cc_start: 0.6478 (m-80) cc_final: 0.5983 (m-80) REVERT: L 185 TYR cc_start: 0.5814 (m-10) cc_final: 0.4964 (m-10) REVERT: L 195 PHE cc_start: 0.8007 (p90) cc_final: 0.7774 (p90) REVERT: L 222 ASP cc_start: 0.4567 (p0) cc_final: 0.4343 (t0) REVERT: L 237 ILE cc_start: 0.6970 (mt) cc_final: 0.6769 (mt) REVERT: L 241 MET cc_start: 0.5841 (ppp) cc_final: 0.5529 (ppp) outliers start: 8 outliers final: 3 residues processed: 319 average time/residue: 0.1353 time to fit residues: 63.6313 Evaluate side-chains 243 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 112 optimal weight: 0.0870 chunk 152 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.140253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107050 restraints weight = 60734.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.108032 restraints weight = 54589.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108820 restraints weight = 39499.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109077 restraints weight = 33198.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109143 restraints weight = 32347.711| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17275 Z= 0.166 Angle : 0.763 12.694 24520 Z= 0.429 Chirality : 0.050 0.288 2736 Planarity : 0.007 0.144 2102 Dihedral : 29.224 158.598 4789 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.37 % Allowed : 2.96 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.22), residues: 1277 helix: 0.17 (0.18), residues: 715 sheet: -1.58 (0.59), residues: 52 loop : -2.16 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 3 TYR 0.040 0.002 TYR E 54 PHE 0.034 0.002 PHE G 27 TRP 0.017 0.002 TRP K 218 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (17262) covalent geometry : angle 0.75611 / 0.43 (24504) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 1.44391 / 0.75 ( 4) hydrogen bonds : bond 0.05387 / 3.57 ( 858) hydrogen bonds : angle 4.28473 / 3.09 ( 2210) metal coordination : bond 0.00598 / 0.27 ( 8) metal coordination : angle 4.52736 / 2.30 ( 12) Misc. bond : bond 0.02190 / 1.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7895 (m-80) cc_final: 0.7476 (m-10) REVERT: A 86 SER cc_start: 0.8784 (m) cc_final: 0.8583 (m) REVERT: A 90 MET cc_start: 0.8218 (mmp) cc_final: 0.7699 (mmt) REVERT: A 126 LEU cc_start: 0.8729 (tp) cc_final: 0.8523 (tp) REVERT: B 29 ILE cc_start: 0.8571 (mm) cc_final: 0.8303 (mm) REVERT: D 34 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7274 (mmtt) REVERT: D 99 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7528 (mtp180) REVERT: D 120 LYS cc_start: 0.7466 (mttt) cc_final: 0.6807 (tptp) REVERT: F 24 ASP cc_start: 0.8015 (p0) cc_final: 0.7228 (p0) REVERT: F 25 ASN cc_start: 0.9364 (m-40) cc_final: 0.8281 (m-40) REVERT: F 84 MET cc_start: 0.7587 (tpp) cc_final: 0.7201 (tpp) REVERT: F 88 TYR cc_start: 0.8293 (m-10) cc_final: 0.8053 (m-10) REVERT: H 37 TYR cc_start: 0.8838 (m-80) cc_final: 0.8590 (m-80) REVERT: H 47 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7363 (tm-30) REVERT: H 68 ASP cc_start: 0.9043 (t70) cc_final: 0.8756 (t0) REVERT: K 173 MET cc_start: 0.4350 (mmp) cc_final: 0.2419 (ttp) REVERT: K 186 LEU cc_start: 0.7218 (mt) cc_final: 0.6929 (pp) REVERT: K 188 MET cc_start: 0.4711 (pmm) cc_final: 0.4314 (pmm) REVERT: K 265 LEU cc_start: 0.5859 (mm) cc_final: 0.5620 (mp) REVERT: K 