Starting phenix.real_space_refine on Thu Feb 5 08:17:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eam_47836/02_2026/9eam_47836.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eam_47836/02_2026/9eam_47836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eam_47836/02_2026/9eam_47836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eam_47836/02_2026/9eam_47836.map" model { file = "/net/cci-nas-00/data/ceres_data/9eam_47836/02_2026/9eam_47836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eam_47836/02_2026/9eam_47836.cif" } resolution = 2.97 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= 0.002 sd= 0.007 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 P 6 5.49 5 Mg 2 5.21 5 S 81 5.16 5 C 10011 2.51 5 N 2712 2.21 5 O 2966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15778 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3304 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 26, 'TRANS': 386} Chain: "B" Number of atoms: 3014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3014 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 17, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2921 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 356} Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2287 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain: "E" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1422 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 12, 'TRANS': 162} Chain: "F" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1371 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 162} Chain: "G" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1088 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "H" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.50, per 1000 atoms: 0.22 Number of scatterers: 15778 At special positions: 0 Unit cell: (97.584, 135.248, 143.808, 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) S 81 16.00 P 6 15.00 Mg 2 11.99 O 2966 8.00 N 2712 7.00 C 10011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 641.6 milliseconds 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3690 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 23 sheets defined 42.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 85 through 98 removed outlier: 3.657A pdb=" N GLN A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 133 removed outlier: 3.774A pdb=" N ARG A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'A' and resid 153 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.603A pdb=" N GLU A 160 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 161 " --> pdb=" O VAL A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 231 Processing helix chain 'A' and resid 238 through 248 Processing helix chain 'A' and resid 248 through 253 removed outlier: 4.272A pdb=" N TRP A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 253' Processing helix chain 'A' and resid 272 through 276 removed outlier: 3.715A pdb=" N PHE A 276 " --> pdb=" O TYR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.681A pdb=" N ILE A 281 " --> pdb=" O GLY A 278 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 284 through 288 removed outlier: 3.699A pdb=" N ALA A 288 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 removed outlier: 3.567A pdb=" N ASN A 306 " --> pdb=" O GLU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 removed outlier: 6.386A pdb=" N ASP A 310 " --> pdb=" O CYS A 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.551A pdb=" N LEU A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 317 " --> pdb=" O ARG A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 311 through 317' Processing helix chain 'A' and resid 330 through 355 removed outlier: 4.048A pdb=" N ARG A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 386 Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.505A pdb=" N PHE A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 392 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.819A pdb=" N ILE A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 64 removed outlier: 3.569A pdb=" N GLU B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 64' Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.526A pdb=" N MET B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.665A pdb=" N ARG B 120 " --> pdb=" O PRO B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'B' and resid 176 through 179 removed outlier: 3.823A pdb=" N THR B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 179' Processing helix chain 'B' and resid 185 through 199 removed outlier: 3.584A pdb=" N ILE B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.118A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 256 through 261 removed outlier: 3.840A pdb=" N GLU B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.778A pdb=" N LEU B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 272 removed outlier: 3.578A pdb=" N LEU B 270 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 272 " --> pdb=" O HIS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.561A pdb=" N PHE B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS B 299 " --> pdb=" O SER B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 329 removed outlier: 3.538A pdb=" N ARG B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.012A pdb=" N SER B 338 " --> pdb=" O GLU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 375 through 381 Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.890A pdb=" N GLU B 387 " --> pdb=" O ARG B 384 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 312 removed outlier: 6.252A pdb=" N MET C 300 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 364 Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.717A