Starting phenix.real_space_refine on Sun Aug 24 01:22:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrg_34055/08_2025/7yrg_34055.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrg_34055/08_2025/7yrg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2025/7yrg_34055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2025/7yrg_34055.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2025/7yrg_34055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrg_34055/08_2025/7yrg_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-2.0-5787/lib/python3.9/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: 4.62, per 1000 atoms: 0.28 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: 1.60 Conformation dependent library (CDL) restraints added in 540.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.55 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: 3.40 Time building geometry restraints manager: 2.07 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: 24014 2.33 - 4.66: 395 4.66 - 6.99: 63 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: 2641 0.103 - 0.207: 85 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: 0.550 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 20.950 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 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 : 0.008 0.346 17275 Z= 0.570 Angle : 0.824 11.650 24520 Z= 0.469 Chirality : 0.048 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 aren 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 covalent geometry : bond 0.00739 (17262) covalent geometry : angle 0.81652 (24504) SS BOND : bond 0.00284 ( 2) SS BOND : angle 0.83745 ( 4) hydrogen bonds : bond 0.12965 ( 858) hydrogen bonds : angle 5.59357 ( 2210) metal coordination : bond 0.01074 ( 8) metal coordination : angle 5.07934 ( 12) Misc. bond : bond 0.30713 ( 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 : 0.469 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 74 ILE cc_start: 0.8165 (mt) cc_final: 0.7964 (mt) REVERT: B 88 TYR cc_start: 0.6529 (m-80) cc_final: 0.6064 (m-10) REVERT: D 34 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7209 (mmtt) REVERT: D 95 GLN cc_start: 0.7759 (tt0) cc_final: 0.7466 (tt0) REVERT: H 39 ILE cc_start: 0.8379 (pt) cc_final: 0.7846 (tt) REVERT: H 54 ILE cc_start: 0.8631 (tt) cc_final: 0.8394 (tt) REVERT: K 173 MET cc_start: 0.4822 (mmp) cc_final: 0.2941 (ttp) REVERT: K 195 PHE cc_start: 0.6801 (p90) cc_final: 0.6496 (p90) REVERT: K 354 THR cc_start: 0.2865 (p) cc_final: 0.2056 (p) REVERT: L 72 MET cc_start: 0.3021 (pmm) cc_final: 0.2727 (ptt) outliers start: 8 outliers final: 0 residues processed: 456 average time/residue: 0.1700 time to fit residues: 105.9315 Evaluate side-chains 237 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 0.2980 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: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN 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 = 0.4125 r_free = 0.4125 target = 0.143395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111464 restraints weight = 45830.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.112297 restraints weight = 40045.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.112439 restraints weight = 33947.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.112796 restraints weight = 30535.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.112878 restraints weight = 27646.146| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3608 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3608 r_free = 0.3608 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3607 r_free = 0.3607 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17275 Z= 0.201 Angle : 0.738 9.379 24520 Z= 0.418 Chirality : 0.042 0.243 2736 Planarity : 0.006 0.092 2102 Dihedral : 28.649 152.789 4789 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.46 % Allowed : 4.07 % Favored : 95.47 % 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 aren not related in a simple way. whole: -0.77 (0.22), residues: 1277 helix: 0.63 (0.19), residues: 713 sheet: -1.50 (0.57), residues: 52 loop : -2.06 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 357 TYR 0.014 0.002 TYR E 54 PHE 0.024 0.002 PHE L 183 TRP 0.008 0.001 TRP K 264 HIS 0.009 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00442 (17262) covalent geometry : angle 0.73069 (24504) SS BOND : bond 0.00476 ( 2) SS BOND : angle 1.50396 ( 4) hydrogen bonds : bond 0.05133 ( 858) hydrogen bonds : angle 4.23015 ( 2210) metal coordination : bond 0.00634 ( 8) metal coordination : angle 4.74341 ( 12) Misc. bond : bond 0.00454 ( 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 306 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.489 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: symmetry clash REVERT: A 120 MET cc_start: 0.7662 (mtp) cc_final: 0.7433 (mtp) REVERT: B 88 TYR cc_start: 0.6799 (m-10) cc_final: 