283 SER cc_start: 0.4776 (t) cc_final: 0.4137 (p) REVERT: K 358 LEU cc_start: 0.6745 (mt) cc_final: 0.5996 (pp) REVERT: L 100 MET cc_start: 0.6712 (mmm) cc_final: 0.5428 (tpp) REVERT: L 183 PHE cc_start: 0.6312 (m-80) cc_final: 0.6080 (m-80) REVERT: L 195 PHE cc_start: 0.7658 (p90) cc_final: 0.7451 (p90) REVERT: L 222 ASP cc_start: 0.5167 (p0) cc_final: 0.4468 (t0) REVERT: L 360 ARG cc_start: 0.6989 (mmp80) cc_final: 0.5912 (tmt170) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1325 time to fit residues: 61.1013 Evaluate side-chains 236 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 143 optimal weight: 0.0970 chunk 155 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 124 optimal weight: 10.0000 chunk 24 optimal weight: 50.0000 chunk 118 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 68 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.136216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.102849 restraints weight = 66628.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103907 restraints weight = 50923.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.104549 restraints weight = 41478.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104747 restraints weight = 32520.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104988 restraints weight = 31319.270| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17275 Z= 0.248 Angle : 0.854 15.436 24520 Z= 0.468 Chirality : 0.052 0.283 2736 Planarity : 0.007 0.085 2102 Dihedral : 29.345 161.484 4789 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.46 % Allowed : 3.33 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.21), residues: 1277 helix: 0.05 (0.18), residues: 712 sheet: -2.53 (0.63), residues: 38 loop : -2.25 (0.23), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG F 23 TYR 0.028 0.003 TYR G 53 PHE 0.022 0.003 PHE G 27 TRP 0.024 0.004 TRP K 218 HIS 0.009 0.002 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.25 (17262) covalent geometry : angle 0.84706 / 0.47 (24504) SS BOND : bond 0.00084 / 0.04 ( 2) SS BOND : angle 1.55024 / 0.82 ( 4) hydrogen bonds : bond 0.06484 / 4.33 ( 858) hydrogen bonds : angle 4.56434 / 3.32 ( 2210) metal coordination : bond 0.01990 / 0.79 ( 8) metal coordination : angle 4.85750 / 2.36 ( 12) Misc. bond : bond 0.00075 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 291 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7567 (pp20) cc_final: 0.7257 (pp20) REVERT: A 60 LEU cc_start: 0.8414 (tp) cc_final: 0.7691 (tp) REVERT: A 86 SER cc_start: 0.8972 (m) cc_final: 0.8501 (t) REVERT: A 126 LEU cc_start: 0.9184 (tp) cc_final: 0.8868 (tp) REVERT: B 18 HIS cc_start: 0.4710 (t70) cc_final: 0.4180 (t70) REVERT: B 29 ILE cc_start: 0.9057 (mm) cc_final: 0.8703 (mm) REVERT: B 84 MET cc_start: 0.7687 (tpt) cc_final: 0.7101 (tpp) REVERT: B 88 TYR cc_start: 0.8015 (m-10) cc_final: 0.7399 (m-10) REVERT: C 52 VAL cc_start: 0.9431 (m) cc_final: 0.9071 (p) REVERT: C 59 GLU cc_start: 0.8504 (tt0) cc_final: 0.8197 (tt0) REVERT: D 34 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7442 (mmtt) REVERT: D 40 TYR cc_start: 0.8481 (m-80) cc_final: 0.8172 (m-80) REVERT: D 120 LYS cc_start: 0.7750 (mttt) cc_final: 0.6821 (tptp) REVERT: E 39 HIS cc_start: 0.4998 (t-90) cc_final: 0.3450 (m-70) REVERT: E 54 TYR cc_start: 0.7993 (m-10) cc_final: 0.7745 (m-10) REVERT: E 113 HIS cc_start: 0.8461 (t70) cc_final: 0.8158 (t-90) REVERT: F 24 ASP cc_start: 0.8617 (p0) cc_final: 0.7730 (p0) REVERT: F 25 ASN cc_start: 0.9426 (m-40) cc_final: 0.9035 (m-40) REVERT: F 27 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.7937 (mm110) REVERT: F 74 GLU cc_start: 0.8666 (tt0) cc_final: 0.8120 (tt0) REVERT: G 53 TYR cc_start: 0.9340 (t80) cc_final: 0.8988 (t80) REVERT: H 47 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7605 (tm-30) REVERT: H 59 MET cc_start: 0.8635 (tpp) cc_final: 0.8415 (tpp) REVERT: H 68 ASP cc_start: 0.9022 (t70) cc_final: 0.8776 (t0) REVERT: K 173 MET cc_start: 0.4478 (mmp) cc_final: 0.2354 (ttp) REVERT: K 188 MET cc_start: 0.5269 (pmm) cc_final: 0.4884 (pmm) REVERT: K 195 PHE cc_start: 0.7039 (p90) cc_final: 0.6688 (p90) REVERT: K 265 LEU cc_start: 0.6161 (mm) cc_final: 0.5864 (mp) REVERT: K 288 THR cc_start: 0.6756 (m) cc_final: 0.6495 (m) REVERT: K 358 LEU cc_start: 0.6831 (mt) cc_final: 0.6151 (pp) REVERT: L 80 ASN cc_start: 0.8313 (m110) cc_final: 0.8004 (m-40) REVERT: L 100 MET cc_start: 0.6573 (mmm) cc_final: 0.5295 (tpp) REVERT: L 183 PHE cc_start: 0.6550 (m-80) cc_final: 0.6176 (m-80) REVERT: L 195 PHE cc_start: 0.8056 (p90) cc_final: 0.7839 (p90) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.1270 time to fit residues: 55.8257 Evaluate side-chains 225 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 33 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 87 GLN G 114 HIS K 80 ASN K 181 HIS K 262 GLN K 273 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.138905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.105903 restraints weight = 57629.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106936 restraints weight = 53600.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107336 restraints weight = 42657.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.107737 restraints weight = 35370.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107912 restraints weight = 32530.328| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17275 Z= 0.157 Angle : 0.745 13.542 24520 Z= 0.416 Chirality : 0.049 0.273 2736 Planarity : 0.007 0.196 2102 Dihedral : 29.263 161.729 4789 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.56 % Allowed : 1.94 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.22), residues: 1277 helix: 0.42 (0.19), residues: 713 sheet: -1.91 (0.64), residues: 50 loop : -2.18 (0.24), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 23 TYR 0.038 0.002 TYR F 88 PHE 0.015 0.002 PHE G 27 TRP 0.019 0.002 TRP K 218 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (17262) covalent geometry : angle 0.73694 / 0.42 (24504) SS BOND : bond 0.00047 / 0.02 ( 2) SS BOND : angle 1.43310 / 0.74 ( 4) hydrogen bonds : bond 0.05134 / 3.43 ( 858) hydrogen bonds : angle 4.08291 / 2.94 ( 2210) metal coordination : bond 0.00911 / 0.34 ( 8) metal coordination : angle 4.94099 / 2.27 ( 12) Misc. bond : bond 0.01152 / 0.