Starting phenix.real_space_refine on Fri Jul 3 20:03:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yrg_34055/07_2026/7yrg_34055.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 290 5.49 5 S 51 5.16 5 C 9376 2.51 5 N 3024 2.21 5 O 3634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16377 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "C" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 790 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 841 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 791 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 100} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ECX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 836 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 2056 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 259, 2051 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 252} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 2082 Chain: "L" Number of atoms: 1921 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 240, 1916 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 21 Conformer: "B" Number of residues, atoms: 240, 1916 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 4 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 21 bond proxies already assigned to first conformer: 1942 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13798 SG CYS K 275 34.989 21.023 55.188 1.00 81.78 S ATOM 14142 SG CYS K 319 32.495 18.444 53.871 1.00 86.30 S ATOM 14157 SG CYS K 321 36.070 17.784 53.089 1.00 93.19 S ATOM 14182 SG CYS K 324 34.891 17.744 56.692 1.00 91.94 S ATOM 15719 SG CYS L 275 79.466 77.873 56.063 1.00 81.78 S ATOM 16063 SG CYS L 319 81.952 80.476 54.778 1.00 86.30 S ATOM 16078 SG CYS L 321 78.374 81.144 54.021 1.00 93.19 S ATOM 16103 SG CYS L 324 79.567 81.128 57.619 1.00 91.94 S Time building chain proxies: 4.34, per 1000 atoms: 0.27 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: 1.33 Conformation dependent library (CDL) restraints added in 794.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 275 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 324 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 319 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 321 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 275 " Number of angles added : 12 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 15 sheets defined 55.7% alpha, 6.5% beta 136 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 2.95 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: 3.51 Time building geometry restraints manager: 1.87 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: 23780 2.33 - 4.66: 620 4.66 - 6.99: 72 6.99 - 9.32: 28 9.32 - 11.65: 4 Bond angle restraints: 24504 Sorted by residual: angle pdb=" C LEU L 361 " pdb=" N LYS L 362 " pdb=" CA LYS L 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" C LEU K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" N LYS L 356 " pdb=" CA LYS L 356 " pdb=" C LYS L 356 " ideal model delta sigma weight residual 111.14 118.03 -6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N LYS K 356 " pdb=" CA LYS K 356 " pdb=" C LYS K 356 " ideal model delta sigma weight residual 111.14 118.01 -6.87 1.08e+00 8.57e-01 4.05e+01 angle pdb=" N GLY F 9 " pdb=" CA GLY F 9 " pdb=" C GLY F 9 " ideal model delta sigma weight residual 112.49 119.26 -6.77 1.21e+00 6.83e-01 3.13e+01 ... (remaining 24499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 8031 31.24 - 62.49: 1669 62.49 - 93.73: 62 93.73 - 124.98: 1 124.98 - 156.22: 4 Dihedral angle restraints: 9767 sinusoidal: 5989 harmonic: 3778 Sorted by residual: dihedral pdb=" CB CYS K 279 " pdb=" SG CYS K 279 " pdb=" SG CYS K 305 " pdb=" CB CYS K 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.86 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS L 279 " pdb=" SG CYS L 279 " pdb=" SG CYS L 305 " pdb=" CB CYS L 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.84 50.84 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" C ECX F 20 " pdb=" N ECX F 20 " pdb=" CA ECX F 20 " pdb=" CB ECX F 20 " ideal model delta harmonic sigma weight residual -122.60 -108.05 -14.55 0 2.50e+00 1.60e-01 3.39e+01 ... (remaining 9764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2606 0.103 - 0.207: 120 0.207 - 0.310: 4 0.310 - 0.414: 2 0.414 - 0.517: 4 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CB VAL F 21 " pdb=" CA VAL F 21 " pdb=" CG1 VAL F 21 " pdb=" CG2 VAL F 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 2733 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 362 " 0.025 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS K 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS K 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS K 