0.6334 (m-10) REVERT: B 96 THR cc_start: 0.8169 (m) cc_final: 0.7668 (p) REVERT: D 34 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7137 (mmtt) REVERT: E 54 TYR cc_start: 0.7195 (m-10) cc_final: 0.6965 (m-10) REVERT: F 61 PHE cc_start: 0.9190 (t80) cc_final: 0.8946 (t80) REVERT: F 88 TYR cc_start: 0.8529 (m-10) cc_final: 0.8081 (m-10) REVERT: H 39 ILE cc_start: 0.8374 (pt) cc_final: 0.8038 (tp) REVERT: K 77 LEU cc_start: 0.8114 (tp) cc_final: 0.7862 (mt) REVERT: K 100 MET cc_start: 0.5723 (ptt) cc_final: 0.5513 (ptt) REVERT: K 173 MET cc_start: 0.4090 (mmp) cc_final: 0.2356 (ttp) REVERT: K 186 LEU cc_start: 0.7435 (mt) cc_final: 0.7111 (pp) REVERT: K 283 SER cc_start: 0.4816 (t) cc_final: 0.4513 (p) REVERT: K 358 LEU cc_start: 0.6862 (mt) cc_final: 0.6036 (pp) REVERT: L 100 MET cc_start: 0.6425 (mmm) cc_final: 0.5217 (tpp) REVERT: L 187 ARG cc_start: 0.7733 (mpp80) cc_final: 0.7500 (mtp180) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.1351 time to fit residues: 59.9755 Evaluate side-chains 225 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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: 7.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS F 25 ASN G 33 HIS ** 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 262 GLN ** K 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.132915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.099486 restraints weight = 55239.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100648 restraints weight = 43451.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101103 restraints weight = 35670.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101284 restraints weight = 30222.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.101345 restraints weight = 28878.119| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 17275 Z= 0.328 Angle : 0.884 15.252 24520 Z= 0.490 Chirality : 0.048 0.249 2736 Planarity : 0.007 0.066 2102 Dihedral : 29.271 170.940 4789 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.56 % Allowed : 6.20 % Favored : 93.25 % 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 aren not related in a simple way. whole: -1.60 (0.21), residues: 1277 helix: -0.17 (0.18), residues: 712 sheet: -1.85 (0.65), residues: 49 loop : -2.22 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG F 23 TYR 0.026 0.003 TYR K 254 PHE 0.034 0.003 PHE G 27 TRP 0.018 0.002 TRP L 264 HIS 0.013 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00735 (17262) covalent geometry : angle 0.87659 (24504) SS BOND : bond 0.00185 ( 2) SS BOND : angle 1.37674 ( 4) hydrogen bonds : bond 0.06778 ( 858) hydrogen bonds : angle 4.81990 ( 2210) metal coordination : bond 0.00778 ( 8) metal coordination : angle 5.04314 ( 12) Misc. bond : bond 0.00097 ( 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 345 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 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: A 86 SER cc_start: 0.9138 (m) cc_final: 0.8791 (t) REVERT: A 94 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8007 (mm-30) REVERT: A 101 VAL cc_start: 0.9363 (t) cc_final: 0.9077 (p) REVERT: A 120 MET cc_start: 0.8621 (mtp) cc_final: 0.7988 (mtp) REVERT: A 122 LYS cc_start: 0.8998 (pttt) cc_final: 0.8609 (tttt) REVERT: A 126 LEU cc_start: 0.9521 (tp) cc_final: 0.9091 (tp) REVERT: B 29 ILE cc_start: 0.9410 (mm) cc_final: 0.9034 (mm) REVERT: B 36 ARG cc_start: 0.9066 (mtm-85) cc_final: 0.8857 (mtm110) REVERT: B 84 MET cc_start: 0.7733 (tpp) cc_final: 0.7379 (tpp) REVERT: B 88 TYR cc_start: 0.8333 (m-10) cc_final: 0.7824 (m-10) REVERT: C 71 ASN cc_start: 0.8188 (m-40) cc_final: 0.7880 (t0) REVERT: C 82 THR cc_start: 0.9639 (p) cc_final: 0.9303 (t) REVERT: C 87 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8661 (tp40) REVERT: D 34 LYS cc_start: 0.7895 (ptpt) cc_final: 0.7560 (mmtt) REVERT: D 41 VAL cc_start: 0.9335 (t) cc_final: 0.9062 (p) REVERT: D 51 ASP cc_start: 0.7443 (p0) cc_final: 0.7199 (p0) REVERT: E 39 HIS cc_start: 0.5403 (t-90) cc_final: 0.3800 (m-70) REVERT: E 45 THR cc_start: 0.6343 (t) cc_final: 0.6049 (m) REVERT: E 73 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7386 (tm-30) REVERT: E 94 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7896 (tp30) REVERT: E 96 SER cc_start: 0.9559 (m) cc_final: 0.9219 (t) REVERT: E 97 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8083 (mt-10) REVERT: E 113 HIS cc_start: 0.9266 (t70) cc_final: 0.8716 (t70) REVERT: E 120 MET cc_start: 0.8792 (mmm) cc_final: 0.8380 (mmm) REVERT: F 25 ASN cc_start: 0.8999 (m110) cc_final: 0.8571 (m-40) REVERT: F 88 TYR cc_start: 0.8290 (m-10) cc_final: 0.7748 (m-10) REVERT: F 96 THR cc_start: 0.9347 (m) cc_final: 0.8797 (p) REVERT: G 19 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.8335 (ttp-170) REVERT: H 47 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7831 (tm-30) REVERT: H 88 THR cc_start: 0.9245 (m) cc_final: 0.8880 (p) REVERT: H 93 GLU cc_start: 0.9156 (mp0) cc_final: 0.8745 (mp0) REVERT: K 100 MET cc_start: 0.5996 (ptt) cc_final: 0.5632 (ptt) REVERT: K 173 MET cc_start: 0.4456 (mmp) cc_final: 0.2059 (ttt) REVERT: K 188 MET cc_start: 0.4374 (pmm) cc_final: 0.4063 (pmm) REVERT: K 195 PHE cc_start: 0.7119 (p90) cc_final: 0.6683 (p90) REVERT: K 352 ARG cc_start: 0.8236 (ptm-80) cc_final: 0.7251 (ppt170) REVERT: L 89 LEU cc_start: 0.7885 (mp) cc_final: 0.7631 (mp) REVERT: L 100 MET cc_start: 0.6972 (mmm) cc_final: 0.5790 (tpp) REVERT: L 195 PHE cc_start: 0.8160 (p90) cc_final: 0.7955 (p90) REVERT: L 256 THR cc_start: 0.8142 (m) cc_final: 0.7761 (p) outliers start: 3 outliers final: 2 residues processed: 343 average time/residue: 0.1224 time to fit residues: 62.5389 Evaluate side-chains 248 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 9.9990 chunk 51 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN K 96 GLN K 181 HIS L 96 GLN L 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.136933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103663 restraints weight = 60734.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105198 restraints weight = 45931.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.105710 restraints weight = 37941.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.105838 restraints weight = 29148.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106079 restraints weight = 27637.620| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 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 = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.7530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17275 Z= 0.179 Angle : 0.694 8.547 24520 Z= 0.398 Chirality : 0.041 0.191 2736 Planarity : 0.008 0.291 2102 Dihedral : 29.025 168.871 4789 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.37 % Allowed : 2.78 % Favored : 96.85 % 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 aren not related in a simple way. whole: -0.94 (0.22), residues: 1277 helix: 0.52 (0.19), residues: 712 sheet: -1.70 (0.63), residues: 58 loop : -2.17 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 352 TYR 0.028 0.002 TYR D 40 PHE 0.016 0.002 PHE G 27 TRP 0.021 0.003 TRP K 218 HIS 0.006 0.001 HIS L 98 Details of bonding type rmsd covalent geometry : bond 0.00389 (17262) covalent geometry : angle 0.68842 (24504) SS BOND : bond 0.00227 ( 2) SS BOND : angle 1.63071 ( 4) hydrogen bonds : bond 0.04804 ( 858) hydrogen bonds : angle 4.10255 ( 2210) metal coordination : bond 0.00700 ( 8) metal coordination : angle 4.05851 ( 12) Misc. bond : bond 0.00815 ( 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 335 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 334 time to evaluate : 0.468 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 86 SER cc_start: 0.9052 (m) cc_final: 0.8721 (t) REVERT: A 94 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7903 (mm-30) REVERT: A 122 LYS cc_start: 0.8905 (pttt) cc_final: 0.8395 (tttt) REVERT: A 133 GLU cc_start: 0.8088 (pp20) cc_final: 0.7692 (pt0) REVERT: B 16 LYS cc_start: 0.5709 (pttp) cc_final: 0.5445 (tptm) REVERT: B 29 ILE cc_start: 0.9513 (mm) cc_final: 0.9177 (mm) REVERT: B 88 TYR cc_start: 0.7911 (m-10) cc_final: 0.7651 (m-10) REVERT: C 26 GLN cc_start: 0.8227 (mm110) cc_final: 0.7860 (mp10) REVERT: C 71 ASN cc_start: 0.8359 (m-40) cc_final: 0.8149 (t0) REVERT: C 87 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8616 (tp-100) REVERT: D 34 LYS cc_start: 0.7814 (ptpt) cc_final: 0.7530 (mmtt) REVERT: D 51 ASP cc_start: 0.7416 (p0) cc_final: 0.7192 (p0) REVERT: E 45 THR cc_start: 0.6207 (t) cc_final: 0.5880 (m) REVERT: E 87 SER cc_start: 0.9021 (p) cc_final: 0.8715 (t) REVERT: E 97 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8099 (mt-10) REVERT: E 120 MET cc_start: 0.8732 (mmm) cc_final: 0.8201 (mmm) REVERT: F 24 ASP cc_start: 0.8652 (p0) cc_final: 0.8310 (p0) REVERT: F 82 THR cc_start: 0.9330 (m) cc_final: 0.9122 (m) REVERT: H 59 MET cc_start: 0.8718 (tpp) cc_final: 0.8330 (tpp) REVERT: H 88 THR cc_start: 0.9289 (m) cc_final: 0.9030 (p) REVERT: K 173 MET cc_start: 0.4430 (mmp) cc_final: 0.2365 (ttt) REVERT: K 195 PHE cc_start: 0.6897 (p90) cc_final: 0.6516 (p90) REVERT: K 358 LEU cc_start: 0.7046 (mt) cc_final: 0.6078 (tt) REVERT: L 100 MET cc_start: 0.7035 (mmm) cc_final: 0.5793 (tpp) REVERT: L 183 PHE cc_start: 0.7413 (t80) cc_final: 0.7085 (t80) REVERT: L 242 LEU cc_start: 0.6939 (mt) cc_final: 0.6719 (mt) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.1230 time to fit residues: 60.6981 Evaluate side-chains 248 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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: 10.0000 chunk 141 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 147 optimal weight: 7.9990 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS K 80 ASN L 80 ASN L 98 HIS L 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.134586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.100993 restraints weight = 69811.