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7435 (pp20) cc_final: 0.7217 (pp20) REVERT: A 60 LEU cc_start: 0.8378 (tp) cc_final: 0.7416 (tp) REVERT: A 86 SER cc_start: 0.8922 (m) cc_final: 0.8416 (t) REVERT: B 18 HIS cc_start: 0.4304 (t70) cc_final: 0.3518 (t70) REVERT: B 36 ARG cc_start: 0.8908 (mtm-85) cc_final: 0.7844 (mtm-85) REVERT: B 84 MET cc_start: 0.7459 (tpt) cc_final: 0.7168 (tpp) REVERT: B 88 TYR cc_start: 0.7787 (m-10) cc_final: 0.7197 (m-10) REVERT: C 45 ARG cc_start: 0.8204 (mtp85) cc_final: 0.7875 (mtp85) REVERT: C 52 VAL cc_start: 0.9367 (m) cc_final: 0.9099 (p) REVERT: D 34 LYS cc_start: 0.7957 (ptpt) cc_final: 0.7416 (mmtt) REVERT: D 120 LYS cc_start: 0.7763 (mttt) cc_final: 0.6868 (tptp) REVERT: E 50 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7808 (mt-10) REVERT: E 76 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: F 24 ASP cc_start: 0.8332 (p0) cc_final: 0.7609 (p0) REVERT: F 25 ASN cc_start: 0.9309 (m-40) cc_final: 0.8336 (m-40) REVERT: F 46 ILE cc_start: 0.8983 (mt) cc_final: 0.8770 (mt) REVERT: G 60 TYR cc_start: 0.9202 (t80) cc_final: 0.8937 (t80) REVERT: K 173 MET cc_start: 0.4534 (mmp) cc_final: 0.2525 (ttp) REVERT: K 188 MET cc_start: 0.5206 (pmm) cc_final: 0.4873 (pmm) REVERT: K 195 PHE cc_start: 0.6886 (p90) cc_final: 0.6465 (p90) REVERT: K 358 LEU cc_start: 0.6732 (mt) cc_final: 0.6199 (pp) REVERT: L 100 MET cc_start: 0.6691 (mmm) cc_final: 0.5436 (tpp) REVERT: L 183 PHE cc_start: 0.6418 (m-80) cc_final: 0.6114 (m-80) REVERT: L 195 PHE cc_start: 0.7827 (p90) cc_final: 0.7626 (p90) outliers start: 2 outliers final: 1 residues processed: 293 average time/residue: 0.1193 time to fit residues: 52.5489 Evaluate side-chains 230 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 27 optimal weight: 30.0000 chunk 118 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.136373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.104313 restraints weight = 45940.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104242 restraints weight = 41524.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.104575 restraints weight = 35725.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104933 restraints weight = 31985.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104963 restraints weight = 31060.599| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3475 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17275 Z= 0.204 Angle : 0.772 14.271 24520 Z= 0.430 Chirality : 0.049 0.283 2736 Planarity : 0.009 0.347 2102 Dihedral : 29.289 163.409 4789 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.37 % Allowed : 0.93 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1277 helix: 0.31 (0.19), residues: 718 sheet: -1.78 (0.65), residues: 50 loop : -2.16 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 23 TYR 0.035 0.002 TYR D 40 PHE 0.023 0.002 PHE G 27 TRP 0.017 0.002 TRP K 218 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (17262) covalent geometry : angle 0.76636 / 0.43 (24504) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 1.51017 / 0.81 ( 4) hydrogen bonds : bond 0.05545 / 3.72 ( 858) hydrogen bonds : angle 4.22334 / 3.06 ( 2210) metal coordination : bond 0.00770 / 0.32 ( 8) metal coordination : angle 4.18556 / 1.90 ( 12) Misc. bond : bond 0.01040 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7515 (pp20) cc_final: 0.7246 (pp20) REVERT: A 60 LEU cc_start: 0.8596 (tp) cc_final: 0.7579 (tt) REVERT: A 86 SER cc_start: 0.8902 (m) cc_final: 0.8504 (t) REVERT: A 94 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7808 (mm-30) REVERT: A 126 LEU cc_start: 0.9298 (tp) cc_final: 0.9075 (tp) REVERT: B 29 ILE cc_start: 0.9153 (mm) cc_final: 