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 362 " 0.025 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C LYS L 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS L 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS L 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 21 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C VAL F 21 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL F 21 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU F 22 " 0.022 2.00e-02 2.50e+03 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.81: 11 1.81 - 2.58: 237 2.58 - 3.35: 19887 3.35 - 4.13: 45935 4.13 - 4.90: 74331 Nonbonded interactions: 140401 Sorted by model distance: nonbonded pdb=" OE2 GLU E 73 " pdb=" CG ARG F 23 " model vdw 1.035 3.440 nonbonded pdb=" O LEU C 117 " pdb=" NZ LYS F 44 " model vdw 1.189 3.120 nonbonded pdb=" OD1 ASP E 77 " pdb=" O LEU F 10 " model vdw 1.254 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 1.434 3.040 nonbonded pdb=" O SER E 57 " pdb=" NH2 ARG F 40 " model vdw 1.578 3.120 ... (remaining 140396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 118)) selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 62 through 135 or resid 137 through 152 or resid 171 throu \ gh 200 or resid 202 through 402)) selection = (chain 'L' and (resid 62 through 151 or (resid 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 through 200 or resid 202 through 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 22.080 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.346 17275 Z= 0.728 Angle : 0.920 11.650 24520 Z= 0.712 Chirality : 0.053 0.517 2736 Planarity : 0.006 0.073 2102 Dihedral : 25.617 156.219 7331 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 27.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.11 % Allowed : 1.20 % Favored : 97.69 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.22), residues: 1277 helix: 0.28 (0.19), residues: 704 sheet: -1.44 (0.48), residues: 80 loop : -2.33 (0.24), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 357 TYR 0.012 0.001 TYR G 60 PHE 0.013 0.002 PHE K 154 TRP 0.007 0.001 TRP K 264 HIS 0.011 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.61 (17262) covalent geometry : angle 0.91296 / 0.71 (24504) SS BOND : bond 0.00284 / 0.14 ( 2) SS BOND : angle 0.83745 / 0.43 ( 4) hydrogen bonds : bond 0.12965 / 8.55 ( 858) hydrogen bonds : angle 5.59357 / 4.12 ( 2210) metal coordination : bond 0.01074 / 0.45 ( 8) metal coordination : angle 5.07934 / 2.46 ( 12) Misc. bond : bond 0.30713 / 15.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2554 Ramachandran restraints generated. 1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 451 time to evaluate : 0.462 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: 0.7963 (mt) REVERT: B 88 TYR cc_start: 0.6529 (m-80) cc_final: 0.6065 (m-10) REVERT: D 34 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7211 (mmtt) REVERT: D 95 GLN cc_start: 0.7758 (tt0) cc_final: 0.7461 (tt0) REVERT: E 54 TYR cc_start: 0.6552 (m-80) cc_final: 0.6351 (m-10) REVERT: H 39 ILE cc_start: 0.8380 (pt) cc_final: 0.7851 (tt) REVERT: H 54 ILE cc_start: 0.8631 (tt) cc_final: 0.8395 (tt) REVERT: K 173 MET cc_start: 0.4822 (mmp) cc_final: 0.2934 (ttp) REVERT: K 195 PHE cc_start: 0.6802 (p90) cc_final: 0.6567 (p90) REVERT: K 354 THR cc_start: 0.2864 (p) cc_final: 0.2094 (p) REVERT: L 72 MET cc_start: 0.3021 (pmm) cc_final: 0.2723 (ptt) outliers start: 8 outliers final: 0 residues processed: 456 average time/residue: 0.1560 time to fit residues: 98.4168 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 : 0.448 ------------------------------------------------------------------------------- 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: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS L 96 GLN L 149 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.146369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.115979 restraints weight = 45940.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.117027 restraints weight = 38934.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.117223 restraints weight = 33021.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.117741 restraints weight = 29319.