Starting phenix.real_space_refine on Tue Dec 31 14:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yrg_34055/12_2024/7yrg_34055.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yrg_34055/12_2024/7yrg_34055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yrg_34055/12_2024/7yrg_34055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yrg_34055/12_2024/7yrg_34055.map" model { file = "/net/cci-nas-00/data/ceres_data/7yrg_34055/12_2024/7yrg_34055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yrg_34055/12_2024/7yrg_34055.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLU:plan': 4, 'ARG:plan': 2, '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: {'GLU:plan': 4, 'ARG:plan': 1} 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: {'GLU:plan': 4, 'ARG:plan': 1} 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: 11.98, per 1000 atoms: 0.73 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: 4.62 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 7.84 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: 7.97 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1981 1.29 - 1.42: 5694 1.42 - 1.55: 8914 1.55 - 1.68: 594 1.68 - 1.81: 79 Bond restraints: 17262 Sorted by residual: bond pdb=" N ARG K 357 " pdb=" CA ARG K 357 " ideal model delta sigma weight residual 1.459 1.344 0.115 1.23e-02 6.61e+03 8.71e+01 bond pdb=" N ARG L 357 " pdb=" CA ARG L 357 " ideal model delta sigma weight residual 1.459 1.345 0.115 1.23e-02 6.61e+03 8.67e+01 bond pdb=" CA LYS L 362 " pdb=" C LYS L 362 " ideal model delta sigma weight residual 1.524 1.639 -0.115 1.27e-02 6.20e+03 8.19e+01 bond pdb=" CA LYS K 362 " pdb=" C LYS K 362 " ideal model delta sigma weight residual 1.524 1.638 -0.115 1.27e-02 6.20e+03 8.14e+01 bond pdb=" CA LEU L 358 " pdb=" C LEU L 358 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.35e-02 5.49e+03 6.05e+01 ... (remaining 17257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 24014 2.33 - 4.66: 395 4.66 - 6.99: 63 6.99 - 9.32: 28 9.32 - 11.65: 4 Bond angle restraints: 24504 Sorted by residual: angle pdb=" C LEU L 361 " pdb=" N LYS L 362 " pdb=" CA LYS L 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" C LEU K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta sigma weight residual 120.44 111.16 9.28 1.30e+00 5.92e-01 5.09e+01 angle pdb=" N LYS L 356 " pdb=" CA LYS L 356 " pdb=" C LYS L 356 " ideal model delta sigma weight residual 111.14 118.03 -6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" N LYS K 356 " pdb=" CA LYS K 356 " pdb=" C LYS K 356 " ideal model delta sigma weight residual 111.14 118.01 -6.87 1.08e+00 8.57e-01 4.05e+01 angle pdb=" N GLY F 9 " pdb=" CA GLY F 9 " pdb=" C GLY F 9 " ideal model delta sigma weight residual 112.49 119.26 -6.77 1.21e+00 6.83e-01 3.13e+01 ... (remaining 24499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 8031 31.24 - 62.49: 1669 62.49 - 93.73: 62 93.73 - 124.98: 1 124.98 - 156.22: 4 Dihedral angle restraints: 9767 sinusoidal: 5989 harmonic: 3778 Sorted by residual: dihedral pdb=" CB CYS K 279 " pdb=" SG CYS K 279 " pdb=" SG CYS K 305 " pdb=" CB CYS K 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.86 50.86 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS L 279 " pdb=" SG CYS L 279 " pdb=" SG CYS L 305 " pdb=" CB CYS L 305 " ideal model delta sinusoidal sigma weight residual -86.00 -136.84 50.84 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" C ECX F 20 " pdb=" N ECX F 20 " pdb=" CA ECX F 20 " pdb=" CB ECX F 20 " ideal model delta harmonic sigma weight residual -122.60 -108.05 -14.55 0 2.50e+00 1.60e-01 3.39e+01 ... (remaining 9764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2641 0.103 - 0.207: 85 0.207 - 0.310: 4 0.310 - 0.414: 2 0.414 - 0.517: 4 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA VAL F 21 " pdb=" N VAL F 21 " pdb=" C VAL F 21 " pdb=" CB VAL F 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA VAL B 21 " pdb=" N VAL B 21 " pdb=" C VAL B 21 " pdb=" CB VAL B 21 " both_signs ideal model delta sigma weight residual False 2.44 1.92 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CB VAL F 21 " pdb=" CA VAL F 21 " pdb=" CG1 VAL F 21 " pdb=" CG2 VAL