0.8879 (mm) REVERT: B 82 THR cc_start: 0.9232 (m) cc_final: 0.8746 (m) REVERT: B 84 MET cc_start: 0.7685 (tpt) cc_final: 0.7204 (tpp) REVERT: B 88 TYR cc_start: 0.7907 (m-10) cc_final: 0.7405 (m-10) REVERT: C 45 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7936 (mtp85) REVERT: C 52 VAL cc_start: 0.9414 (m) cc_final: 0.9128 (p) REVERT: C 87 GLN cc_start: 0.8664 (tp40) cc_final: 0.8306 (tp40) REVERT: D 34 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7391 (mmtt) REVERT: D 120 LYS cc_start: 0.8014 (mttt) cc_final: 0.6944 (tptp) REVERT: E 39 HIS cc_start: 0.5016 (t-90) cc_final: 0.3559 (m-70) REVERT: E 50 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7795 (mt-10) REVERT: E 76 GLN cc_start: 0.8252 (tt0) cc_final: 0.7792 (tm-30) REVERT: E 112 ILE cc_start: 0.9207 (tt) cc_final: 0.8994 (tp) REVERT: F 46 ILE cc_start: 0.8975 (mt) cc_final: 0.8708 (mt) REVERT: F 84 MET cc_start: 0.8079 (tpp) cc_final: 0.7878 (tpp) REVERT: G 21 GLN cc_start: 0.8433 (pt0) cc_final: 0.8129 (pp30) REVERT: G 53 TYR cc_start: 0.9287 (t80) cc_final: 0.8967 (t80) REVERT: G 60 TYR cc_start: 0.9233 (t80) cc_final: 0.8958 (t80) REVERT: H 46 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8305 (mmmt) REVERT: H 59 MET cc_start: 0.8623 (tpp) cc_final: 0.8285 (tpp) REVERT: K 173 MET cc_start: 0.4393 (mmp) cc_final: 0.2483 (ttp) REVERT: K 195 PHE cc_start: 0.7016 (p90) cc_final: 0.6588 (p90) REVERT: K 358 LEU cc_start: 0.6691 (mt) cc_final: 0.6202 (pp) REVERT: L 100 MET cc_start: 0.6851 (mmm) cc_final: 0.5586 (tpp) REVERT: L 183 PHE cc_start: 0.6388 (m-80) cc_final: 0.6053 (m-80) REVERT: L 284 THR cc_start: 0.8070 (p) cc_final: 0.7696 (p) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1215 time to fit residues: 52.4564 Evaluate side-chains 229 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 13 optimal weight: 0.9990 chunk 31 optimal weight: 40.0000 chunk 16 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 24 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.135709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.101291 restraints weight = 57895.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.103030 restraints weight = 48226.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103402 restraints weight = 34294.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103620 restraints weight = 30001.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.103632 restraints weight = 28720.482| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17275 Z= 0.213 Angle : 0.782 15.085 24520 Z= 0.434 Chirality : 0.050 0.289 2736 Planarity : 0.008 0.293 2102 Dihedral : 29.340 165.021 4789 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.28 % Allowed : 1.48 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.22), residues: 1277 helix: 0.29 (0.19), residues: 717 sheet: -2.19 (0.72), residues: 38 loop : -2.08 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 23 TYR 0.030 0.003 TYR H 40 PHE 0.027 0.002 PHE G 27 TRP 0.016 0.002 TRP K 218 HIS 0.010 0.001 HIS L 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (17262) covalent geometry : angle 0.77738 / 0.43 (24504) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 1.47107 / 0.78 ( 4) hydrogen bonds : bond 0.05472 / 3.66 ( 858) hydrogen bonds : angle 4.24841 / 3.08 ( 2210) metal coordination : bond 0.00688 / 