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101812 restraints weight = 55057.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102562 restraints weight = 49594.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102825 restraints weight = 36335.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103284 restraints weight = 33087.825| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.8132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 17275 Z= 0.214 Angle : 0.716 10.691 24520 Z= 0.408 Chirality : 0.042 0.208 2736 Planarity : 0.007 0.239 2102 Dihedral : 29.026 173.447 4789 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.28 % Allowed : 2.59 % Favored : 97.13 % 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 aren not related in a simple way. whole: -0.89 (0.22), residues: 1277 helix: 0.52 (0.19), residues: 712 sheet: -1.92 (0.64), residues: 58 loop : -2.07 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 128 TYR 0.038 0.002 TYR H 40 PHE 0.035 0.002 PHE L 281 TRP 0.033 0.004 TRP K 218 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00480 (17262) covalent geometry : angle 0.71052 (24504) SS BOND : bond 0.00029 ( 2) SS BOND : angle 1.67801 ( 4) hydrogen bonds : bond 0.05078 ( 858) hydrogen bonds : angle 4.19727 ( 2210) metal coordination : bond 0.00727 ( 8) metal coordination : angle 4.11496 ( 12) Misc. bond : bond 0.00179 ( 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 302 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.384 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 77 ASP cc_start: 0.7470 (t0) cc_final: 0.6992 (t0) REVERT: A 86 SER cc_start: 0.9033 (m) cc_final: 0.8648 (t) REVERT: A 101 VAL cc_start: 0.9471 (t) cc_final: 0.9245 (p) REVERT: A 122 LYS cc_start: 0.9065 (pttt) cc_final: 0.8508 (tttt) REVERT: B 16 LYS cc_start: 0.6020 (pttp) cc_final: 0.5056 (tptp) REVERT: B 60 VAL cc_start: 0.9539 (t) cc_final: 0.9327 (t) REVERT: B 82 THR cc_start: 0.9407 (m) cc_final: 0.9113 (m) REVERT: C 57 ILE cc_start: 0.9660 (mm) cc_final: 0.9451 (tp) REVERT: C 87 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8625 (tp40) REVERT: D 34 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7516 (mmtt) REVERT: E 39 HIS cc_start: 0.5272 (t-90) cc_final: 0.4012 (m-70) REVERT: E 45 THR cc_start: 0.6277 (t) cc_final: 0.5952 (m) REVERT: E 73 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7437 (tm-30) REVERT: E 87 SER cc_start: 0.9060 (p) cc_final: 0.8712 (t) REVERT: E 120 MET cc_start: 0.8825 (mmm) cc_final: 0.8340 (mmm) REVERT: F 24 ASP cc_start: 0.8904 (p0) cc_final: 0.8353 (p0) REVERT: F 47 SER cc_start: 0.9348 (p) cc_final: 0.9055 (p) REVERT: F 82 THR cc_start: 0.9244 (m) cc_final: 0.9026 (m) REVERT: G 58 LEU cc_start: 0.9497 (mt) cc_final: 0.9262 (mt) REVERT: H 88 THR cc_start: 0.9290 (m) cc_final: 0.9082 (p) REVERT: H 95 GLN cc_start: 0.8569 (tt0) cc_final: 0.8243 (tt0) REVERT: K 173 MET cc_start: 0.4371 (mmp) cc_final: 0.2365 (ttt) REVERT: K 188 MET cc_start: 0.5428 (pmm) cc_final: 0.5060 (pmm) REVERT: K 195 PHE cc_start: 0.6994 (p90) cc_final: 0.6663 (p90) REVERT: K 349 TYR cc_start: 0.7656 (m-10) cc_final: 0.7251 (m-10) REVERT: K 358 LEU cc_start: 0.7071 (mt) cc_final: 0.6232 (tt) REVERT: L 100 MET cc_start: 0.6780 (mmm) cc_final: 0.5605 (tpp) REVERT: L 183 PHE cc_start: 0.7552 (t80) cc_final: 0.7064 (t80) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1138 time to fit residues: 51.8494 Evaluate side-chains 228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.9990 chunk 137 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN F 27 GLN K 80 ASN L 80 ASN L 181 HIS L 273 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.133602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100059 restraints weight = 59631.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.100631 restraints weight = 51359.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101349 restraints weight = 42191.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.101604 restraints weight = 33581.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.101710 restraints weight = 31452.640| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 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 = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17275 Z= 0.217 Angle : 0.723 14.727 24520 Z= 0.408 Chirality : 0.042 0.196 2736 Planarity : 0.009 0.364 2102 Dihedral : 29.072 174.110 4789 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.28 % Allowed : 2.68 % Favored : 97.04 % 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 aren not related in a simple way. whole: -0.91 (0.23), residues: 1277 helix: 0.53 (0.19), residues: 710 sheet: -2.02 (0.61), residues: 68 loop : -2.07 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 23 TYR 0.038 0.002 TYR H 40 PHE 0.015 0.002 PHE D 70 TRP 0.012 0.002 TRP K 264 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00490 (17262) covalent