F 21 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 2733 not shown) Planarity restraints: 2102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 362 " 0.025 2.00e-02 2.50e+03 5.33e-02 2.84e+01 pdb=" C LYS K 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS K 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS K 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 362 " 0.025 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C LYS L 362 " -0.092 2.00e-02 2.50e+03 pdb=" O LYS L 362 " 0.036 2.00e-02 2.50e+03 pdb=" N LYS L 363 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 21 " 0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C VAL F 21 " -0.070 2.00e-02 2.50e+03 pdb=" O VAL F 21 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU F 22 " 0.022 2.00e-02 2.50e+03 ... (remaining 2099 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.81: 11 1.81 - 2.58: 237 2.58 - 3.35: 19887 3.35 - 4.13: 45935 4.13 - 4.90: 74331 Nonbonded interactions: 140401 Sorted by model distance: nonbonded pdb=" OE2 GLU E 73 " pdb=" CG ARG F 23 " model vdw 1.035 3.440 nonbonded pdb=" O LEU C 117 " pdb=" NZ LYS F 44 " model vdw 1.189 3.120 nonbonded pdb=" OD1 ASP E 77 " pdb=" O LEU F 10 " model vdw 1.254 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 1.434 3.040 nonbonded pdb=" O SER E 57 " pdb=" NH2 ARG F 40 " model vdw 1.578 3.120 ... (remaining 140396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 36 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and ((resid 15 through 16 and (name N or name CA or name C or name O \ or name CB )) or resid 17 through 118)) selection = (chain 'G' and resid 15 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'K' and (resid 62 through 135 or resid 137 through 152 or resid 171 throu \ gh 200 or resid 202 through 363 or resid 401 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 363 or \ resid 401 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 51.540 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.148 17262 Z= 0.488 Angle : 0.817 11.650 24504 Z= 0.469 Chirality : 0.048 0.517 2736 Planarity : 0.006 0.073 2102 Dihedral : 25.617 156.219 7331 Min Nonbonded Distance : 1.035 Molprobity Statistics. All-atom Clashscore : 27.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP K 264 HIS 0.011 0.001 HIS F 75 PHE 0.013 0.002 PHE K 154 TYR 0.012 0.001 TYR G 60 ARG 0.011 0.001 ARG L 357 *********************** 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 : 1.525 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: 0.6066 (m-10) REVERT: D 34 LYS cc_start: 0.7632 (ptpt) cc_final: 0.7211 (mmtt) REVERT: D 95 GLN cc_start: 0.7759 (tt0) cc_final: 0.7461 (tt0) REVERT: E 54 TYR cc_start: 0.6553 (m-80) cc_final: 0.6351 (m-10) REVERT: H 39 ILE cc_start: 0.8379 (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: 0.6801 (p90) cc_final: 0.6567 (p90) REVERT: K 354 THR cc_start: 0.2865 (p) cc_final: 0.2094 (p) REVERT: L 72 MET cc_start: 0.3021 (pmm) cc_final: 0.2724 (ptt) outliers start: 8 outliers final: 0 residues processed: 456 average time/residue: 0.3918 time to fit residues: 244.8100 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 : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN L 149 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17262 Z= 0.265 Angle : 0.730 9.909 24504 Z= 0.418 Chirality : 0.042 0.233 2736 Planarity : 0.006 0.091 2102 Dihedral : 28.682 153.139 4789 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.56 % Allowed : 4.26 % Favored : 95.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1277 helix: 0.57 (0.19), residues: 713 sheet: -1.38 (0.64), residues: 38 loop : -2.00 (0.24), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 264 HIS 0.009 0.001 HIS F 75 PHE 0.025 0.002 PHE L 183 TYR 0.012 0.002 TYR A 99 ARG 0.009 0.001 ARG F 23 *********************** 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 305 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 1.494 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 120 MET cc_start: 0.7596 (mtp) cc_final: 0.7371 (mtp) REVERT: A 126 LEU cc_start: 0.8454 (tp) cc_final: 0.8092 (tp) REVERT: B 88 TYR cc_start: 0.7031 (m-10) cc_final: 