pdb=" N ALA D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.943A pdb=" N GLY D 50 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 removed outlier: 3.563A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS D 70 " --> pdb=" O GLU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 80 removed outlier: 4.328A pdb=" N LEU D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.574A pdb=" N VAL D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET D 115 " --> pdb=" O HIS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 135 removed outlier: 4.788A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL D 124 " --> pdb=" O CYS D 120 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN D 132 " --> pdb=" O TYR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 188 removed outlier: 3.703A pdb=" N VAL D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 176 " --> pdb=" O ASP D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 245 removed outlier: 3.696A pdb=" N HIS D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 280 removed outlier: 4.247A pdb=" N ARG D 267 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS D 269 " --> pdb=" O ARG D 265 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA D 280 " --> pdb=" O VAL D 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 53 removed outlier: 4.731A pdb=" N LYS E 50 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA E 51 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 85 removed outlier: 4.115A pdb=" N THR E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS E 85 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 101 removed outlier: 3.636A pdb=" N THR E 97 " --> pdb=" O LYS E 93 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 removed outlier: 4.219A pdb=" N GLU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.812A pdb=" N ASN E 170 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 19 removed outlier: 3.922A pdb=" N ALA F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 41 Processing helix chain 'F' and resid 43 through 47 removed outlier: 3.754A pdb=" N LEU F 46 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU F 47 " --> pdb=" O LYS F 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 43 through 47' Processing helix chain 'F' and resid 80 through 97 removed outlier: 4.020A pdb=" N ARG F 97 " --> pdb=" O PHE F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 167 removed outlier: 3.603A pdb=" N LEU F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASP F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 14 removed outlier: 3.584A pdb=" N LYS G 13 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G 14 " --> pdb=" O PHE G 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 10 through 14' Processing helix chain 'G' and resid 16 through 20 removed outlier: 3.563A pdb=" N TYR G 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 49 removed outlier: 4.139A pdb=" N VAL G 42 " --> pdb=" O ASP G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 68 through 84 removed outlier: 4.172A pdb=" N LYS G 72 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 96 removed outlier: 3.656A pdb=" N ALA G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 114 Processing helix chain 'G' and resid 120 through 137 removed outlier: 4.094A pdb=" N VAL G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 146 removed outlier: 3.629A pdb=" N VAL G 142 " --> pdb=" O VAL G 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 889 through 904 removed outlier: 3.638A pdb=" N LEU H 904 " --> pdb=" O MET H 900 " (cutoff:3.500A) Processing helix chain 'H' and resid 911 through 916 removed outlier: 3.623A pdb=" N SER H 915 " --> pdb=" O PRO H 912 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE H 916 " --> pdb=" O GLN H 913 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.611A pdb=" N CYS A 8 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N THR A 113 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N VAL A 10 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 185 removed outlier: 6.348A pdb=" N THR A 166 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N SER A 322 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE A 168 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 319 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 254 through 259 Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 33 removed outlier: 3.581A pdb=" N CYS B 11 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR B 110 " --> pdb=" O CYS B 11 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASN B 13 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 135 " --> pdb=" O CYS B 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 136 " --> pdb=" O MET B 373 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 373 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 56 through 57 removed outlier: 3.534A pdb=" N MET B 56 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 174 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 174 removed outlier: 6.476A pdb=" N VAL B 155 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N SER B 304 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL B 157 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE B 301 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 Processing sheet with id=AB3, first strand: chain 'C' and resid 2 through 5 removed outlier: 4.695A pdb=" N ALA C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY C 347 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C 329 " --> pdb=" O THR C 346 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 16 removed outlier: 5.913A pdb=" N LYS C 36 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS C 44 " --> pdb=" O