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.117653 restraints weight = 27702.694| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3690 r_free = 0.3690 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2876 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= 0.188 Angle : 0.796 10.660 24520 Z= 0.447 Chirality : 0.051 0.267 2736 Planarity : 0.006 0.104 2102 Dihedral : 29.224 151.025 4789 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.56 % Allowed : 3.33 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.22), residues: 1277 helix: 0.52 (0.19), residues: 711 sheet: -1.21 (0.52), residues: 66 loop : -2.34 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG K 244 TYR 0.022 0.002 TYR F 72 PHE 0.024 0.003 PHE L 183 TRP 0.004 0.001 TRP K 264 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (17262) covalent geometry : angle 0.78797 / 0.45 (24504) SS BOND : bond 0.00221 / 0.11 ( 2) SS BOND : angle 1.42666 / 0.80 ( 4) hydrogen bonds : bond 0.06344 / 4.17 ( 858) hydrogen bonds : angle 4.43182 / 3.19 ( 2210) metal coordination : bond 0.00676 / 0.30 ( 8) metal coordination : angle 5.13409 / 2.47 ( 12) Misc. bond : bond 0.01413 / 0.72 ( 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 298 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 296 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7155 (mtp) cc_final: 0.6860 (mtp) REVERT: D 34 LYS cc_start: 0.7571 (ptpt) cc_final: 0.7186 (mmtt) REVERT: F 61 PHE cc_start: 0.9111 (t80) cc_final: 0.8906 (t80) REVERT: G 68 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6425 (mt) REVERT: G 104 ILE cc_start: 0.8875 (mm) cc_final: 0.8651 (mm) REVERT: H 39 ILE cc_start: 0.8200 (pt) cc_final: 0.7821 (tt) REVERT: K 173 MET cc_start: 0.4358 (mmp) cc_final: 0.2396 (ttt) REVERT: K 273 HIS cc_start: 0.5892 (t70) cc_final: 0.5170 (t70) REVERT: K 283 SER cc_start: 0.4345 (t) cc_final: 0.3754 (p) REVERT: K 354 THR cc_start: 0.3428 (p) cc_final: 0.2606 (t) REVERT: L 89 LEU cc_start: 0.7664 (mp) cc_final: 0.7215 (mp) REVERT: L 100 MET cc_start: 0.6153 (mmm) cc_final: 0.5279 (tpp) REVERT: L 183 PHE cc_start: 0.6558 (m-80) cc_final: 0.6215 (m-80) outliers start: 2 outliers final: 1 residues processed: 297 average time/residue: 0.1247 time to fit residues: 54.8540 Evaluate side-chains 223 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 0.2980 chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 43 optimal weight: 30.0000 chunk 100 optimal weight: 9.9990 chunk 23 optimal weight: 40.0000 chunk 29 optimal weight: 30.0000 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.144270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113117 restraints weight = 57275.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.114414 restraints weight = 52227.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115046 restraints weight = 36247.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115018 restraints weight = 31183.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115055 restraints weight = 29673.247| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17275 Z= 0.206 Angle : 0.782 11.989 24520 Z= 0.444 Chirality : 0.050 0.328 2736 Planarity : 0.006 0.133 2102 Dihedral : 29.116 154.131 4789 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.46 % Allowed : 4.53 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.22), residues: 1277 helix: 0.37 (0.19), residues: 715 sheet: -1.44 (0.56), residues: 52 loop : -2.12 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG F 23 TYR 0.020 0.003 TYR L 254 PHE 0.024 0.002 PHE L 183 TRP 0.018 0.003 TRP L 264 HIS 0.011 0.001 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (17262) covalent geometry : angle 0.77679 / 0.44 (24504) SS BOND : bond 0.00144 / 0.07 ( 2) SS BOND : angle 1.38330 / 0.77 ( 4) hydrogen bonds : bond 0.05804 / 3.85 ( 858) hydrogen bonds : angle 4.39748 / 3.16 ( 2210) metal coordination : bond 0.00561 / 0.25 ( 8) metal coordination : angle 4.00392 / 1.89 ( 12) Misc. bond : bond 0.01156 / 0.55 ( 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 273 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 0.417 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 60 LEU cc_start: 0.7321 (mm) cc_final: 0.6905 (mm) REVERT: A 86 SER cc_start: 0.8306 (m) cc_final: 0.8101 (m) REVERT: A 122 LYS cc_start: 0.7704 (pttt) cc_final: 0.7439 (mttt) REVERT: D 34 LYS cc_start: 0.7509 (ptpt) cc_final: 0.7168 (mmtt) REVERT: F 24 ASP cc_start: 0.8280 (p0) cc_final: 0.7465 (p0) REVERT: F 88 TYR cc_start: 0.8434 (m-10) cc_final: 0.8106 (m-10) REVERT: H 39 ILE cc_start: 0.8447 (pt) cc_final: 0.8062 (tp) REVERT: K 173 MET cc_start: 0.4210 (mmp) cc_final: 0.2331 (ttp) REVERT: K 181 HIS cc_start: 0.3386 (t-170) cc_final: 0.3090 (t-170) REVERT: K 288 THR cc_start: 0.5576 (t) cc_final: 0.5356 (t) REVERT: K 358 LEU cc_start: 0.6447 (mt) cc_final: 0.5561 (pp) REVERT: L 100 MET cc_start: 0.6226 (mmm) cc_final: 0.5475 (tpp) REVERT: L 181 HIS cc_start: 0.5431 (t70) cc_final: 0.4624 (t70) REVERT: L 183 PHE cc_start: 0.6354 (m-80) cc_final: 0.5975 (m-80) REVERT: L 185 TYR cc_start: 0.5825 (m-10) cc_final: 0.5438 (m-10) REVERT: L 222 ASP cc_start: 0.4841 (p0) cc_final: 0.4283 (t0) outliers start: 1 outliers final: 1 residues processed: 272 average time/residue: 0.1222 time to fit residues: 50.1667 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 30.0000 chunk 152 optimal weight: 0.4980 chunk 120 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 0.0040 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 93 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS K 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.144703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113046 restraints weight = 61345.