geometry : angle 0.71808 (24504) SS BOND : bond 0.00310 ( 2) SS BOND : angle 1.48482 ( 4) hydrogen bonds : bond 0.05027 ( 858) hydrogen bonds : angle 4.18081 ( 2210) metal coordination : bond 0.00667 ( 8) metal coordination : angle 3.60589 ( 12) Misc. bond : bond 0.00477 ( 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 296 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7757 (t0) cc_final: 0.7423 (t0) REVERT: A 86 SER cc_start: 0.9073 (m) cc_final: 0.8741 (t) REVERT: A 120 MET cc_start: 0.8595 (mtp) cc_final: 0.8270 (mtp) REVERT: A 122 LYS cc_start: 0.9093 (pttt) cc_final: 0.8448 (tttt) REVERT: B 16 LYS cc_start: 0.5293 (pttp) cc_final: 0.4627 (tptp) REVERT: B 88 TYR cc_start: 0.7880 (m-10) cc_final: 0.7344 (m-10) REVERT: C 25 LEU cc_start: 0.9050 (mm) cc_final: 0.8848 (mm) REVERT: C 87 GLN cc_start: 0.8958 (tp-100) cc_final: 0.8731 (tp40) REVERT: C 91 ARG cc_start: 0.9074 (mmp80) cc_final: 0.8727 (mmp80) REVERT: C 95 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 34 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7571 (mmtt) REVERT: D 45 LEU cc_start: 0.9469 (tp) cc_final: 0.9263 (tp) REVERT: D 93 GLU cc_start: 0.8924 (mp0) cc_final: 0.8617 (mp0) REVERT: D 106 LEU cc_start: 0.9456 (mt) cc_final: 0.9219 (mp) REVERT: E 39 HIS cc_start: 0.5370 (t-90) cc_final: 0.4285 (m-70) REVERT: E 45 THR cc_start: 0.6212 (t) cc_final: 0.5953 (m) REVERT: E 50 GLU cc_start: 0.8450 (tt0) cc_final: 0.8088 (tt0) REVERT: E 73 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7623 (tm-30) REVERT: E 83 ARG cc_start: 0.8450 (ttm170) cc_final: 0.8067 (mmt90) REVERT: E 87 SER cc_start: 0.9030 (p) cc_final: 0.8683 (t) REVERT: E 120 MET cc_start: 0.8905 (mmm) cc_final: 0.8237 (mmm) REVERT: F 47 SER cc_start: 0.9375 (p) cc_final: 0.9086 (p) REVERT: F 96 THR cc_start: 0.9194 (m) cc_final: 0.8859 (p) REVERT: H 71 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8266 (tp30) REVERT: H 85 LYS cc_start: 0.8281 (mttp) cc_final: 0.8009 (mmtt) REVERT: H 88 THR cc_start: 0.9339 (m) cc_final: 0.8921 (p) REVERT: H 93 GLU cc_start: 0.9068 (mp0) cc_final: 0.8806 (mp0) REVERT: K 173 MET cc_start: 0.4348 (mmp) cc_final: 0.2394 (ttt) REVERT: K 188 MET cc_start: 0.5431 (pmm) cc_final: 0.4808 (pmm) REVERT: K 195 PHE cc_start: 0.6944 (p90) cc_final: 0.6489 (p90) REVERT: K 354 THR cc_start: 0.4846 (p) cc_final: 0.4590 (p) REVERT: K 358 LEU cc_start: 0.7154 (mt) cc_final: 0.6323 (tt) REVERT: L 100 MET cc_start: 0.6869 (mmm) cc_final: 0.5769 (tpp) REVERT: L 241 MET cc_start: 0.5491 (ppp) cc_final: 0.5179 (ppp) REVERT: L 242 LEU cc_start: 0.7078 (mt) cc_final: 0.6863 (mt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1136 time to fit residues: 50.5078 Evaluate side-chains 225 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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: 20.0000 chunk 91 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 136 optimal weight: 30.0000 chunk 40 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN K 181 HIS L 80 ASN L 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.135557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.103091 restraints weight = 47145.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102821 restraints weight = 42144.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102837 restraints weight = 41255.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103148 restraints weight = 35228.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.103193 restraints weight = 34398.611| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3459 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3459 r_free = 0.3459 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3459 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.8929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 17275 Z= 0.186 Angle : 0.692 12.458 24520 Z= 0.393 Chirality : 0.040 0.209 2736 Planarity : 0.010 0.430 2102 Dihedral : 29.050 174.692 4789 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.28 % Allowed : 1.57 % Favored : 98.15 % 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 aren not related in a simple way. whole: -0.76 (0.23), residues: 1277 helix: 0.64 (0.19), residues: 714 sheet: -2.09 (0.60), residues: 68 loop : -1.98 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 23 TYR 0.035 0.002 TYR H 40 PHE 0.012 0.002 PHE D 70 TRP 0.034 0.004 TRP K 218 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00417 (17262) covalent geometry : angle 0.68918 (24504) SS BOND : bond 0.00309 ( 2) SS BOND : angle 1.46064 ( 4) hydrogen bonds : bond 0.04675 ( 858) hydrogen bonds : angle 4.07846 ( 2210) metal coordination : bond 0.00538 ( 8) metal coordination : angle 2.98488 ( 12) Misc. bond : bond 0.00430 ( 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 298 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.465 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 86 SER cc_start: 0.9088 (m) cc_final: 0.8755 (t) REVERT: A 122 LYS cc_start: 0.9106 (pttt) cc_final: 0.8451 (tttt) REVERT: A 133 GLU cc_start: 0.8080 (pt0) cc_final: 0.7878 (pt0) REVERT: B 16 LYS cc_start: 0.4912 (pttp) cc_final: 0.4396 (tptp) REVERT: C 25 LEU cc_start: 0.8849 (mm) cc_final: 0.8578 (mm) REVERT: C 87 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8630 (tp40) REVERT: C 95 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8282 (tm-30) REVERT: C 110 ILE cc_start: 0.8899 (mm) cc_final: 0.8647 (pt) REVERT: D 34 LYS cc_start: 0.7857 (ptpt) cc_final: 0.7524 (mmtt) REVERT: D 51 ASP cc_start: 0.7309 (p0) cc_final: 0.7058 (p0) REVERT: E 39 HIS cc_start: 0.5258 (t-90) cc_final: 0.4267 (m-70) REVERT: E 83 ARG cc_start: 0.8312 (ttm170) cc_final: 0.8042 (mmt90) REVERT: E 87 SER cc_start: 0.8994 (p) cc_final: 0.8664 (t) REVERT: F 82 THR cc_start: 0.9302 (m) cc_final: 0.9042 (m) REVERT: G 60 TYR cc_start: 0.9371 (t80) cc_final: 0.9097 (t80) REVERT: H 46 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8481 (mmmt) REVERT: H 85 LYS cc_start: 0.8160 (mttp) cc_final: 0.7928 (mmtt) REVERT: H 88 THR cc_start: 0.9298 (m) cc_final: 0.9087 (p) REVERT: K 173 MET cc_start: 0.4358 (mmp) cc_final: 0.2345 (ttt) REVERT: K 358 LEU cc_start: 0.6866 (mt) cc_final: 0.6164 (tt) REVERT: L 100 MET cc_start: 0.6811 (mmm) cc_final: 0.5815 (tpp) REVERT: L 241 MET cc_start: 0.5405 (ppp) cc_final: 0.5076 (ppp) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1145 time to fit residues: 51.3805 Evaluate side-chains 231 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 127 optimal weight: 40.0000 chunk 7 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 107 optimal weight: 0.0270 chunk 24 optimal weight: 10.0000 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS K 80 ASN K 181 HIS ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** 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 = 0.4052 r_free = 0.4052 target = 0.136768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.103144 restraints weight = 58713.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103617 restraints weight = 53930.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.104543 restraints weight = 46503.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.104548 restraints weight = 34964.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104830 restraints weight = 32348.394| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 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 = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.9193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17275 Z= 0.172 Angle : 0.685 11.718 24520 Z= 0.387 Chirality : 0.040 0.193 2736 Planarity : 0.006 0.188 2102 Dihedral : 29.008 175.579 4789 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.28 % Allowed : 1.30 % Favored : 98.43 % 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 aren not related in a simple way. whole: -0.72 (0.23), residues: 1277 helix: 0.70 (0.19), residues: 714 sheet: -2.06 (0.77), residues: 44 loop : -2.03 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 23 TYR 0.016 0.002 TYR D 40 PHE 0.021 0.002 PHE K 281 TRP 0.015 0.002 TRP L 264 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (17262) covalent geometry : angle 0.68236 (24504) SS BOND : bond 0.00245 ( 2) SS BOND : angle 1.37954 ( 4) hydrogen bonds : bond 0.04420 ( 858) hydrogen bonds : angle 3.99393 ( 2210) metal coordination : bond 0.00516 ( 8) metal coordination : angle 2.74977 ( 12) Misc. bond : bond 0.00487 ( 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 307 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9066 (m) cc_final: 0.8751 (t) REVERT: A 120 MET cc_start: 0.8507 (mtp) cc_final: 0.8175 (mtp) REVERT: A 122 LYS cc_start: 0.9118 (pttt) cc_final: 0.8388 (tttt) REVERT: A 133 GLU cc_start: 0.8167 (pt0) cc_final: 0.7964 (pt0) REVERT: B 16 LYS cc_start: 0.4791 (pttp) cc_final: 0.4141 (tttp) REVERT: B 82 THR cc_start: 0.9352 (m) cc_final: 0.9097 (m) REVERT: C 87 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8668 (tp40) REVERT: C 110 ILE cc_start: 0.8815 (mm) cc_final: 0.8584 (pt) REVERT: D 34 LYS cc_start: 0.7871 (ptpt) cc_final: 0.7587 (mmtt) REVERT: D 51 ASP cc_start: 0.7346 (p0) cc_final: 0.7111 (p0) REVERT: E 39 HIS cc_start: 0.5168 (t-90) cc_final: 0.4255 (m-70) REVERT: E 83 ARG cc_start: 0.8323 (ttm170) cc_final: 0.7805 (mmt90) REVERT: E 87 SER cc_start: 0.8979 (p) cc_final: 0.8647 (t) REVERT: E 94 GLU cc_start: 0.8242 (tp30) cc_final: 0.7727 (tp30) REVERT: E 133 GLU cc_start: 0.7718 (mp0) cc_final: 0.6944 (tp30) REVERT: G 60 TYR cc_start: 0.9331 (t80) cc_final: 0.8986 (t80) REVERT: G 87 GLN cc_start: 0.8872 (mm110) cc_final: 0.8462 (mm110) REVERT: H 46 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8435 (mmmt) REVERT: H 85 LYS cc_start: 0.8134 (mttp) cc_final: 0.7857 (mmtt) REVERT: H 88 THR cc_start: 0.9296 (m) cc_final: 0.8834 (p) REVERT: K 173 MET cc_start: 0.4258 (mmp) cc_final: 0.2159 (ttt) REVERT: K 188 