LYS C 36 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASN C 38 " --> pdb=" O TRP C 42 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 55 through 60 removed outlier: 4.179A pdb=" N ALA C 76 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 104 removed outlier: 6.551A pdb=" N GLY C 114 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL C 102 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA C 112 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TRP C 104 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LYS C 110 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 145 through 150 removed outlier: 6.832A pdb=" N GLY C 160 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU C 148 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA C 158 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP C 150 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU C 156 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS C 166 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU C 197 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL C 168 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 209 through 212 removed outlier: 3.931A pdb=" N GLY C 209 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 249 through 254 removed outlier: 3.555A pdb=" N ALA C 263 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 284 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN C 273 " --> pdb=" O PHE C 282 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N PHE C 282 " --> pdb=" O ASN C 273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.562A pdb=" N PHE D 35 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL D 93 " --> pdb=" O ILE D 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.562A pdb=" N PHE D 35 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 142 through 144 removed outlier: 3.691A pdb=" N THR D 151 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN D 197 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 149 through 150 removed outlier: 3.766A pdb=" N LYS E 155 " --> pdb=" O ASP E 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 51 through 54 675 hydrogen bonds defined for protein. 1878 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4883 1.34 - 1.46: 2884 1.46 - 1.58: 8209 1.58 - 1.69: 14 1.69 - 1.81: 130 Bond restraints: 16120 Sorted by residual: bond pdb=" CG ARG C 302 " pdb=" CD ARG C 302 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.17e+00 bond pdb=" CB ASN G 89 " pdb=" CG ASN G 89 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 6.04e+00 bond pdb=" CB ILE C 293 " pdb=" CG2 ILE C 293 " ideal model delta sigma weight residual 1.521 1.598 -0.077 3.30e-02 9.18e+02 5.47e+00 bond pdb=" C ARG F 6 " pdb=" N PRO F 7 " ideal model delta sigma weight residual 1.335 1.364 -0.030 1.28e-02 6.10e+03 5.44e+00 bond pdb=" N LYS C 290 " pdb=" CA LYS C 290 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.32e+00 ... (remaining 16115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 21665 4.09 - 8.17: 122 8.17 - 12.26: 14 12.26 - 16.35: 0 16.35 - 20.43: 1 Bond angle restraints: 21802 Sorted by residual: angle pdb=" CG1 ILE C 293 " pdb=" CB ILE C 293 " pdb=" CG2 ILE C 293 " ideal model delta sigma weight residual 110.70 90.27 20.43 3.00e+00 1.11e-01 4.64e+01 angle pdb=" N ARG C 302 " pdb=" CA ARG C 302 " pdb=" CB ARG C 302 " ideal model delta sigma weight residual 110.44 120.04 -9.60 1.56e+00 4.11e-01 3.79e+01 angle pdb=" C HIS D 202 " pdb=" N ARG D 203 " pdb=" CA ARG D 203 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C SER C 292 " pdb=" N ILE C 293 " pdb=" CA ILE C 293 " ideal model delta sigma weight residual 121.97 131.13 -9.16 1.80e+00 3.09e-01 2.59e+01 angle pdb=" C PHE F 101 " pdb=" N PHE F 102 " pdb=" CA PHE F 102 " ideal model delta sigma weight residual 121.54 130.67 -9.13 1.91e+00 2.74e-01 2.28e+01 ... (remaining 21797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 8873 17.31 - 34.63: 764 34.63 - 51.94: 111 51.94 - 69.25: 17 69.25 - 86.57: 13 Dihedral angle restraints: 9778 sinusoidal: 4062 harmonic: 5716 Sorted by residual: dihedral pdb=" CA ARG A 49 " pdb=" C ARG A 49 " pdb=" N ARG A 50 " pdb=" CA ARG A 50 " ideal model delta harmonic sigma weight residual -180.00 -149.62 -30.38 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA ASN E 122 " pdb=" C ASN E 122 " pdb=" N LYS E 123 " pdb=" CA LYS E 123 " ideal model delta harmonic sigma weight residual -180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET C 189 " pdb=" C MET C 189 " pdb=" N PRO C 190 " pdb=" CA PRO C 190 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 2240 0.114 - 0.229: 134 0.229 - 0.343: 6 0.343 - 0.457: 2 0.457 - 0.571: 2 Chirality restraints: 2384 Sorted by residual: chirality pdb=" CB ILE C 293 " pdb=" CA ILE C 293 " pdb=" CG1 ILE C 293 " pdb=" CG2 ILE C 293 " both_signs ideal model delta sigma weight residual False 2.64 3.22 -0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CB ILE C 288 " pdb=" CA ILE C 288 " pdb=" CG1 ILE C 288 " pdb=" CG2 ILE C 288 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CB VAL H 919 " pdb=" CA VAL H 919 " pdb=" CG1 VAL H 919 " pdb=" CG2 VAL H 919 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 2381 not shown) Planarity restraints: 2812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 298 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C SER C 298 " -0.063 2.00e-02 2.50e+03 pdb=" O SER C 298 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA C 299 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 131 " -0.019 2.00e-02 2.50e+03 2.00e-02 9.97e+00 pdb=" CG TRP C 131 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP C 131 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 131 