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.113873 restraints weight = 56468.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.114729 restraints weight = 41279.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.115041 restraints weight = 33805.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.115164 restraints weight = 33247.805| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17275 Z= 0.153 Angle : 0.708 9.314 24520 Z= 0.406 Chirality : 0.048 0.277 2736 Planarity : 0.006 0.126 2102 Dihedral : 29.104 157.625 4789 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.46 % Allowed : 2.50 % 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 are not related in a simple way. whole: -0.84 (0.22), residues: 1277 helix: 0.60 (0.19), residues: 716 sheet: -1.53 (0.57), residues: 52 loop : -2.17 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 23 TYR 0.025 0.002 TYR K 185 PHE 0.022 0.002 PHE G 27 TRP 0.013 0.002 TRP K 218 HIS 0.006 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (17262) covalent geometry : angle 0.70095 / 0.41 (24504) SS BOND : bond 0.00072 / 0.03 ( 2) SS BOND : angle 1.37889 / 0.75 ( 4) hydrogen bonds : bond 0.05026 / 3.35 ( 858) hydrogen bonds : angle 4.09393 / 2.93 ( 2210) metal coordination : bond 0.01084 / 0.53 ( 8) metal coordination : angle 4.59028 / 2.32 ( 12) Misc. bond : bond 0.00321 / 0.15 ( 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 269 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 0.437 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 60 LEU cc_start: 0.7190 (mm) cc_final: 0.6987 (mt) REVERT: B 96 THR cc_start: 0.7677 (m) cc_final: 0.7296 (p) REVERT: D 34 LYS cc_start: 0.7637 (ptpt) cc_final: 0.7230 (mmtt) REVERT: D 88 THR cc_start: 0.8821 (m) cc_final: 0.8601 (p) REVERT: F 24 ASP cc_start: 0.8362 (p0) cc_final: 0.7349 (p0) REVERT: F 84 MET cc_start: 0.7619 (tpp) cc_final: 0.7194 (tpp) REVERT: F 88 TYR cc_start: 0.8425 (m-10) cc_final: 0.8075 (m-10) REVERT: H 39 ILE cc_start: 0.8356 (pt) cc_final: 0.8001 (tp) REVERT: K 173 MET cc_start: 0.4241 (mmp) cc_final: 0.2366 (ttp) REVERT: L 100 MET cc_start: 0.6553 (mmm) cc_final: 0.5711 (tpp) REVERT: L 183 PHE cc_start: 0.6488 (m-80) cc_final: 0.6106 (m-80) REVERT: L 242 LEU cc_start: 0.6986 (mt) cc_final: 0.6759 (mt) outliers start: 1 outliers final: 1 residues processed: 268 average time/residue: 0.1171 time to fit residues: 47.6705 Evaluate side-chains 203 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 0.9980 chunk 141 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 155 optimal weight: 30.0000 chunk 37 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 24 optimal weight: 50.0000 chunk 118 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 76 GLN F 18 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS L 221 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.140318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107535 restraints weight = 68120.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108306 restraints weight = 62127.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109173 restraints weight = 49607.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.109572 restraints weight = 38929.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109710 restraints weight = 35927.430| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17275 Z= 0.206 Angle : 0.785 11.556 24520 Z= 0.437 Chirality : 0.049 0.288 2736 Planarity : 0.007 0.089 2102 Dihedral : 29.204 161.555 4789 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.37 % Allowed : 3.52 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.22), residues: 1277 helix: 0.33 (0.19), residues: 717 sheet: -1.95 (0.63), residues: 38 loop : -2.04 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 19 TYR 0.040 0.002 TYR G 60 PHE 0.046 0.003 PHE L 281 TRP 0.013 0.003 TRP K 218 HIS 0.011 0.002 HIS K 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (17262) covalent geometry : angle 0.77755 / 0.44 (24504) SS BOND : bond 0.00110 / 0.06 ( 2) SS BOND : angle 1.69178 / 0.90 ( 4) hydrogen bonds : bond 0.05809 / 3.87 ( 858) hydrogen bonds : angle 4.26735 / 3.10 ( 2210) metal coordination : bond 0.02340 / 0.91 ( 8) metal coordination : angle 4.74311 / 2.37 ( 12) Misc. bond : bond 0.00140 / 0.07 ( 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 279 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7160 (pp20) cc_final: 0.6875 (pp20) REVERT: A 60 LEU cc_start: 0.7564 (mm) cc_final: 0.7189 (mm) REVERT: A 126 LEU cc_start: 0.8704 (tp) cc_final: 0.8500 (tp) REVERT: B 96 THR cc_start: 0.8389 (m) cc_final: 0.8126 (p) REVERT: D 34 LYS cc_start: 0.7762 (ptpt) cc_final: 0.7267 (mmtt) REVERT: D 120 LYS cc_start: 0.7505 (mttt) cc_final: 0.6966 (tptp) REVERT: F 74 GLU cc_start: 0.8545 (tt0) cc_final: 0.8140 (tt0) REVERT: K 173 MET cc_start: 0.4400 (mmp) cc_final: 0.2410 (ttp) REVERT: K 188 MET cc_start: 0.4450 (pmm) cc_final: 0.4108 (pmm) REVERT: K 309 ASP cc_start: 0.5767 (m-30) cc_final: 0.5564 (m-30) REVERT: K 354 THR cc_start: 0.4209 (p) cc_final: 0.3927 (p) REVERT: K 358 LEU cc_start: 0.6783 (mt) cc_final: 0.5983 (tt) REVERT: L 72 MET cc_start: 0.3360 (ptp) cc_final: 0.3084 (ptp) REVERT: L 100 MET cc_start: 0.6482 (mmm) cc_final: 0.5179 (tpp) REVERT: L 183 PHE cc_start: 0.6371 (m-80) cc_final: 0.6059 (m-80) REVERT: L 242 LEU cc_start: 0.7074 (mt) cc_final: 0.6854 (mt) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.1152 time to fit residues: 48.4303 Evaluate side-chains 205 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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: 4.9990 chunk 137 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 45 optimal weight: 40.0000 chunk 136 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 76 GLN F 25 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 ASN K 181 HIS K 273 HIS L 98 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.140522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.107410 restraints weight = 57986.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.108832 restraints weight = 50090.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.109392 restraints weight = 37460.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109681 restraints weight = 32762.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109708 restraints weight = 31708.068| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3557 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3557 r_free = 0.3557 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3557 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17275 Z= 0.172 Angle : 0.726 9.755 24520 Z= 0.409 Chirality : 0.048 0.293 2736 Planarity : 0.005 0.068 2102 Dihedral : 29.177 162.319 4789 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.28 % Allowed : 2.04 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.22), residues: 1277 helix: 0.55 (0.19), residues: 716 sheet: -1.86 (0.66), residues: 48 loop : -2.10 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 116 TYR 0.039 0.002 TYR H 40 PHE 0.028 0.002 PHE K 281 TRP 0.027 0.003 TRP K 218 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (17262) covalent geometry : angle 0.71931 / 0.41 (24504) SS BOND : bond 0.00189 / 0.09 ( 2) SS BOND : angle 1.50481 / 0.78 ( 4) hydrogen bonds : bond 0.04960 / 3.31 ( 858) hydrogen bonds : angle 4.06428 / 2.93 ( 2210) metal coordination : bond 0.00804 / 0.31 ( 8) metal coordination : angle 4.40307 / 1.97 ( 12) Misc. bond : bond 0.00863 / 0.41 ( 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 269 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.410 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: B 16 LYS cc_start: 0.5611 (pttp) cc_final: 0.5391 (pttp) REVERT: B 29 ILE cc_start: 0.8772 (mm) cc_final: 0.8512 (mm) REVERT: D 34 LYS cc_start: 0.7842 (ptpt) cc_final: 0.7321 (mmtt) REVERT: D 120 LYS cc_start: 0.7413 (mttt) cc_final: 0.6856 (tptp) REVERT: E 45 THR cc_start: 0.5075 (t) cc_final: 0.4773 (m) REVERT: E 50 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7627 (mt-10) REVERT: F 24 ASP cc_start: 0.8351 (p0) cc_final: 0.7831 (p0) REVERT: H 68 ASP cc_start: 0.9166 (t70) cc_final: 0.8840 (t0) REVERT: H 88 THR cc_start: 0.8617 (m) cc_final: 0.8378 (p) REVERT: K 77 LEU cc_start: 0.7649 (mt) cc_final: 0.7405 (mt) REVERT: K 173 MET cc_start: 0.4258 (mmp) cc_final: 0.2366 (ttp) REVERT: K 195 PHE cc_start: 0.6809 (p90) cc_final: 0.6405 (p90) REVERT: K 358 LEU cc_start: 0.6667 (mt) cc_final: 0.5904 (pp) REVERT: L 100 MET cc_start: 0.6731 (mmm) cc_final: 0.5426 (tpp) REVERT: L 183 PHE cc_start: 0.6466 (m-80) cc_final: 0.6199 (m-80) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.1075 time to fit residues: 43.9818 Evaluate side-chains 217 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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: 0.4980 chunk 91 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 27 optimal weight: 40.0000 chunk 118 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 0.0570 chunk 136 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN G 114 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.140861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109650 restraints weight = 45544.