0.28 ( 8) metal coordination : angle 3.93940 / 1.79 ( 12) Misc. bond : bond 0.00849 / 0.41 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8979 (m) cc_final: 0.8474 (t) REVERT: A 94 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7987 (mm-30) REVERT: A 126 LEU cc_start: 0.9408 (tp) cc_final: 0.9080 (tp) REVERT: B 16 LYS cc_start: 0.5802 (pttp) cc_final: 0.5144 (tptm) REVERT: B 29 ILE cc_start: 0.9247 (mm) cc_final: 0.9009 (mm) REVERT: B 84 MET cc_start: 0.7777 (tpt) cc_final: 0.7501 (tpp) REVERT: C 52 VAL cc_start: 0.9415 (m) cc_final: 0.9157 (p) REVERT: C 87 GLN cc_start: 0.8715 (tp40) cc_final: 0.8496 (tp40) REVERT: D 34 LYS cc_start: 0.7875 (ptpt) cc_final: 0.7365 (mmtt) REVERT: E 39 HIS cc_start: 0.5328 (t-90) cc_final: 0.3698 (m-70) REVERT: E 76 GLN cc_start: 0.8301 (tt0) cc_final: 0.7471 (tm-30) REVERT: E 112 ILE cc_start: 0.9282 (tt) cc_final: 0.9080 (tp) REVERT: E 113 HIS cc_start: 0.9057 (t70) cc_final: 0.8799 (t-90) REVERT: E 120 MET cc_start: 0.8391 (mmm) cc_final: 0.7938 (mmm) REVERT: F 46 ILE cc_start: 0.9017 (mt) cc_final: 0.8785 (mt) REVERT: G 21 GLN cc_start: 0.8388 (pt0) cc_final: 0.8143 (pp30) REVERT: G 53 TYR cc_start: 0.9338 (t80) cc_final: 0.9059 (t80) REVERT: G 60 TYR cc_start: 0.9299 (t80) cc_final: 0.8960 (t80) REVERT: H 46 LYS cc_start: 0.8822 (mmmt) cc_final: 0.8415 (mmmt) REVERT: K 173 MET cc_start: 0.4421 (mmp) cc_final: 0.2565 (ttp) REVERT: K 188 MET cc_start: 0.4748 (pmm) cc_final: 0.4427 (pmm) REVERT: K 195 PHE cc_start: 0.7054 (p90) cc_final: 0.6643 (p90) REVERT: K 358 LEU cc_start: 0.6805 (mt) cc_final: 0.6246 (pp) REVERT: L 100 MET cc_start: 0.6929 (mmm) cc_final: 0.5689 (tpp) REVERT: L 183 PHE cc_start: 0.6480 (m-80) cc_final: 0.6141 (m-80) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1067 time to fit residues: 46.9778 Evaluate side-chains 226 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 137 optimal weight: 0.3980 chunk 34 optimal weight: 50.0000 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.137889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.104749 restraints weight = 66437.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.105754 restraints weight = 53898.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.106427 restraints weight = 44151.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106737 restraints weight = 34462.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106923 restraints weight = 32425.943| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17275 Z= 0.157 Angle : 0.734 9.632 24520 Z= 0.412 Chirality : 0.048 0.286 2736 Planarity : 0.006 0.171 2102 Dihedral : 29.297 165.102 4789 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.22), residues: 1277 helix: 0.42 (0.19), residues: 717 sheet: -1.70 (0.67), residues: 50 loop : -2.14 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 45 TYR 0.022 0.002 TYR G 53 PHE 0.019 0.002 PHE G 27 TRP 0.032 0.003 TRP K 218 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (17262) covalent geometry : angle 0.72936 / 0.41 (24504) SS BOND : bond 0.00073 / 0.04 ( 2) SS BOND : angle 1.52293 / 0.80 ( 4) hydrogen bonds : bond 0.04914 / 3.28 ( 858) hydrogen bonds : angle 4.04721 / 2.91 ( 2210) metal coordination : bond 0.00632 / 0.25 ( 8) metal coordination : angle 3.76018 / 1.67 ( 12) Misc. bond : bond 0.00220 