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 131 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 131 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 131 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 131 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 131 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 131 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 228 " 0.048 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO D 229 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " 0.040 5.00e-02 4.00e+02 ... (remaining 2809 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 100 2.64 - 3.21: 12151 3.21 - 3.77: 21830 3.77 - 4.34: 30539 4.34 - 4.90: 51717 Nonbonded interactions: 116337 Sorted by model distance: nonbonded pdb=" O2B ATP A 500 " pdb="MG MG A 501 " model vdw 2.078 2.170 nonbonded pdb=" O1G ATP A 500 " pdb="MG MG A 501 " model vdw 2.104 2.170 nonbonded pdb=" O3B ATP B 500 " pdb="MG MG B 501 " model vdw 2.107 2.170 nonbonded pdb=" O2G ATP B 500 " pdb="MG MG B 501 " model vdw 2.174 2.170 nonbonded pdb=" O1B ATP B 500 " pdb="MG MG B 501 " model vdw 2.246 2.170 ... (remaining 116332 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.010 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: 0.260 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 0.005 0.091 16120 Z= 0.238 Angle : 0.856 20.432 21802 Z= 0.478 Chirality : 0.059 0.571 2384 Planarity : 0.008 0.072 2812 Dihedral : 13.119 86.566 6088 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.17), residues: 1949 helix: -2.43 (0.13), residues: 687 sheet: 0.95 (0.27), residues: 386 loop : -1.49 (0.18), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 10 TYR 0.018 0.002 TYR C 333 PHE 0.030 0.002 PHE F 138 TRP 0.054 0.002 TRP C 131 HIS 0.006 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00463 (16120) covalent geometry : angle 0.85566 (21802) hydrogen bonds : bond 0.16010 ( 662) hydrogen bonds : angle 6.15098 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.7708 (tpt) cc_final: 0.7151 (tpp) REVERT: C 1 MET cc_start: 0.8108 (mtt) cc_final: 0.7741 (mmm) REVERT: C 297 MET cc_start: 0.7354 (ptt) cc_final: 0.7126 (pmt) REVERT: C 365 GLN cc_start: 0.9108 (mm110) cc_final: 0.8721 (mp10) REVERT: D 172 ASP cc_start: 0.8914 (m-30) cc_final: 0.8529 (p0) REVERT: D 182 MET cc_start: 0.9158 (mmm) cc_final: 0.8867 (mmm) REVERT: D 183 GLN cc_start: 0.8869 (tp-100) cc_final: 0.8542 (tp-100) REVERT: E 43 ASP cc_start: 0.8773 (m-30) cc_final: 0.8494 (m-30) REVERT: E 150 ASP cc_start: 0.8387 (t70) cc_final: 0.8059 (t0) REVERT: F 167 ASN cc_start: 0.8791 (m110) cc_final: 0.8468 (m110) REVERT: G 18 GLU cc_start: 0.9145 (pp20) cc_final: 0.8864 (pp20) REVERT: G 51 MET cc_start: 0.8929 (mmp) cc_final: 0.8650 (mmp) REVERT: G 61 ASN cc_start: 0.7952 (t0) cc_final: 0.7558 (t0) REVERT: H 898 ASN cc_start: 0.8650 (m-40) cc_final: 0.8285 (m-40) REVERT: H 907 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8355 (mtp180) REVERT: H 921 GLU cc_start: 0.8718 (tp30) cc_final: 0.8315 (tp30) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.7567 time to fit residues: 106.9585 Evaluate side-chains 108 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 176 HIS B 141 GLN G 48 GLN G 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.053340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.035248 restraints weight = 60409.886| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.70 r_work: 0.2518 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 16120 Z= 0.356 Angle : 0.677 7.426 21802 Z= 0.364 Chirality : 0.049 0.153 2384 Planarity : 0.006 0.056 2812 Dihedral : 6.495 81.773 2206 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 0.76 % Allowed : 5.00 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: -0.46 (0.18), residues: 1949 helix: 0.23 (0.19), residues: 714 sheet: 0.85 (0.27), residues: 380 loop : -1.28 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 47 TYR 0.019 0.002 TYR D 253 PHE 0.028 0.002 PHE F 90 TRP 0.042 0.002 TRP C 131 HIS 0.008 0.002 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00870 (16120) covalent geometry : angle 0.67674 (21802) hydrogen bonds : bond 0.07894 ( 662) hydrogen bonds : angle 4.54425 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.675 Fit side-chains REVERT: B 1 MET cc_start: 0.7975 (tpt) cc_final: 0.7492 (tpp) REVERT: B 74 MET cc_start: 0.7915 (ttm) cc_final: 0.7629 (ttt) REVERT: B 365 MET cc_start: 0.8873 (tpp) cc_final: 0.8350 (tpp) REVERT: C 54 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.8093 (t-90) REVERT: C 297 MET cc_start: 0.7445 (ptt) cc_final: 0.6689 (mtt) REVERT: C 365 GLN cc_start: 0.9110 (mm110) cc_final: 0.8689 (mp10) REVERT: C 370 MET cc_start: 0.7210 (ptt) cc_final: 0.6905 (ppp) REVERT: D 172 ASP cc_start: 0.8967 (m-30) cc_final: 0.8626 (p0) REVERT: D 182 MET cc_start: 0.9189 (mmm) cc_final: 0.8948 (mmm) REVERT: D 183 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8551 (tp-100) REVERT: E 150 ASP cc_start: 0.8370 (t70) cc_final: 0.8004 (t0) REVERT: G 18 GLU cc_start: 0.9090 (pp20) cc_final: 0.8791 (pp20) REVERT: G 27 GLU cc_start: 0.7640 (tp30) cc_final: 0.7349 (tp30) REVERT: G 51 MET cc_start: 0.8774 (mmp) cc_final: 0.8538 (mmp) REVERT: G 61 ASN cc_start: 0.7863 (t0) cc_final: 0.7445 (t0) REVERT: G 89 ASN cc_start: 0.9560 (m-40) cc_final: 0.9072 (p0) REVERT: H 898 ASN cc_start: 0.8636 (m-40) cc_final: 0.8143 (m-40) REVERT: H 903 LYS cc_start: 0.9096 (tppp) cc_final: 0.8739 (tttp) REVERT: H 921 GLU cc_start: 0.8842 (tp30) cc_final: 0.8376 (tp30) outliers start: 13 outliers final: 6 residues processed: 119 average time/residue: 0.7774 time to fit residues: 100.7484 Evaluate side-chains 117 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 897 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 45 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN A 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.055677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.037612 restraints weight = 60231.419| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.74 r_work: 0.2603 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16120 Z= 0.109 Angle : 0.490 6.694 21802 Z= 0.262 Chirality : 0.042 0.147 2384 Planarity : 0.004 0.052 2812 Dihedral : 5.727 78.260 2206 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.05 % Favored : 97.85 % Rotamer: Outliers : 0.46 % Allowed : 6.57 % Favored : 92.