0.6548 (m-10) REVERT: B 96 THR cc_start: 0.8193 (m) cc_final: 0.7704 (p) REVERT: D 34 LYS cc_start: 0.7589 (ptpt) cc_final: 0.7212 (mmtt) REVERT: D 88 THR cc_start: 0.8832 (m) cc_final: 0.8621 (p) REVERT: E 50 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7603 (mt-10) REVERT: E 76 GLN cc_start: 0.7697 (tt0) cc_final: 0.7266 (tm-30) REVERT: F 59 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8752 (ttpp) REVERT: F 61 PHE cc_start: 0.9208 (t80) cc_final: 0.8971 (t80) REVERT: F 88 TYR cc_start: 0.8618 (m-10) cc_final: 0.8145 (m-10) REVERT: H 39 ILE cc_start: 0.8456 (pt) cc_final: 0.8099 (tp) REVERT: H 84 ASN cc_start: 0.7979 (m110) cc_final: 0.7691 (m-40) REVERT: K 173 MET cc_start: 0.4133 (mmp) cc_final: 0.2371 (ttp) REVERT: K 283 SER cc_start: 0.4777 (t) cc_final: 0.4534 (p) REVERT: L 100 MET cc_start: 0.6448 (mmm) cc_final: 0.5323 (tpp) REVERT: L 187 ARG cc_start: 0.7712 (mpp80) cc_final: 0.7292 (mtp180) outliers start: 2 outliers final: 1 residues processed: 304 average time/residue: 0.2993 time to fit residues: 132.7671 Evaluate side-chains 225 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 96 optimal weight: 0.0030 chunk 39 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 113 optimal weight: 0.0970 overall best weight: 4.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN F 18 HIS F 25 ASN G 33 HIS G 87 GLN K 262 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17262 Z= 0.325 Angle : 0.767 12.263 24504 Z= 0.435 Chirality : 0.044 0.273 2736 Planarity : 0.006 0.087 2102 Dihedral : 28.956 170.003 4789 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.28 % Allowed : 4.90 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.22), residues: 1277 helix: 0.29 (0.19), residues: 717 sheet: -1.89 (0.71), residues: 36 loop : -2.09 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 218 HIS 0.009 0.002 HIS K 181 PHE 0.017 0.003 PHE A 104 TYR 0.024 0.002 TYR G 60 ARG 0.022 0.001 ARG F 23 *********************** 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 328 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.7809 (mm) cc_final: 0.7038 (mm) REVERT: A 86 SER cc_start: 0.8949 (m) cc_final: 0.8442 (t) REVERT: A 94 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 120 MET cc_start: 0.8407 (mtp) cc_final: 0.7866 (mtp) REVERT: A 122 LYS cc_start: 0.8777 (pttt) cc_final: 0.8453 (mttt) REVERT: B 29 ILE cc_start: 0.9194 (mm) cc_final: 0.8755 (mm) REVERT: B 84 MET cc_start: 0.7471 (tpp) cc_final: 0.6985 (tpp) REVERT: B 88 TYR cc_start: 0.8100 (m-10) cc_final: 0.7479 (m-10) REVERT: C 52 VAL cc_start: 0.9554 (m) cc_final: 0.9236 (p) REVERT: C 82 THR cc_start: 0.9479 (p) cc_final: 0.9144 (t) REVERT: C 87 GLN cc_start: 0.8792 (tp40) cc_final: 0.8424 (tp40) REVERT: D 34 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7521 (mmtt) REVERT: D 51 ASP cc_start: 0.7470 (p0) cc_final: 0.7226 (p0) REVERT: D 120 LYS cc_start: 0.7931 (mttt) cc_final: 0.6863 (tptp) REVERT: E 45 THR cc_start: 0.5381 (t) cc_final: 0.4987 (m) REVERT: E 94 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7953 (tp30) REVERT: E 120 MET cc_start: 0.8774 (mmm) cc_final: 0.8564 (mmm) REVERT: F 24 ASP cc_start: 0.8702 (p0) cc_final: 0.7951 (p0) REVERT: F 61 PHE cc_start: 0.9194 (t80) cc_final: 0.8933 (t80) REVERT: F 88 TYR cc_start: 0.8498 (m-10) cc_final: 0.7925 (m-10) REVERT: G 53 TYR cc_start: 0.9504 (t80) cc_final: 0.9285 (t80) REVERT: K 173 MET cc_start: 0.4498 (mmp) cc_final: 0.2153 (ttt) REVERT: K 195 PHE cc_start: 0.6926 (p90) cc_final: 0.6570 (p90) REVERT: L 100 MET cc_start: 0.6847 (mmm) cc_final: 0.5626 (tpp) REVERT: L 183 PHE cc_start: 0.7158 (t80) cc_final: 0.6744 (t80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2985 time to fit residues: 142.5299 Evaluate side-chains 241 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 HIS ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17262 Z= 0.216 Angle : 0.665 10.068 24504 Z= 0.384 Chirality : 0.040 0.184 2736 Planarity : 0.009 0.286 2102 Dihedral : 28.790 170.152 4789 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.37 % Allowed : 2.22 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.22), residues: 1277 helix: 0.74 (0.19), residues: 