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109822 restraints weight = 36354.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.109720 restraints weight = 32470.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109924 restraints weight = 30550.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.109963 restraints weight = 28934.504| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17275 Z= 0.157 Angle : 0.700 9.839 24520 Z= 0.398 Chirality : 0.047 0.285 2736 Planarity : 0.006 0.192 2102 Dihedral : 29.163 163.029 4789 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.28 % Allowed : 0.46 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.22), residues: 1277 helix: 0.70 (0.19), residues: 716 sheet: -1.83 (0.66), residues: 48 loop : -2.13 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 23 TYR 0.040 0.002 TYR D 40 PHE 0.025 0.002 PHE G 27 TRP 0.020 0.004 TRP K 218 HIS 0.004 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (17262) covalent geometry : angle 0.69405 / 0.40 (24504) SS BOND : bond 0.00079 / 0.04 ( 2) SS BOND : angle 1.24607 / 0.70 ( 4) hydrogen bonds : bond 0.04826 / 3.24 ( 858) hydrogen bonds : angle 4.03838 / 2.90 ( 2210) metal coordination : bond 0.00625 / 0.27 ( 8) metal coordination : angle 3.97272 / 1.79 ( 12) Misc. bond : bond 0.00373 / 0.18 ( 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 270 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.475 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 126 LEU cc_start: 0.9089 (tp) cc_final: 0.8767 (tp) REVERT: B 29 ILE cc_start: 0.8813 (mm) cc_final: 0.8603 (mm) REVERT: C 95 GLU cc_start: 0.4866 (pp20) cc_final: 0.4042 (pp20) REVERT: D 34 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7182 (mmtt) REVERT: D 36 SER cc_start: 0.8430 (p) cc_final: 0.8122 (m) REVERT: D 71 GLU cc_start: 0.7683 (tt0) cc_final: 0.7480 (tt0) REVERT: D 120 LYS cc_start: 0.7505 (mttt) cc_final: 0.6878 (tptp) REVERT: E 50 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7666 (mt-10) REVERT: F 24 ASP cc_start: 0.8565 (p0) cc_final: 0.7911 (p0) REVERT: H 68 ASP cc_start: 0.9000 (t70) cc_final: 0.8769 (t0) REVERT: K 77 LEU cc_start: 0.7632 (mt) cc_final: 0.7387 (mt) REVERT: K 100 MET cc_start: 0.5503 (ptt) cc_final: 0.5113 (mtm) REVERT: K 173 MET cc_start: 0.4320 (mmp) cc_final: 0.2449 (ttp) REVERT: K 188 MET cc_start: 0.4749 (pmm) cc_final: 0.4539 (pmm) REVERT: K 195 PHE cc_start: 0.6873 (p90) cc_final: 0.6550 (p90) REVERT: K 358 LEU cc_start: 0.6563 (mt) cc_final: 0.5922 (pp) REVERT: L 72 MET cc_start: 0.3323 (ptp) cc_final: 0.3039 (ptp) REVERT: L 100 MET cc_start: 0.6659 (mmm) cc_final: 0.5340 (tpp) REVERT: L 183 PHE cc_start: 0.6394 (m-80) cc_final: 0.6146 (m-80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1109 time to fit residues: 45.8243 Evaluate side-chains 213 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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: 40.0000 chunk 16 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 123 optimal weight: 0.0770 chunk 121 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 107 optimal weight: 0.6980 chunk 24 optimal weight: 50.0000 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 HIS L 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.140270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108944 restraints weight = 57696.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.108918 restraints weight = 51865.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109195 restraints weight = 45140.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109660 restraints weight = 38331.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109858 restraints weight = 35064.724| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17275 Z= 0.164 Angle : 0.709 9.877 24520 Z= 0.402 Chirality : 0.047 0.284 2736 Planarity : 0.005 0.096 2102 Dihedral : 29.153 164.230 4789 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.37 % Allowed : 1.20 % 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 are not related in a simple way. whole: -0.80 (0.22), residues: 1277 helix: 0.65 (0.19), residues: 718 sheet: -1.62 (0.59), residues: 62 loop : -2.17 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 23 TYR 0.026 0.002 TYR D 40 PHE 0.035 0.002 PHE L 281 TRP 0.039 0.005 TRP K 218 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (17262) covalent geometry : angle 0.70504 / 0.40 (24504) SS BOND : bond 0.00030 / 0.01 ( 2) SS BOND : angle 1.42196 / 0.74 ( 4) hydrogen bonds : bond 0.04797 / 3.23 ( 858) hydrogen bonds : angle 4.01496 / 2.88 ( 2210) metal coordination : bond 0.00575 / 0.25 ( 8) metal coordination : angle 3.52517 / 1.54 ( 12) Misc. bond : bond 0.00366 / 0.17 ( 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 275 