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.28 (0.19), residues: 1949 helix: 1.15 (0.20), residues: 709 sheet: 1.00 (0.27), residues: 384 loop : -1.02 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 47 TYR 0.013 0.001 TYR D 250 PHE 0.021 0.001 PHE F 138 TRP 0.049 0.001 TRP C 131 HIS 0.003 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00244 (16120) covalent geometry : angle 0.49011 (21802) hydrogen bonds : bond 0.04791 ( 662) hydrogen bonds : angle 3.99798 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.658 Fit side-chains REVERT: B 1 MET cc_start: 0.7821 (tpt) cc_final: 0.7361 (tpp) REVERT: B 74 MET cc_start: 0.7929 (ttm) cc_final: 0.7573 (ttt) REVERT: B 365 MET cc_start: 0.8829 (tpp) cc_final: 0.8618 (tpt) REVERT: C 54 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.8068 (t-90) REVERT: C 365 GLN cc_start: 0.9114 (mm110) cc_final: 0.8711 (mp10) REVERT: C 370 MET cc_start: 0.6977 (ptt) cc_final: 0.6752 (ppp) REVERT: D 172 ASP cc_start: 0.8862 (m-30) cc_final: 0.8523 (p0) REVERT: D 182 MET cc_start: 0.9225 (mmm) cc_final: 0.9003 (mmm) REVERT: D 183 GLN cc_start: 0.8895 (tp-100) cc_final: 0.8586 (tp-100) REVERT: E 150 ASP cc_start: 0.8380 (t70) cc_final: 0.7479 (p0) REVERT: G 18 GLU cc_start: 0.9091 (pp20) cc_final: 0.8809 (pp20) REVERT: G 27 GLU cc_start: 0.7899 (tp30) cc_final: 0.7581 (tp30) REVERT: G 51 MET cc_start: 0.8737 (mmp) cc_final: 0.8492 (mmp) REVERT: G 61 ASN cc_start: 0.7924 (t0) cc_final: 0.7482 (t0) REVERT: G 89 ASN cc_start: 0.9498 (m-40) cc_final: 0.9018 (p0) REVERT: H 898 ASN cc_start: 0.8585 (m-40) cc_final: 0.8137 (m-40) REVERT: H 903 LYS cc_start: 0.9104 (tppp) cc_final: 0.8848 (tttp) REVERT: H 921 GLU cc_start: 0.8864 (tp30) cc_final: 0.8434 (tp30) outliers start: 8 outliers final: 2 residues processed: 116 average time/residue: 0.7491 time to fit residues: 94.9147 Evaluate side-chains 112 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain F residue 94 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 100 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 11 optimal weight: 0.3980 chunk 178 optimal weight: 50.0000 chunk 166 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 161 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.055109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.036945 restraints weight = 60290.060| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.74 r_work: 0.2582 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16120 Z= 0.144 Angle : 0.500 7.332 21802 Z= 0.265 Chirality : 0.043 0.142 2384 Planarity : 0.004 0.050 2812 Dihedral : 5.483 75.359 2206 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 0.87 % Allowed : 7.38 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.64 (0.19), residues: 1949 helix: 1.64 (0.21), residues: 706 sheet: 1.04 (0.27), residues: 384 loop : -0.91 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 47 TYR 0.013 0.001 TYR D 250 PHE 0.014 0.001 PHE F 138 TRP 0.051 0.001 TRP C 131 HIS 0.005 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00342 (16120) covalent geometry : angle 0.50029 (21802) hydrogen bonds : bond 0.05234 ( 662) hydrogen bonds : angle 3.92030 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.613 Fit side-chains REVERT: A 383 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.8643 (mmp) REVERT: B 1 MET cc_start: 0.7901 (tpt) cc_final: 0.7459 (tpp) REVERT: B 74 MET cc_start: 0.7895 (ttm) cc_final: 0.7527 (ttt) REVERT: B 365 MET cc_start: 0.8791 (tpp) cc_final: 0.8548 (tpt) REVERT: C 54 HIS cc_start: 0.8318 (OUTLIER) cc_final: 0.8085 (t-90) REVERT: C 365 GLN cc_start: 0.9101 (mm110) cc_final: 0.8685 (mp10) REVERT: C 370 MET cc_start: 0.7063 (ptt) cc_final: 0.6736 (ppp) REVERT: D 172 ASP cc_start: 0.8825 (m-30) cc_final: 0.8476 (p0) REVERT: D 182 MET cc_start: 0.9220 (mmm) cc_final: 0.8998 (mmm) REVERT: D 183 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8554 (tp-100) REVERT: E 150 ASP cc_start: 0.8260 (t70) cc_final: 0.7906 (t0) REVERT: G 18 GLU cc_start: 0.9051 (pp20) cc_final: 0.8828 (pp20) REVERT: G 27 GLU cc_start: 0.8084 (tp30) cc_final: 0.7827 (tp30) REVERT: G 61 ASN cc_start: 0.7907 (t0) cc_final: 0.7462 (t0) REVERT: G 89 ASN cc_start: 0.9470 (m-40) cc_final: 0.8987 (p0) REVERT: G 115 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: G 120 ASN cc_start: 0.8738 (p0) cc_final: 0.8480 (p0) REVERT: H 898 ASN cc_start: 0.8549 (m-40) cc_final: 0.8136 (m-40) REVERT: H 903 LYS cc_start: 0.9086 (tppp) cc_final: 0.8847 (tttp) REVERT: H 921 GLU cc_start: 0.8883 (tp30) cc_final: 0.8429 (tp30) outliers start: 15 outliers final: 5 residues processed: 120 average time/residue: 0.7433 time to fit residues: 97.6299 Evaluate side-chains 116 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 148 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 191 optimal weight: 0.7980 chunk 174 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.054606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.036592 restraints weight = 60231.599| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.72 r_work: 0.2565 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16120 