714 sheet: -1.58 (0.59), residues: 62 loop : -2.05 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 218 HIS 0.005 0.001 HIS F 18 PHE 0.018 0.002 PHE G 27 TYR 0.015 0.001 TYR K 254 ARG 0.026 0.001 ARG F 23 *********************** 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 328 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7702 (t0) cc_final: 0.7487 (t0) REVERT: A 86 SER cc_start: 0.8944 (m) cc_final: 0.8449 (t) REVERT: A 94 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 122 LYS cc_start: 0.8616 (pttt) cc_final: 0.8230 (mttt) REVERT: A 126 LEU cc_start: 0.9391 (tp) cc_final: 0.9150 (tp) REVERT: B 29 ILE cc_start: 0.9375 (mm) cc_final: 0.9166 (mm) REVERT: B 78 ARG cc_start: 0.8364 (mtm180) cc_final: 0.8103 (mtm180) REVERT: B 82 THR cc_start: 0.9337 (m) cc_final: 0.8885 (m) REVERT: B 88 TYR cc_start: 0.7795 (m-10) cc_final: 0.7354 (m-10) REVERT: C 52 VAL cc_start: 0.9469 (m) cc_final: 0.9170 (p) REVERT: C 87 GLN cc_start: 0.8912 (tp40) cc_final: 0.8422 (tp40) REVERT: D 34 LYS cc_start: 0.7982 (ptpt) cc_final: 0.7600 (mmtt) REVERT: E 50 GLU cc_start: 0.8379 (tt0) cc_final: 0.7983 (tt0) REVERT: E 87 SER cc_start: 0.8941 (p) cc_final: 0.8732 (t) REVERT: E 120 MET cc_start: 0.8610 (mmm) cc_final: 0.8027 (mmm) REVERT: F 24 ASP cc_start: 0.8772 (p0) cc_final: 0.8227 (p0) REVERT: F 82 THR cc_start: 0.9319 (m) cc_final: 0.8975 (m) REVERT: F 84 MET cc_start: 0.7704 (tpp) cc_final: 0.7425 (tpp) REVERT: F 85 ASP cc_start: 0.8346 (m-30) cc_final: 0.8097 (m-30) REVERT: F 88 TYR cc_start: 0.8237 (m-10) cc_final: 0.7819 (m-10) REVERT: G 60 TYR cc_start: 0.9193 (t80) cc_final: 0.8891 (t80) REVERT: K 173 MET cc_start: 0.4435 (mmp) cc_final: 0.2374 (ttt) REVERT: K 195 PHE cc_start: 0.6909 (p90) cc_final: 0.6589 (p90) REVERT: K 288 THR cc_start: 0.6622 (m) cc_final: 0.6394 (m) REVERT: K 358 LEU cc_start: 0.6901 (mt) cc_final: 0.6289 (tt) REVERT: L 100 MET cc_start: 0.6808 (mmm) cc_final: 0.5629 (tpp) REVERT: L 181 HIS cc_start: 0.5457 (t70) cc_final: 0.4679 (t-90) REVERT: L 254 TYR cc_start: 0.6288 (t80) cc_final: 0.6076 (t80) REVERT: L 264 TRP cc_start: 0.7811 (t60) cc_final: 0.7521 (t60) outliers start: 1 outliers final: 0 residues processed: 327 average time/residue: 0.3038 time to fit residues: 143.6420 Evaluate side-chains 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 HIS ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 27 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17262 Z= 0.277 Angle : 0.692 10.820 24504 Z= 0.398 Chirality : 0.041 0.200 2736 Planarity : 0.005 0.094 2102 Dihedral : 28.887 174.331 4789 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.28 % Allowed : 2.68 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.22), residues: 1277 helix: 0.75 (0.19), residues: 704 sheet: -1.51 (0.65), residues: 50 loop : -2.03 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 218 HIS 0.005 0.001 HIS B 75 PHE 0.041 0.002 PHE L 281 TYR 0.038 0.002 TYR H 40 ARG 0.007 0.001 ARG A 129 *********************** 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 300 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.291 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: 0.9011 (m) cc_final: 0.8588 (t) REVERT: A 94 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 122 LYS cc_start: 0.8956 (pttt) cc_final: 0.8414 (tttt) REVERT: A 126 LEU cc_start: 0.9414 (tp) cc_final: 0.8537 (tp) REVERT: B 16 LYS cc_start: 0.5453 (pttp) cc_final: 0.5132 (tptm) REVERT: B 84 MET cc_start: 0.7776 (tpp) cc_final: 0.7550 (tpp) REVERT: B 88 TYR cc_start: 0.7919 (m-10) cc_final: 0.7351 (m-10) REVERT: C 26 GLN cc_start: 0.8133 (mm110) cc_final: 0.7822 (mp10) REVERT: C 82 THR cc_start: 0.9470 (p) cc_final: 0.9206 (t) REVERT: C 87 GLN cc_start: 0.8932 (tp40) cc_final: 0.8639 (tp40) REVERT: D 34 LYS cc_start: 0.7905 (ptpt) cc_final: 0.7524 (mmtt) REVERT: D 51 ASP cc_start: 0.7523 (p0) cc_final: 0.7212 (p0) REVERT: E 87 SER cc_start: 0.9089 (p) cc_final: 0.8786 (t) REVERT: E 94 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8045 (tp30) REVERT: E 120 MET cc_start: 0.8812 (mmm) cc_final: 0.8266 (mmm) REVERT: E 133 GLU cc_start: 0.7809 (mp0) cc_final: 0.6884 (tm-30) REVERT: F 