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.470 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 86 SER cc_start: 0.8787 (m) cc_final: 0.8289 (t) REVERT: A 126 LEU cc_start: 0.9059 (tp) cc_final: 0.8826 (tp) REVERT: B 29 ILE cc_start: 0.9046 (mm) cc_final: 0.8775 (mm) REVERT: C 27 PHE cc_start: 0.8805 (m-80) cc_final: 0.8480 (m-80) REVERT: C 53 TYR cc_start: 0.9207 (t80) cc_final: 0.8745 (t80) REVERT: D 34 LYS cc_start: 0.7734 (ptpt) cc_final: 0.7161 (mmtt) REVERT: D 36 SER cc_start: 0.8518 (p) cc_final: 0.8282 (m) REVERT: D 120 LYS cc_start: 0.7617 (mttt) cc_final: 0.6853 (tptp) REVERT: E 50 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7740 (mt-10) REVERT: F 24 ASP cc_start: 0.8612 (p0) cc_final: 0.8051 (p0) REVERT: F 74 GLU cc_start: 0.8459 (tt0) cc_final: 0.8204 (tt0) REVERT: H 68 ASP cc_start: 0.9008 (t70) cc_final: 0.8805 (t0) REVERT: K 77 LEU cc_start: 0.7641 (mt) cc_final: 0.7441 (mt) REVERT: K 173 MET cc_start: 0.4314 (mmp) cc_final: 0.2463 (ttp) REVERT: K 188 MET cc_start: 0.4892 (pmm) cc_final: 0.4662 (pmm) REVERT: K 195 PHE cc_start: 0.6811 (p90) cc_final: 0.6439 (p90) REVERT: K 358 LEU cc_start: 0.6736 (mt) cc_final: 0.6053 (pp) REVERT: L 72 MET cc_start: 0.3050 (ptp) cc_final: 0.2798 (ptp) REVERT: L 100 MET cc_start: 0.6665 (mmm) cc_final: 0.5443 (tpp) REVERT: L 183 PHE cc_start: 0.6393 (m-80) cc_final: 0.6144 (m-80) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.1207 time to fit residues: 50.2031 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.1980 chunk 6 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 34 optimal weight: 40.0000 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.139688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.108090 restraints weight = 65367.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108052 restraints weight = 77206.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109326 restraints weight = 57947.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109758 restraints weight = 43855.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.109922 restraints weight = 40654.520| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17275 Z= 0.165 Angle : 0.729 13.438 24520 Z= 0.409 Chirality : 0.047 0.284 2736 Planarity : 0.009 0.327 2102 Dihedral : 29.171 165.213 4789 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.37 % Allowed : 0.19 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.22), residues: 1277 helix: 0.63 (0.19), residues: 718 sheet: -1.55 (0.66), residues: 52 loop : -2.21 (0.24), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 352 TYR 0.030 0.002 TYR H 40 PHE 0.027 0.002 PHE G 27 TRP 0.054 0.005 TRP L 264 HIS 0.006 0.001 HIS L 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (17262) covalent geometry : angle 0.72507 / 0.41 (24504) SS BOND : bond 0.00191 / 0.09 ( 2) SS BOND : angle 1.53740 / 0.80 ( 4) hydrogen bonds : bond 0.04833 / 3.24 ( 858) hydrogen bonds : angle 4.05157 / 2.91 ( 2210) metal coordination : bond 0.00490 / 0.21 ( 8) metal coordination : angle 3.24764 / 1.41 ( 12) Misc. bond : bond 0.00786 / 0.38 ( 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 275 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8810 (m) cc_final: 0.8407 (t) REVERT: A 126 LEU cc_start: 0.9123 (tp) cc_final: 0.8873 (tp) REVERT: B 16 LYS cc_start: 0.5546 (pttp) cc_final: 0.4297 (tttm) REVERT: B 18 HIS cc_start: 0.4333 (t70) cc_final: 0.3923 (t70) REVERT: B 29 ILE cc_start: 0.9064 (mm) cc_final: 0.8804 (mm) REVERT: B 36 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8500 (mtm110) REVERT: D 34 LYS cc_start: 0.7735 (ptpt) cc_final: 0.7174 (mmtt) REVERT: D 120 LYS cc_start: 0.7644 (mttt) cc_final: 0.6889 (tptp) REVERT: E 76 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: E 94 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7779 (tp30) REVERT: F 59 LYS cc_start: 0.9245 (ttmt) cc_final: 0.8968 (tttt) REVERT: G 94 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7076 (tm-30) REVERT: K 173 MET cc_start: 0.4282 (mmp) cc_final: 0.2272 (ttt) REVERT: K 188 MET cc_start: 0.4920 (pmm) cc_final: 0.4588 (pmm) REVERT: K 195 PHE cc_start: 0.6830 (p90) cc_final: 0.6425 (p90) REVERT: K 358 LEU cc_start: 0.6627 (mt) cc_final: 0.6085 (tt) REVERT: L 72 MET cc_start: 0.3078 (ptp) cc_final: 0.2803 (ptp) REVERT: L 100 MET cc_start: 0.6592 (mmm) cc_final: 0.5382 (tpp) REVERT: L 183 PHE cc_start: 0.6244 (m-80) cc_final: 0.5978 (m-80) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.1140 time to fit residues: 48.2502 Evaluate side-chains 220 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 30.0000 chunk 72 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 128 optimal weight: 0.1980 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.141075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108098 restraints weight = 59196.