Z= 0.181 Angle : 0.539 10.420 21802 Z= 0.283 Chirality : 0.044 0.200 2384 Planarity : 0.004 0.058 2812 Dihedral : 5.531 76.298 2206 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 1.10 % Allowed : 7.55 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.77 (0.20), residues: 1949 helix: 1.73 (0.21), residues: 714 sheet: 1.04 (0.28), residues: 384 loop : -0.81 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 47 TYR 0.015 0.001 TYR D 250 PHE 0.013 0.001 PHE F 138 TRP 0.054 0.001 TRP C 131 HIS 0.005 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00440 (16120) covalent geometry : angle 0.53923 (21802) hydrogen bonds : bond 0.05570 ( 662) hydrogen bonds : angle 3.94041 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.671 Fit side-chains REVERT: A 383 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8646 (mmp) REVERT: B 1 MET cc_start: 0.7958 (tpt) cc_final: 0.7504 (tpp) REVERT: B 74 MET cc_start: 0.7970 (ttm) cc_final: 0.7578 (ttt) REVERT: C 54 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.8175 (t-90) REVERT: C 370 MET cc_start: 0.7020 (ptt) cc_final: 0.6699 (ppp) REVERT: D 172 ASP cc_start: 0.8830 (m-30) cc_final: 0.8526 (p0) REVERT: D 182 MET cc_start: 0.9224 (mmm) cc_final: 0.8995 (mmm) REVERT: D 183 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8539 (tp-100) REVERT: E 9 MET cc_start: 0.9007 (mmm) cc_final: 0.8517 (tpp) REVERT: E 150 ASP cc_start: 0.8418 (t70) cc_final: 0.7546 (p0) REVERT: G 18 GLU cc_start: 0.9003 (pp20) cc_final: 0.8796 (pp20) REVERT: G 27 GLU cc_start: 0.8244 (tp30) cc_final: 0.8000 (tp30) REVERT: G 61 ASN cc_start: 0.7929 (t0) cc_final: 0.7463 (t0) REVERT: G 89 ASN cc_start: 0.9473 (m-40) cc_final: 0.9052 (p0) REVERT: G 115 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: G 120 ASN cc_start: 0.8678 (p0) cc_final: 0.8391 (p0) REVERT: H 898 ASN cc_start: 0.8572 (m-40) cc_final: 0.8164 (m-40) REVERT: H 903 LYS cc_start: 0.9089 (tppp) cc_final: 0.8839 (tttp) REVERT: H 921 GLU cc_start: 0.8921 (tp30) cc_final: 0.8496 (tp30) outliers start: 19 outliers final: 9 residues processed: 116 average time/residue: 0.6988 time to fit residues: 88.5124 Evaluate side-chains 118 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 70 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.054578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.036820 restraints weight = 59565.237| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.67 r_work: 0.2571 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16120 Z= 0.172 Angle : 0.534 10.504 21802 Z= 0.280 Chirality : 0.044 0.181 2384 Planarity : 0.004 0.050 2812 Dihedral : 5.484 76.142 2206 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.87 % Favored : 97.02 % Rotamer: Outliers : 0.87 % Allowed : 8.72 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.85 (0.20), residues: 1949 helix: 1.79 (0.20), residues: 714 sheet: 1.02 (0.27), residues: 384 loop : -0.72 (0.21), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 47 TYR 0.014 0.001 TYR D 250 PHE 0.014 0.001 PHE F 138 TRP 0.053 0.001 TRP C 131 HIS 0.005 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00418 (16120) covalent geometry : angle 0.53417 (21802) hydrogen bonds : bond 0.05420 ( 662) hydrogen bonds : angle 3.91204 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.668 Fit side-chains REVERT: A 383 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8684 (mmp) REVERT: B 1 MET cc_start: 0.7998 (tpt) cc_final: 0.7531 (tpp) REVERT: B 74 MET cc_start: 0.8110 (ttm) cc_final: 0.7717 (ttt) REVERT: B 127 MET cc_start: 0.8953 (mmm) cc_final: 0.8683 (mmp) REVERT: C 54 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.8212 (t-90) REVERT: C 370 MET cc_start: 0.7072 (ptt) cc_final: 0.6611 (ppp) REVERT: D 172 ASP cc_start: 0.8797 (m-30) cc_final: 0.8535 (p0) REVERT: D 182 MET cc_start: 0.9243 (mmm) cc_final: 0.9042 (mmm) REVERT: D 183 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8541 (tp-100) REVERT: E 9 MET cc_start: 0.9032 (mmm) cc_final: 0.8626 (tpp) REVERT: E 95 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9020 (mmp) REVERT: E 150 ASP cc_start: 0.8391 (t70) cc_final: 0.7575 (p0) REVERT: G 27 GLU cc_start: 0.8280 (tp30) cc_final: 0.8048 (tp30) REVERT: G 51 MET cc_start: 0.8765 (mmt) cc_final: 0.8433 (mmp) REVERT: G 61 ASN cc_start: 0.7960 (t0) cc_final: 0.7468 (t0) REVERT: G 89 ASN cc_start: 0.9473 (m-40) cc_final: 0.9136 (p0) REVERT: G 115 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: G 120 ASN cc_start: 0.8639 (p0) cc_final: 0.8354 (p0) REVERT: H 898 ASN cc_start: 0.8603 (m-40) cc_final: 0.8183 (m-40) REVERT: H 903 LYS cc_start: 0.9078 (tppp) cc_final: 0.8831 (tttp) REVERT: H 921 GLU cc_start: 0.8845 (tp30) cc_final: 0.8436 (tp30) outliers start: 15 outliers final: 9 residues processed: 115 average time/residue: 0.7186 time to fit residues: 90.5914 Evaluate side-chains 118 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 101 optimal weight: 0.0050 chunk 71 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 117 optimal weight: 0.0370 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 overall best weight: 1.