24 ASP cc_start: 0.8809 (p0) cc_final: 0.8296 (p0) REVERT: F 47 SER cc_start: 0.9408 (p) cc_final: 0.9055 (p) REVERT: F 82 THR cc_start: 0.9306 (m) cc_final: 0.8995 (m) REVERT: F 85 ASP cc_start: 0.8431 (m-30) cc_final: 0.8196 (m-30) REVERT: F 88 TYR cc_start: 0.8233 (m-10) cc_final: 0.7822 (m-10) REVERT: G 21 GLN cc_start: 0.8528 (pt0) cc_final: 0.8115 (pp30) REVERT: G 60 TYR cc_start: 0.9385 (t80) cc_final: 0.9000 (t80) REVERT: G 68 LEU cc_start: 0.8796 (mm) cc_final: 0.8589 (mt) REVERT: G 93 ASP cc_start: 0.8220 (p0) cc_final: 0.7997 (p0) REVERT: H 46 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8523 (mmmt) REVERT: H 95 GLN cc_start: 0.8724 (tt0) cc_final: 0.8305 (tt0) REVERT: K 173 MET cc_start: 0.4511 (mmp) cc_final: 0.2422 (ttt) REVERT: K 188 MET cc_start: 0.4925 (pmm) cc_final: 0.4635 (pmm) REVERT: K 195 PHE cc_start: 0.6855 (p90) cc_final: 0.6543 (p90) REVERT: K 358 LEU cc_start: 0.6952 (mt) cc_final: 0.6342 (tt) REVERT: L 100 MET cc_start: 0.6935 (mmm) cc_final: 0.5718 (tpp) REVERT: L 195 PHE cc_start: 0.8000 (p90) cc_final: 0.7781 (p90) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2799 time to fit residues: 124.5879 Evaluate side-chains 228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 85 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17262 Z= 0.239 Angle : 0.669 11.469 24504 Z= 0.383 Chirality : 0.040 0.199 2736 Planarity : 0.005 0.077 2102 Dihedral : 28.861 174.146 4789 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.37 % Allowed : 2.22 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.23), residues: 1277 helix: 0.82 (0.19), residues: 707 sheet: -1.65 (0.64), residues: 50 loop : -2.06 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP K 218 HIS 0.005 0.001 HIS B 75 PHE 0.018 0.002 PHE G 27 TYR 0.035 0.002 TYR H 40 ARG 0.012 0.001 ARG L 187 *********************** 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 303 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 1.296 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: 0.8960 (m) cc_final: 0.8501 (t) REVERT: A 94 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7856 (mm-30) REVERT: A 101 VAL cc_start: 0.9410 (t) cc_final: 0.9160 (m) REVERT: A 122 LYS cc_start: 0.8967 (pttt) cc_final: 0.8384 (tttt) REVERT: B 16 LYS cc_start: 0.5274 (pttp) cc_final: 0.4422 (tptp) REVERT: B 84 MET cc_start: 0.7808 (tpp) cc_final: 0.7498 (tpp) REVERT: B 88 TYR cc_start: 0.7897 (m-10) cc_final: 0.7332 (m-10) REVERT: C 26 GLN cc_start: 0.8157 (mm110) cc_final: 0.7839 (mp10) REVERT: C 52 VAL cc_start: 0.9408 (m) cc_final: 0.9097 (p) REVERT: C 87 GLN cc_start: 0.8891 (tp40) cc_final: 0.8612 (tp40) REVERT: D 34 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7612 (mmtt) REVERT: D 45 LEU cc_start: 0.9525 (tp) cc_final: 0.9240 (tp) REVERT: D 51 ASP cc_start: 0.7560 (p0) cc_final: 0.7249 (p0) REVERT: E 87 SER cc_start: 0.9138 (p) cc_final: 0.8742 (t) REVERT: E 94 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8142 (tp30) REVERT: E 120 MET cc_start: 0.8834 (mmm) cc_final: 0.8279 (mmm) REVERT: F 24 ASP cc_start: 0.8872 (p0) cc_final: 0.8533 (p0) REVERT: F 47 SER cc_start: 0.9419 (p) cc_final: 0.9099 (p) REVERT: F 49 LEU cc_start: 0.9021 (mm) cc_final: 0.8783 (mm) REVERT: F 85 ASP cc_start: 0.8396 (m-30) cc_final: 0.8165 (m-30) REVERT: F 88 TYR cc_start: 0.8261 (m-10) cc_final: 0.7818 (m-10) REVERT: G 21 GLN cc_start: 0.8510 (pt0) cc_final: 0.8123 (pp30) REVERT: G 60 TYR cc_start: 0.9367 (t80) cc_final: 0.8926 (t80) REVERT: H 46 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8522 (mmmt) REVERT: K 173 MET cc_start: 0.4553 (mmp) cc_final: 0.2385 (ttt) REVERT: K 188 MET cc_start: 0.4964 (pmm) cc_final: 0.4735 (pmm) REVERT: K 195 PHE cc_start: 0.6946 (p90) cc_final: 0.6519 (p90) REVERT: K 358 LEU cc_start: 0.6925 (mt) cc_final: 0.6322 (tt) REVERT: L 100 MET cc_start: 0.6873 (mmm) cc_final: 0.5764 (tpp) REVERT: L 187 ARG cc_start: 0.8319 (mpt-90) cc_final: 0.8080 (mmm-85) REVERT: L 241 MET cc_start: 0.5811 (ppp) cc_final: 0.5401 (ppp) outliers start: 1 outliers final: 1 residues processed: 302 average time/residue: 0.2924 time to fit residues: 129.4519 Evaluate side-chains 233 