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109641 restraints weight = 47900.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110338 restraints weight = 34572.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110537 restraints weight = 30262.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110659 restraints weight = 29300.015| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3571 r_free = 0.3571 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17275 Z= 0.146 Angle : 0.703 13.645 24520 Z= 0.396 Chirality : 0.046 0.278 2736 Planarity : 0.011 0.445 2102 Dihedral : 29.174 165.647 4789 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.28 % Allowed : 0.37 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1277 helix: 0.68 (0.19), residues: 719 sheet: -1.49 (0.67), residues: 52 loop : -2.17 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG F 23 TYR 0.027 0.002 TYR G 60 PHE 0.027 0.002 PHE G 27 TRP 0.031 0.004 TRP L 264 HIS 0.006 0.001 HIS K 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (17262) covalent geometry : angle 0.69768 / 0.40 (24504) SS BOND : bond 0.00140 / 0.07 ( 2) SS BOND : angle 1.52753 / 0.78 ( 4) hydrogen bonds : bond 0.04591 / 3.08 ( 858) hydrogen bonds : angle 3.95841 / 2.82 ( 2210) metal coordination : bond 0.00900 / 0.43 ( 8) metal coordination : angle 3.93450 / 1.67 ( 12) Misc. bond : bond 0.00310 / 0.15 ( 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 271 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 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: 0.8813 (m) cc_final: 0.8385 (t) REVERT: B 16 LYS cc_start: 0.5384 (pttp) cc_final: 0.4260 (tttm) REVERT: B 18 HIS cc_start: 0.4493 (t70) cc_final: 0.3947 (t70) REVERT: B 36 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.8573 (mtm110) REVERT: C 26 GLN cc_start: 0.8055 (mm110) cc_final: 0.7854 (mp10) REVERT: C 52 VAL cc_start: 0.9318 (m) cc_final: 0.9031 (p) REVERT: D 34 LYS cc_start: 0.7705 (ptpt) cc_final: 0.7178 (mmtt) REVERT: D 120 LYS cc_start: 0.7641 (mttt) cc_final: 0.6884 (tptp) REVERT: E 50 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7839 (mt-10) REVERT: E 94 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7831 (tp30) REVERT: G 21 GLN cc_start: 0.8281 (pt0) cc_final: 0.7875 (pp30) REVERT: G 93 ASP cc_start: 0.8227 (p0) cc_final: 0.8001 (p0) REVERT: K 173 MET cc_start: 0.4288 (mmp) cc_final: 0.2309 (ttt) REVERT: K 195 PHE cc_start: 0.6887 (p90) cc_final: 0.6465 (p90) REVERT: K 358 LEU cc_start: 0.6616 (mt) cc_final: 0.6161 (tt) REVERT: L 72 MET cc_start: 0.3198 (ptp) cc_final: 0.2931 (ptp) REVERT: L 100 MET cc_start: 0.6585 (mmm) cc_final: 0.5388 (tpp) REVERT: L 183 PHE cc_start: 0.6362 (m-80) cc_final: 0.6050 (m-80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.1114 time to fit residues: 46.4657 Evaluate side-chains 221 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 0.8980 chunk 117 optimal weight: 30.0000 chunk 153 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 138 optimal weight: 0.8980 chunk 152 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 chunk 25 optimal weight: 40.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS F 93 GLN G 21 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.139757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.107258 restraints weight = 51543.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.107983 restraints weight = 45799.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.108242 restraints weight = 37691.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.108562 restraints weight = 34020.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.108715 restraints weight = 30736.020| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17275 Z= 0.159 Angle : 0.705 12.111 24520 Z= 0.397 Chirality : 0.047 0.277 2736 Planarity : 0.009 0.366 2102 Dihedral : 29.208 166.884 4789 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.28 % Allowed : 0.46 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1277 helix: 0.59 (0.19), residues: 719 sheet: -1.59 (0.66), residues: 52 loop : -2.16 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 23 TYR 0.016 0.002 TYR K 254 PHE 0.020 0.002 PHE G 27 TRP 0.031 0.004 TRP L 264 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (17262) covalent geometry : angle 0.70216 / 0.40 (24504) SS BOND : bond 0.00020 / 0.01 ( 2) SS BOND : angle 1.42194 / 0.77 ( 4) hydrogen bonds : bond 0.04706 / 3.16 ( 858) hydrogen bonds : angle 3.97668 / 2.83 ( 2210) metal coordination : bond 0.00412 / 0.17 ( 8) metal coordination : angle 2.98443 / 1.28 ( 12) Misc. bond : bond 0.00571 / 0.27 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.54 seconds wall clock time: 43 minutes 44.70 seconds (2624.70 seconds total)