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.054966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.036984 restraints weight = 59614.754| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.71 r_work: 0.2581 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16120 Z= 0.141 Angle : 0.527 8.787 21802 Z= 0.275 Chirality : 0.043 0.166 2384 Planarity : 0.004 0.073 2812 Dihedral : 5.355 75.149 2206 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.46 % Favored : 97.43 % Rotamer: Outliers : 0.87 % Allowed : 9.41 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.95 (0.20), residues: 1949 helix: 1.83 (0.20), residues: 720 sheet: 1.05 (0.27), residues: 384 loop : -0.62 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 47 TYR 0.014 0.001 TYR D 250 PHE 0.016 0.001 PHE F 138 TRP 0.057 0.001 TRP C 131 HIS 0.004 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00339 (16120) covalent geometry : angle 0.52745 (21802) hydrogen bonds : bond 0.04981 ( 662) hydrogen bonds : angle 3.81263 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.657 Fit side-chains REVERT: A 383 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8630 (mmp) REVERT: B 1 MET cc_start: 0.8014 (tpt) cc_final: 0.7537 (tpp) REVERT: B 365 MET cc_start: 0.8546 (tpp) cc_final: 0.8312 (tpp) REVERT: C 54 HIS cc_start: 0.8387 (OUTLIER) cc_final: 0.8184 (t-90) REVERT: C 370 MET cc_start: 0.7122 (ptt) cc_final: 0.6582 (ppp) REVERT: D 172 ASP cc_start: 0.8769 (m-30) cc_final: 0.8478 (p0) REVERT: D 182 MET cc_start: 0.9226 (mmm) cc_final: 0.8987 (mmm) REVERT: D 183 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8476 (tp-100) REVERT: E 9 MET cc_start: 0.8998 (mmm) cc_final: 0.8661 (tpp) REVERT: E 95 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.9005 (mmp) REVERT: E 150 ASP cc_start: 0.8328 (t70) cc_final: 0.7730 (t0) REVERT: G 27 GLU cc_start: 0.8293 (tp30) cc_final: 0.7989 (tp30) REVERT: G 51 MET cc_start: 0.8744 (mmt) cc_final: 0.8417 (mmp) REVERT: G 61 ASN cc_start: 0.7924 (t0) cc_final: 0.7434 (t0) REVERT: G 89 ASN cc_start: 0.9562 (m-40) cc_final: 0.9094 (p0) REVERT: G 115 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: G 120 ASN cc_start: 0.8630 (p0) cc_final: 0.8047 (p0) REVERT: H 898 ASN cc_start: 0.8570 (m-40) cc_final: 0.8132 (m-40) REVERT: H 903 LYS cc_start: 0.9064 (tppp) cc_final: 0.8823 (tttp) REVERT: H 921 GLU cc_start: 0.8764 (tp30) cc_final: 0.8361 (tp30) outliers start: 15 outliers final: 9 residues processed: 112 average time/residue: 0.7365 time to fit residues: 90.2703 Evaluate side-chains 118 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 128 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 101 optimal weight: 0.4980 chunk 164 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.054741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.036706 restraints weight = 60313.928| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 3.73 r_work: 0.2571 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16120 Z= 0.164 Angle : 0.544 8.804 21802 Z= 0.284 Chirality : 0.043 0.164 2384 Planarity : 0.004 0.048 2812 Dihedral : 5.354 74.659 2206 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 0.93 % Allowed : 9.76 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.20), residues: 1949 helix: 1.87 (0.20), residues: 720 sheet: 1.02 (0.27), residues: 384 loop : -0.58 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 47 TYR 0.014 0.001 TYR D 250 PHE 0.014 0.001 PHE F 138 TRP 0.061 0.001 TRP C 131 HIS 0.005 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00398 (16120) covalent geometry : angle 0.54391 (21802) hydrogen bonds : bond 0.05253 ( 662) hydrogen bonds : angle 3.82976 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.651 Fit side-chains REVERT: A 383 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8617 (mmp) REVERT: B 1 MET cc_start: 0.7986 (tpt) cc_final: 0.7756 (tpt) REVERT: B 74 MET cc_start: 0.8019 (ttm) cc_final: 0.7776 (ttt) REVERT: B 365 MET cc_start: 0.8631 (tpp) cc_final: 0.8225 (tpp) REVERT: C 54 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.8182 (t-90) REVERT: C 370 MET cc_start: 0.7167 (ptt) cc_final: 0.6551 (ppp) REVERT: D 172 ASP cc_start: 0.8782 (m-30) cc_final: 0.8505 (p0) REVERT: D 182 MET cc_start: 0.9224 (mmm) cc_final: 0.8975 (mmm) REVERT: D 183 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8480 (tp-100) REVERT: E 9 MET cc_start: 0.9016 (mmm) cc_final: 0.8718 (tpp) REVERT: E 95 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8985 (mmp) REVERT: E 150 ASP cc_start: 0.8324 (t70) cc_final: 0.7667 (t0) REVERT: G 19 TYR cc_start: 0.8589 (m-80) cc_final: 0.8356 (m-80) REVERT: G 27 GLU cc_start: 0.8351 (tp30) cc_final: 0.8114 (tp30) REVERT: G 51 MET cc_start: 0.8731 (mmt) cc_final: 0.8392 (mmp) REVERT: G 61 ASN cc_start: 0.7886 (t0) cc_final: 0.7394 (t0) REVERT: G 89 ASN cc_start: 0.9523 (m-40) cc_final: 0.9121 (p0) REVERT: G 115 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: G 120 ASN cc_start: 0.8631 (p0) cc_final: 0.8081 (p0) REVERT: H 898 ASN cc_start: 0.8526 (m-40) cc_final: 0.8118 (m-40) REVERT: H 903 LYS cc_start: 0.9056 (tppp) cc_final: 0.8775 (tttp) REVERT: H 921 GLU cc_start: 0.8693 (tp30) cc_final: 0.8282 (tp30) outliers start: 16 outliers final: 10 residues processed: 114 average time/residue: 0.7333 time to fit residues: 91.5668 Evaluate side-chains 121 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 54 HIS Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 168 PHE Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 188 optimal weight: 4.9990 chunk 15 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.054334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.036362 restraints weight = 60156.021| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.70 r_work: 0.2563 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16120 Z= 0.195 Angle : 0.581 12.479 21802 Z= 0.301 Chirality : 0.044 0.167 2384 Planarity : 0.004 0.085 2812 Dihedral : 5.483 76.439 2206 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 0.99 % Allowed : 9.99 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 0.96 (0.20), residues: 1949 helix: 1.86 (0.20), residues: 719 sheet: 1.00 (0.28), residues: 384 loop : -0.60 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG G 47 TYR 0.015 0.001 TYR D 250 PHE 0.014 0.001 PHE F 138 TRP 0.063 0.002 TRP C 131 HIS 0.006 