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 26 GLN H 84 ASN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.8270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17262 Z= 0.205 Angle : 0.659 11.450 24504 Z= 0.377 Chirality : 0.040 0.186 2736 Planarity : 0.008 0.307 2102 Dihedral : 28.775 174.782 4789 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.28 % Allowed : 1.20 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.23), residues: 1277 helix: 0.89 (0.20), residues: 715 sheet: -1.75 (0.69), residues: 46 loop : -2.04 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP K 218 HIS 0.005 0.001 HIS B 75 PHE 0.019 0.001 PHE G 27 TYR 0.032 0.001 TYR H 40 ARG 0.007 0.001 ARG F 92 *********************** 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 295 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.502 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: 0.8912 (m) cc_final: 0.8455 (t) REVERT: A 101 VAL cc_start: 0.9357 (t) cc_final: 0.9114 (m) REVERT: A 120 MET cc_start: 0.8504 (mtp) cc_final: 0.8123 (mtp) REVERT: A 122 LYS cc_start: 0.8970 (pttt) cc_final: 0.8318 (tttt) REVERT: B 16 LYS cc_start: 0.5163 (pttp) cc_final: 0.4461 (tptp) REVERT: B 82 THR cc_start: 0.9299 (m) cc_final: 0.9075 (m) REVERT: B 88 TYR cc_start: 0.7751 (m-10) cc_final: 0.7293 (m-10) REVERT: C 52 VAL cc_start: 0.9392 (m) cc_final: 0.9118 (p) REVERT: C 60 TYR cc_start: 0.9114 (t80) cc_final: 0.8838 (t80) REVERT: C 64 GLU cc_start: 0.8471 (tp30) cc_final: 0.8090 (tt0) REVERT: C 110 ILE cc_start: 0.8424 (mm) cc_final: 0.8112 (pt) REVERT: D 34 LYS cc_start: 0.7785 (ptpt) cc_final: 0.7566 (mmtt) REVERT: E 73 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7658 (tm-30) REVERT: E 87 SER cc_start: 0.9106 (p) cc_final: 0.8711 (t) REVERT: E 94 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8072 (tp30) REVERT: E 120 MET cc_start: 0.8823 (mmm) cc_final: 0.8295 (mmm) REVERT: E 133 GLU cc_start: 0.7752 (mp0) cc_final: 0.6724 (tm-30) REVERT: F 24 ASP cc_start: 0.8880 (p0) cc_final: 0.8540 (p0) REVERT: F 82 THR cc_start: 0.9318 (m) cc_final: 0.9064 (m) REVERT: F 88 TYR cc_start: 0.8091 (m-10) cc_final: 0.7660 (m-10) REVERT: G 21 GLN cc_start: 0.8487 (pt0) cc_final: 0.8151 (pp30) REVERT: G 60 TYR cc_start: 0.9324 (t80) cc_final: 0.9045 (t80) REVERT: H 46 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8450 (mmmt) REVERT: K 173 MET cc_start: 0.4514 (mmp) cc_final: 0.2396 (ttt) REVERT: K 188 MET cc_start: 0.5110 (pmm) cc_final: 0.4865 (pmm) REVERT: K 195 PHE cc_start: 0.6880 (p90) cc_final: 0.6499 (p90) REVERT: K 354 THR cc_start: 0.4551 (p) cc_final: 0.4341 (p) REVERT: K 358 LEU cc_start: 0.6781 (mt) cc_final: 0.6202 (tt) REVERT: L 100 MET cc_start: 0.6978 (mmm) cc_final: 0.5812 (tpp) REVERT: L 241 MET cc_start: 0.5817 (ppp) cc_final: 0.5460 (ppp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2711 time to fit residues: 120.3022 Evaluate side-chains 228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 118 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 273 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.9267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 17262 Z= 0.383 Angle : 0.811 19.020 24504 Z= 0.450 Chirality : 0.046 0.228 2736 Planarity : 0.009 0.346 2102 Dihedral : 29.179 176.528 4789 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.28 % Allowed : 1.48 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1277 helix: 0.23 (0.19), residues: 711 sheet: -1.87 (0.62), residues: 56 loop : -2.11 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP L 264 HIS 0.012 0.002 HIS B 75 PHE 0.017 0.002 PHE D 70 TYR 0.027 0.003 TYR H 40 ARG 0.009 0.001 ARG C 91 *********************** 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 291 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9109 (m) cc_final: 0.8701 (t) REVERT: A 93 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8841 (mm-40) REVERT: A 120 MET cc_start: 0.8794 (mtp) cc_final: 0.8256 (mtp) REVERT: A 122 LYS cc_start: 0.9192 (pttt) cc_final: 0.8477 (tttt) REVERT: B 16 LYS cc_start: 0.4994 (pttp) cc_final: 0.4478 (tptm) REVERT: B 82 THR cc_start: 0.9323 (m) cc_final: 0.9115 (m) REVERT: B 88 TYR cc_start: 0.8076 (m-10) cc_final: 0.7834 (m-10) REVERT: C 52 VAL cc_start: 0.9437 (m) cc_final: 0.9211 (p) REVERT: C 95 GLU cc_start: 0.7614 (mp0) cc_final: 0.7309 (mp0) REVERT: C 110 ILE cc_start: 0.8768 (mm) cc_final: 0.8465 (pt) REVERT: D 111 VAL cc_start: 0.9428 (t) cc_final: 0.9218 (p) REVERT: E 39 HIS cc_start: 0.5377 (t-90) cc_final: 0.4255 (m-70) REVERT: E 50 GLU cc_start: 0.8548 (tt0) cc_final: 0.8325 (tt0) REVERT: E 87 SER cc_start: 0.9251 (p) cc_final: 0.8879 (t) REVERT: E 94 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8146 (tp30) REVERT: E 120 MET cc_start: 0.8923 (mmm) cc_final: 0.8304 (mmm) REVERT: E 126 LEU cc_start: 0.9532 (tp) cc_final: 0.9290 (tt) REVERT: F 59 LYS cc_start: 0.9234 (ttmt) cc_final: 0.8873 (ttpt) REVERT: F 74 GLU cc_start: 0.8963 (tt0) cc_final: 0.8761 (tt0) REVERT: F 82 THR cc_start: 0.9326 (m) cc_final: 0.9025 (m) REVERT: F 88 TYR cc_start: 0.8271 (m-10) cc_final: 0.7906 (m-10) REVERT: G 21 GLN cc_start: 0.8606 (pt0) cc_final: 0.8356 (pp30) REVERT: G 54 SER cc_start: 0.9426 (m) cc_final: 0.9173 (t) REVERT: H 46 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8507 (mmmt) REVERT: K 77 LEU cc_start: 0.7674 (mt) cc_final: 0.7442 (tp) REVERT: K 173 MET cc_start: 0.4636 (mmp) cc_final: 0.2246 (ttt) REVERT: K 195 PHE cc_start: 0.6937 (p90) cc_final: 0.6627 (p90) REVERT: K 358 LEU cc_start: 0.6975 (mt) cc_final: 0.6404 (tt) REVERT: L 100 MET cc_start: 0.7039 (mmm) cc_final: 0.6238 (tpp) REVERT: L 195 PHE cc_start: 0.8228 (p90) cc_final: 0.7869 (p90) REVERT: L 241 MET cc_start: 0.5994 (ppp) cc_final: 0.5540 (ppp) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2841 time to fit residues: 124.5926 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 126 optimal weight: 0.2980 chunk 132 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN G 114 HIS H 84 ASN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.9372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17262 Z= 0.197 Angle : 0.709 17.016 24504 Z= 0.393 Chirality : 0.040 0.252 2736 Planarity : 0.010 0.385 2102 Dihedral : 28.928 173.222 4789 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.37 % Allowed : 1.02 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1277 helix: 0.66 (0.19), residues: 714 sheet: -2.24 (0.65), residues: 46 loop : -2.07 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 264 HIS 0.005 0.001 HIS A 113 PHE 0.026 0.002 PHE K 281 TYR 0.021 0.002 TYR K 203 ARG 0.018 0.001 ARG F 23 *********************** 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 309 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.8971 (m) cc_final: 0.8572 (t) REVERT: A 120 MET cc_start: 0.8495 (mtp) cc_final: 0.8283 (mtp) REVERT: A 122 LYS cc_start: 0.9123 (pttt) cc_final: 0.8438 (tttt) REVERT: A 133 GLU cc_start: 0.7770 (pp20) cc_final: 0.7352 (pp20) REVERT: B 16 LYS cc_start: 0.4660 (pttp) cc_final: 0.4088 (tttp) REVERT: B 29 ILE cc_start: 0.9463 (mm) cc_final: 0.9045 (mm) REVERT: C 52 VAL cc_start: 0.9316 (m) cc_final: 0.9074 (p) REVERT: C 110 ILE cc_start: 0.8537 (mm) cc_final: 0.8327 (pt) REVERT: D 59 MET cc_start: 0.8705 (tpp) cc_final: 0.8268 (tpp) REVERT: E 39 HIS cc_start: 0.4999 (t-90) cc_final: 0.4066 (m-70) REVERT: E 50 GLU cc_start: 0.8509 (tt0) cc_final: 0.8147 (tt0) REVERT: E 87 SER cc_start: 0.9109 (p) cc_final: 0.8778 (t) REVERT: E 94 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8061 (tp30) REVERT: E 120 MET cc_start: 0.8953 (mmm) cc_final: 0.8365 (mmm) REVERT: E 133 GLU cc_start: 0.7773 (mp0) cc_final: 0.6960 (tp30) REVERT: F 36 ARG cc_start: 0.9031 (mtm-85) cc_final: 0.8331 (mtm-85) REVERT: F 47 SER cc_start: 0.9407 (p) cc_final: 0.8974 (p) REVERT: F 82 THR cc_start: 0.9270 (m) cc_final: 0.9070 (m) REVERT: G 21 GLN cc_start: 0.8523 (pt0) cc_final: 0.8166 (pp30) REVERT: G 27 PHE cc_start: 0.7852 (m-10) cc_final: 0.7591 (m-80) REVERT: G 54 SER cc_start: 0.9380 (m) cc_final: 0.9098 (t) REVERT: H 46 LYS cc_start: 0.8868 (mmmt) cc_final: 0.8444 (mmmt) REVERT: K 173 MET cc_start: 0.4702 (mmp) cc_final: 0.2601 (ttt) REVERT: K 349 TYR cc_start: 0.7347 (m-10) cc_final: 0.7042 (m-10) REVERT: K 358 LEU cc_start: 0.6915 (mt) cc_final: 0.6404 (tt) REVERT: L 100 MET cc_start: 0.6666 (mmm) cc_final: 