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8230 (m-80) cc_final: 0.7847 (m-10) REVERT: A 86 SER cc_start: 0.8852 (m) cc_final: 0.8400 (t) REVERT: A 94 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 126 LEU cc_start: 0.9362 (tp) cc_final: 0.9106 (tp) REVERT: B 29 ILE cc_start: 0.9218 (mm) cc_final: 0.8979 (mm) REVERT: B 82 THR cc_start: 0.9157 (m) cc_final: 0.8582 (m) REVERT: C 52 VAL cc_start: 0.9343 (m) cc_final: 0.9115 (p) REVERT: C 87 GLN cc_start: 0.8655 (tp40) cc_final: 0.8405 (tp40) REVERT: D 34 LYS cc_start: 0.7876 (ptpt) cc_final: 0.7318 (mmtt) REVERT: D 105 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7677 (mm-30) REVERT: E 39 HIS cc_start: 0.5245 (t-90) cc_final: 0.3742 (m-70) REVERT: E 94 GLU cc_start: 0.8168 (tp30) cc_final: 0.7842 (tp30) REVERT: E 112 ILE cc_start: 0.9176 (tt) cc_final: 0.8952 (tp) REVERT: E 120 MET cc_start: 0.8301 (mmm) cc_final: 0.7868 (mmm) REVERT: F 46 ILE cc_start: 0.8974 (mt) cc_final: 0.8767 (mt) REVERT: G 21 GLN cc_start: 0.8200 (pt0) cc_final: 0.7999 (pp30) REVERT: G 53 TYR cc_start: 0.9253 (t80) cc_final: 0.8976 (t80) REVERT: H 46 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8539 (mmmt) REVERT: H 59 MET cc_start: 0.8611 (tpp) cc_final: 0.8267 (tpp) REVERT: K 77 LEU cc_start: 0.7626 (mt) cc_final: 0.7406 (tp) REVERT: K 173 MET cc_start: 0.4372 (mmp) cc_final: 0.2423 (ttp) REVERT: K 188 MET cc_start: 0.4731 (pmm) cc_final: 0.4299 (pmm) REVERT: K 195 PHE cc_start: 0.6869 (p90) cc_final: 0.6566 (p90) REVERT: K 358 LEU cc_start: 0.6890 (mt) cc_final: 0.6349 (pp) REVERT: L 100 MET cc_start: 0.7025 (mmm) cc_final: 0.5789 (tpp) REVERT: L 183 PHE cc_start: 0.6402 (m-80) cc_final: 0.6046 (m-80) REVERT: L 284 THR cc_start: 0.8298 (p) cc_final: 0.7997 (p) REVERT: L 311 PHE cc_start: 0.5145 (t80) cc_final: 0.4877 (t80) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.1117 time to fit residues: 51.7448 Evaluate side-chains 232 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 50.0000 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 30.0000 chunk 54 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 108 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.100291 restraints weight = 60293.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100893 restraints weight = 52659.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.101604 restraints weight = 46803.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101824 restraints weight = 36563.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.101955 restraints weight = 34450.851| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17275 Z= 0.254 Angle : 0.823 13.396 24520 Z= 0.454 Chirality : 0.051 0.288 2736 Planarity : 0.006 0.083 2102 Dihedral : 29.408 167.369 4789 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.28 % Allowed : 0.56 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.22), residues: 1277 helix: 0.17 (0.18), residues: 713 sheet: -2.35 (0.71), residues: 38 loop : -2.11 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 78 TYR 0.029 0.003 TYR D 40 PHE 0.039 0.003 PHE E 78 TRP 0.012 0.002 TRP L 264 HIS 0.010 0.002 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (17262) covalent geometry : angle 0.81871 / 0.45 (24504) SS BOND : bond 0.00112 / 0.05 ( 2) SS BOND : angle 1.68889 / 0.91 ( 4) hydrogen bonds : bond 0.06052 / 4.03 ( 