MET cc_start: 0.5313 (pmm) cc_final: 0.4398 (pmm) REVERT: K 358 LEU cc_start: 0.6909 (mt) cc_final: 0.6222 (tt) REVERT: L 100 MET cc_start: 0.6763 (mmm) cc_final: 0.5490 (tpp) REVERT: L 182 VAL cc_start: 0.8976 (t) cc_final: 0.8734 (p) REVERT: L 241 MET cc_start: 0.5670 (ppp) cc_final: 0.5314 (ppp) REVERT: L 264 TRP cc_start: 0.8153 (t60) cc_final: 0.7572 (t60) outliers start: 0 outliers final: 0 residues processed: 307 average time/residue: 0.1128 time to fit residues: 51.2408 Evaluate side-chains 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 6.9990 chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 114 HIS K 80 ASN K 181 HIS ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN L 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.137275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.104067 restraints weight = 66187.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104962 restraints weight = 53073.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.105618 restraints weight = 45542.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.106017 restraints weight = 33346.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106228 restraints weight = 30721.859| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 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 = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.9387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17275 Z= 0.163 Angle : 0.673 11.552 24520 Z= 0.379 Chirality : 0.040 0.210 2736 Planarity : 0.005 0.166 2102 Dihedral : 28.903 175.965 4789 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.28 % Allowed : 0.74 % Favored : 98.98 % 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 aren not related in a simple way. whole: -0.70 (0.23), residues: 1277 helix: 0.69 (0.19), residues: 717 sheet: -2.13 (0.71), residues: 48 loop : -2.01 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 23 TYR 0.013 0.001 TYR D 40 PHE 0.015 0.002 PHE G 27 TRP 0.014 0.002 TRP K 264 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00361 (17262) covalent geometry : angle 0.67096 (24504) SS BOND : bond 0.00126 ( 2) SS BOND : angle 1.26074 ( 4) hydrogen bonds : bond 0.04213 ( 858) hydrogen bonds : angle 3.91119 ( 2210) metal coordination : bond 0.00461 ( 8) metal coordination : angle 2.47439 ( 12) Misc. bond : bond 0.00408 ( 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 294 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9134 (pttt) cc_final: 0.8383 (tttt) REVERT: A 133 GLU cc_start: 0.8219 (pt0) cc_final: 0.7979 (pt0) REVERT: B 16 LYS cc_start: 0.4649 (pttp) cc_final: 0.4089 (tttp) REVERT: B 82 THR cc_start: 0.9316 (m) cc_final: 0.8841 (m) REVERT: B 85 ASP cc_start: 0.8563 (m-30) cc_final: 0.8320 (m-30) REVERT: B 88 TYR cc_start: 0.7741 (m-10) cc_final: 0.7301 (m-10) REVERT: C 87 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8634 (tp40) REVERT: C 110 ILE cc_start: 0.8763 (mm) cc_final: 0.8497 (pt) REVERT: D 34 LYS cc_start: 0.7945 (ptpt) cc_final: 0.7655 (mmtt) REVERT: E 39 HIS cc_start: 0.5188 (t-90) cc_final: 0.4151 (m-70) REVERT: E 83 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7715 (mmt90) REVERT: E 87 SER cc_start: 0.8905 (p) cc_final: 0.8613 (t) REVERT: E 90 MET cc_start: 0.8225 (tpp) cc_final: 0.7982 (tpp) REVERT: E 94 GLU cc_start: 0.8183 (tp30) cc_final: 0.7612 (tp30) REVERT: E 133 GLU cc_start: 0.7591 (mp0) cc_final: 0.6955 (tp30) REVERT: F 35 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7968 (tpp80) REVERT: G 60 TYR cc_start: 0.9301 (t80) cc_final: 0.9059 (t80) REVERT: G 87 GLN cc_start: 0.8853 (mm110) cc_final: 0.8530 (mm110) REVERT: H 46 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8300 (mmmt) REVERT: H 85 LYS cc_start: 0.8053 (mttp) cc_final: 0.7802 (mmtt) REVERT: K 173 MET cc_start: 0.4356 (mmp) cc_final: 0.2283 (ttt) REVERT: K 188 MET cc_start: 0.5361 (pmm) cc_final: 0.4504 (pmm) REVERT: L 100 MET cc_start: 0.6701 (mmm) cc_final: 0.5384 (tpp) REVERT: L 183 PHE cc_start: 0.7454 (t80) cc_final: 0.7244 (t80) REVERT: L 241 MET cc_start: 0.5789 (ppp) cc_final: 0.5462 (ppp) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1005 time to fit residues: 45.0269 Evaluate side-chains 230 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 0.0050 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 139 optimal weight: 40.0000 chunk 102 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 25 ASN K 80 ASN K 181 HIS ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.102634 restraints weight = 65911.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102842 restraints weight = 57834.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.103655 restraints weight = 50293.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.104021 restraints weight = 35654.