0.5513 (tpp) REVERT: L 241 MET cc_start: 0.6103 (ppp) cc_final: 0.5685 (ppp) outliers start: 1 outliers final: 1 residues processed: 308 average time/residue: 0.2763 time to fit residues: 127.8710 Evaluate side-chains 229 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 30.0000 chunk 90 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.9666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 17262 Z= 0.312 Angle : 0.755 24.102 24504 Z= 0.418 Chirality : 0.042 0.265 2736 Planarity : 0.005 0.058 2102 Dihedral : 29.067 177.510 4789 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.28 % Allowed : 0.65 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1277 helix: 0.44 (0.19), residues: 723 sheet: -2.28 (0.64), residues: 46 loop : -2.13 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP K 264 HIS 0.010 0.001 HIS G 114 PHE 0.028 0.002 PHE G 27 TYR 0.019 0.002 TYR C 60 ARG 0.041 0.001 ARG F 23 ********************** 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 270 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.9035 (m) cc_final: 0.8641 (t) REVERT: A 120 MET cc_start: 0.8693 (mtp) cc_final: 0.8318 (mtp) REVERT: A 122 LYS cc_start: 0.9192 (pttt) cc_final: 0.8388 (tttt) REVERT: A 126 LEU cc_start: 0.9231 (tp) cc_final: 0.8894 (tp) REVERT: B 16 LYS cc_start: 0.4750 (pttp) cc_final: 0.4031 (tttp) REVERT: B 60 VAL cc_start: 0.9665 (t) cc_final: 0.9383 (t) REVERT: B 63 GLU cc_start: 0.7834 (pm20) cc_final: 0.7478 (pm20) REVERT: B 82 THR cc_start: 0.9241 (m) cc_final: 0.8892 (m) REVERT: B 88 TYR cc_start: 0.7878 (m-10) cc_final: 0.7641 (m-10) REVERT: C 59 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8554 (mm-30) REVERT: C 110 ILE cc_start: 0.8666 (mm) cc_final: 0.8419 (pt) REVERT: D 93 GLU cc_start: 0.8955 (mp0) cc_final: 0.8321 (mp0) REVERT: E 39 HIS cc_start: 0.5122 (t-90) cc_final: 0.4237 (m-70) REVERT: E 50 GLU cc_start: 0.8471 (tt0) cc_final: 0.8234 (tt0) REVERT: E 87 SER cc_start: 0.9126 (p) cc_final: 0.8826 (t) REVERT: E 94 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8093 (tp30) REVERT: F 36 ARG cc_start: 0.9131 (mtm-85) cc_final: 0.8685 (mtm-85) REVERT: F 82 THR cc_start: 0.9327 (m) cc_final: 0.8904 (m) REVERT: F 88 TYR cc_start: 0.8077 (m-10) cc_final: 0.7704 (m-10) REVERT: G 21 GLN cc_start: 0.8393 (pt0) cc_final: 0.8174 (pp30) REVERT: G 54 SER cc_start: 0.9472 (m) cc_final: 0.9131 (t) REVERT: H 46 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8369 (mmmt) REVERT: K 77 LEU cc_start: 0.8062 (mm) cc_final: 0.7719 (tp) REVERT: K 173 MET cc_start: 0.4624 (mmp) cc_final: 0.2399 (ttt) REVERT: K 188 MET cc_start: 0.5398 (pmm) cc_final: 0.5141 (pmm) REVERT: K 358 LEU cc_start: 0.6956 (mt) cc_final: 0.6425 (tt) REVERT: L 100 MET cc_start: 0.6688 (mmm) cc_final: 0.5954 (tpp) REVERT: L 195 PHE cc_start: 0.8122 (p90) cc_final: 0.7784 (p90) REVERT: L 241 MET cc_start: 0.6200 (ppp) cc_final: 0.5717 (ppp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2662 time to fit residues: 109.9662 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 : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** G 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS L 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.132017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098167 restraints weight = 65291.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.099301 restraints weight = 49623.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099653 restraints weight = 45146.598| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 1.0028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 17262 Z= 0.337 Angle : 0.781 20.955 24504 Z= 0.434 Chirality : 0.044 0.196 2736 Planarity : 0.005 0.045 2102 Dihedral : 29.214 176.933 4789 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.22), residues: 1277 helix: 0.35 (0.19), residues: 714 sheet: -2.13 (0.66), residues: 46 loop : -2.16 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 264 HIS 0.010 0.002 HIS K 181 PHE 0.036 0.002 PHE G 27 TYR 0.036 0.002 TYR D 40 ARG 0.031 0.001 ARG F 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3272.93 seconds wall clock time: 60 minutes 44.22 seconds (3644.22 seconds total)