858) hydrogen bonds : angle 4.40709 / 3.19 ( 2210) metal coordination : bond 0.00739 / 0.31 ( 8) metal coordination : angle 3.68600 / 1.69 ( 12) Misc. bond : bond 0.00383 / 0.18 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9004 (m) cc_final: 0.8535 (t) REVERT: A 126 LEU cc_start: 0.9401 (tp) cc_final: 0.9115 (tp) REVERT: B 16 LYS cc_start: 0.5657 (pttp) cc_final: 0.4607 (tptm) REVERT: B 29 ILE cc_start: 0.9353 (mm) cc_final: 0.9142 (mm) REVERT: D 31 LYS cc_start: 0.4136 (tttt) cc_final: 0.3905 (mmtp) REVERT: D 34 LYS cc_start: 0.7963 (ptpt) cc_final: 0.7504 (mmtt) REVERT: E 39 HIS cc_start: 0.5453 (t-90) cc_final: 0.3881 (m-70) REVERT: E 94 GLU cc_start: 0.8283 (tp30) cc_final: 0.7994 (tp30) REVERT: E 120 MET cc_start: 0.8593 (mmm) cc_final: 0.8173 (mmm) REVERT: F 46 ILE cc_start: 0.8987 (mt) cc_final: 0.8706 (mt) REVERT: G 21 GLN cc_start: 0.8458 (pt0) cc_final: 0.8204 (pp30) REVERT: G 53 TYR cc_start: 0.9408 (t80) cc_final: 0.9110 (t80) REVERT: H 46 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8598 (mmmt) REVERT: H 68 ASP cc_start: 0.9129 (t70) cc_final: 0.8919 (t0) REVERT: K 173 MET cc_start: 0.4394 (mmp) cc_final: 0.2298 (ttt) REVERT: K 188 MET cc_start: 0.5103 (pmm) cc_final: 0.4521 (pmm) REVERT: K 195 PHE cc_start: 0.6941 (p90) cc_final: 0.6496 (p90) REVERT: K 265 LEU cc_start: 0.6557 (mp) cc_final: 0.6302 (mp) REVERT: L 100 MET cc_start: 0.6770 (mmm) cc_final: 0.5500 (tpp) REVERT: L 183 PHE cc_start: 0.6587 (m-80) cc_final: 0.6236 (m-80) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1040 time to fit residues: 42.5968 Evaluate side-chains 217 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 44 optimal weight: 30.0000 chunk 138 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 40.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN K 273 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.137201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.105102 restraints weight = 52500.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105030 restraints weight = 42058.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.105324 restraints weight = 33782.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105558 restraints weight = 32129.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.105611 restraints weight = 31415.127| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17275 Z= 0.156 Angle : 0.758 16.087 24520 Z= 0.420 Chirality : 0.049 0.297 2736 Planarity : 0.008 0.309 2102 Dihedral : 29.377 166.688 4789 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.02 (0.23), residues: 1277 helix: 0.38 (0.19), residues: 716 sheet: -2.10 (0.71), residues: 48 loop : -2.07 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG F 23 TYR 0.020 0.002 TYR G 53 PHE 0.030 0.002 PHE G 27 TRP 0.014 0.002 TRP L 264 HIS 0.010 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (17262) covalent geometry : angle 0.75406 / 0.42 (24504) SS BOND : bond 0.00123 / 0.06 ( 2) SS BOND : angle 1.52537 / 0.84 ( 4) hydrogen bonds : bond 0.05011 / 3.35 ( 858) hydrogen bonds : angle 4.10973 / 2.93 ( 2210) metal coordination : bond 0.00605 / 0.24 ( 8) metal coordination : angle 3.45230 / 1.56 ( 12) Misc. bond : bond 0.00468 / 0.22 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.87 seconds wall clock time: 43 minutes 42.33 seconds (2622.33 seconds total)