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.104255 restraints weight = 33396.815| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3474 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3474 r_free = 0.3474 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 = 0.3474 r_free = 0.3474 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3474 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.9576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17275 Z= 0.177 Angle : 0.683 11.209 24520 Z= 0.384 Chirality : 0.040 0.186 2736 Planarity : 0.005 0.151 2102 Dihedral : 28.924 176.951 4789 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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 aren not related in a simple way. whole: -0.65 (0.23), residues: 1277 helix: 0.73 (0.19), residues: 714 sheet: -2.08 (0.72), residues: 46 loop : -1.96 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 23 TYR 0.034 0.002 TYR H 40 PHE 0.015 0.002 PHE G 27 TRP 0.016 0.002 TRP K 264 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00399 (17262) covalent geometry : angle 0.68119 (24504) SS BOND : bond 0.00148 ( 2) SS BOND : angle 1.42165 ( 4) hydrogen bonds : bond 0.04341 ( 858) hydrogen bonds : angle 3.94496 ( 2210) metal coordination : bond 0.00467 ( 8) metal coordination : angle 2.34237 ( 12) Misc. bond : bond 0.00382 ( 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 280 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.391 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 120 MET cc_start: 0.8564 (mtp) cc_final: 0.8032 (mtp) REVERT: A 122 LYS cc_start: 0.9140 (pttt) cc_final: 0.8446 (tttt) REVERT: A 126 LEU cc_start: 0.9336 (tp) cc_final: 0.9048 (tp) REVERT: B 16 LYS cc_start: 0.4651 (pttp) cc_final: 0.4025 (tttp) REVERT: B 88 TYR cc_start: 0.7757 (m-10) cc_final: 0.7329 (m-10) REVERT: C 87 GLN cc_start: 0.8937 (tp-100) cc_final: 0.8651 (tp40) REVERT: D 34 LYS cc_start: 0.7855 (ptpt) cc_final: 0.7625 (mmtt) REVERT: E 39 HIS cc_start: 0.5192 (t-90) cc_final: 0.4238 (m-70) REVERT: E 81 ASP cc_start: 0.8133 (p0) cc_final: 0.7928 (p0) REVERT: E 83 ARG cc_start: 0.8340 (ttm170) cc_final: 0.8039 (mmt90) REVERT: E 87 SER cc_start: 0.9022 (p) cc_final: 0.8630 (t) REVERT: E 133 GLU cc_start: 0.7641 (mp0) cc_final: 0.6954 (tp30) REVERT: F 49 LEU cc_start: 0.9062 (pt) cc_final: 0.8149 (tt) REVERT: F 82 THR cc_start: 0.9267 (m) cc_final: 0.9029 (m) REVERT: G 87 GLN cc_start: 0.8800 (mm110) cc_final: 0.8456 (mm110) REVERT: H 59 MET cc_start: 0.8649 (tpp) cc_final: 0.8159 (tpp) REVERT: H 85 LYS cc_start: 0.8068 (mttp) cc_final: 0.7831 (mmtt) REVERT: K 173 MET cc_start: 0.4300 (mmp) cc_final: 0.2257 (ttt) REVERT: K 188 MET cc_start: 0.5339 (pmm) cc_final: 0.4500 (pmm) REVERT: L 100 MET cc_start: 0.6700 (mmm) cc_final: 0.5391 (tpp) REVERT: L 183 PHE cc_start: 0.7627 (t80) cc_final: 0.7274 (t80) REVERT: L 241 MET cc_start: 0.5792 (ppp) cc_final: 0.5472 (ppp) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.1064 time to fit residues: 45.5006 Evaluate side-chains 220 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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: 0.9990 chunk 8 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN E 108 ASN G 114 HIS K 80 ASN K 181 HIS ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 ASN L 181 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.138297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.105935 restraints weight = 53413.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.106080 restraints weight = 48151.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.106243 restraints weight = 41257.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.106682 restraints weight = 36645.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106723 restraints weight = 33445.954| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 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 = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.9682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17275 Z= 0.157 Angle : 0.674 10.667 24520 Z= 0.378 Chirality : 0.039 0.275 2736 Planarity : 0.006 0.158 2102 Dihedral : 28.815 175.784 4789 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.37 % Allowed : 0.65 % Favored : 98.98 % 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 aren not related in a simple way. whole: -0.54 (0.23), residues: 1277 helix: 0.83 (0.19), residues: 714 sheet: -2.24 (0.76), residues: 38 loop : -1.93 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 23 TYR 0.017 0.001 TYR C 60 PHE 0.019 0.001 PHE K 281 TRP 0.016 0.003 TRP K 264 HIS 0.008 0.001 HIS G 114 Details of bonding type rmsd covalent geometry : bond 0.00346 (17262) covalent geometry : angle 0.67268 (24504) SS BOND : bond 0.00156 ( 2) SS BOND : angle 1.29978 ( 4) hydrogen bonds : bond 0.04084 ( 858) hydrogen bonds : angle 3.85974 ( 2210) metal coordination : bond 0.00448 ( 8) metal coordination : angle 2.14161 ( 12) Misc. bond : bond 0.00344 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2312.92 seconds wall clock time: 40 minutes 49.96 seconds (2449.96 seconds total)