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00478 (16120) covalent geometry : angle 0.58058 (21802) hydrogen bonds : bond 0.05652 ( 662) hydrogen bonds : angle 3.89162 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.675 Fit side-chains REVERT: A 383 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8644 (mmp) REVERT: B 74 MET cc_start: 0.8000 (ttm) cc_final: 0.7764 (ttt) REVERT: B 365 MET cc_start: 0.8739 (tpp) cc_final: 0.8272 (tpp) REVERT: C 370 MET cc_start: 0.7286 (ptt) cc_final: 0.6602 (ppp) REVERT: D 172 ASP cc_start: 0.8816 (m-30) cc_final: 0.8526 (p0) REVERT: D 182 MET cc_start: 0.9209 (mmm) cc_final: 0.8948 (mmm) REVERT: D 183 GLN cc_start: 0.8835 (tp-100) cc_final: 0.8492 (tp-100) REVERT: E 9 MET cc_start: 0.8983 (mmm) cc_final: 0.8666 (tpp) REVERT: E 150 ASP cc_start: 0.8307 (t70) cc_final: 0.7670 (OUTLIER) REVERT: G 19 TYR cc_start: 0.8562 (m-80) cc_final: 0.8331 (m-80) REVERT: G 27 GLU cc_start: 0.8355 (tp30) cc_final: 0.8139 (tp30) REVERT: G 51 MET cc_start: 0.8707 (mmt) cc_final: 0.8357 (mmp) REVERT: G 61 ASN cc_start: 0.7863 (t0) cc_final: 0.7371 (t0) REVERT: G 89 ASN cc_start: 0.9553 (m-40) cc_final: 0.9101 (p0) REVERT: G 115 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: G 120 ASN cc_start: 0.8664 (p0) cc_final: 0.8141 (p0) REVERT: H 898 ASN cc_start: 0.8474 (m-40) cc_final: 0.8067 (m-40) REVERT: H 900 MET cc_start: 0.8803 (mmp) cc_final: 0.8399 (mmp) REVERT: H 903 LYS cc_start: 0.9012 (tppp) cc_final: 0.8754 (tttp) REVERT: H 921 GLU cc_start: 0.8664 (tp30) cc_final: 0.8268 (tp30) outliers start: 17 outliers final: 10 residues processed: 117 average time/residue: 0.7049 time to fit residues: 90.5374 Evaluate side-chains 115 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 193 HIS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 80 optimal weight: 0.0980 chunk 37 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 138 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 43 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS G 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.056276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.038385 restraints weight = 59686.812| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.71 r_work: 0.2636 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16120 Z= 0.100 Angle : 0.522 11.677 21802 Z= 0.270 Chirality : 0.042 0.147 2384 Planarity : 0.004 0.045 2812 Dihedral : 5.041 73.719 2206 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.90 % Favored : 98.00 % Rotamer: Outliers : 0.35 % Allowed : 10.87 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.16 (0.20), residues: 1949 helix: 2.01 (0.20), residues: 721 sheet: 1.06 (0.27), residues: 387 loop : -0.46 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 34 TYR 0.009 0.001 TYR B 222 PHE 0.019 0.001 PHE F 138 TRP 0.062 0.001 TRP C 131 HIS 0.004 0.001 HIS D 245 Details of bonding type rmsd covalent geometry : bond 0.00221 (16120) covalent geometry : angle 0.52200 (21802) hydrogen bonds : bond 0.03888 ( 662) hydrogen bonds : angle 3.60556 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3898 Ramachandran restraints generated. 1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.653 Fit side-chains REVERT: A 383 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8635 (mmp) REVERT: B 74 MET cc_start: 0.8023 (ttm) cc_final: 0.7798 (ttt) REVERT: C 370 MET cc_start: 0.7194 (ptt) cc_final: 0.6531 (ppp) REVERT: D 172 ASP cc_start: 0.8756 (m-30) cc_final: 0.8474 (p0) REVERT: D 183 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8461 (tp-100) REVERT: E 9 MET cc_start: 0.8962 (mmm) cc_final: 0.8732 (tpp) REVERT: E 150 ASP cc_start: 0.8208 (t70) cc_final: 0.7594 (t0) REVERT: G 18 GLU cc_start: 0.8795 (pp20) cc_final: 0.8594 (pp20) REVERT: G 19 TYR cc_start: 0.8540 (m-80) cc_final: 0.8239 (m-80) REVERT: G 27 GLU cc_start: 0.8419 (tp30) cc_final: 0.8111 (tp30) REVERT: G 51 MET cc_start: 0.8661 (mmt) cc_final: 0.8333 (mmp) REVERT: G 89 ASN cc_start: 0.9527 (m-40) cc_final: 0.9105 (p0) REVERT: G 120 ASN cc_start: 0.8542 (p0) cc_final: 0.7993 (p0) REVERT: H 898 ASN cc_start: 0.8497 (m-40) cc_final: 0.8089 (m-40) REVERT: H 900 MET cc_start: 0.8815 (mmp) cc_final: 0.8313 (mmp) REVERT: H 903 LYS cc_start: 0.9083 (tppp) cc_final: 0.8826 (tttp) REVERT: H 921 GLU cc_start: 0.8624 (tp30) cc_final: 0.8253 (tp30) outliers start: 6 outliers final: 3 residues processed: 112 average time/residue: 0.7415 time to fit residues: 90.7602 Evaluate side-chains 109 residues out of total 1721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain G residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 108 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 110 optimal weight: 0.0570 chunk 190 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 48 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.054134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.036145 restraints weight = 59864.104| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.69 r_work: 0.2553 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16120 Z= 0.238 Angle : 0.611 12.932 21802 Z= 0.315 Chirality : 0.046 0.166 2384 Planarity : 0.004 0.071 2812 Dihedral : 5.446 74.800 2206 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 0.46 % Allowed : 11.33 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % 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: 1.06 (0.20), residues: 1949 helix: 1.96 (0.20), residues: 719 sheet: 1.04 (0.28), residues: 384 loop : -0.55 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 47 TYR 0.016 0.001 TYR D 250 PHE 0.014 0.001 PHE C 254 TRP 0.060 0.002 TRP C 131 HIS 0.006 0.001 HIS F 129 Details of bonding type rmsd covalent geometry : bond 0.00585 (16120) covalent geometry : angle 0.61081 (21802) hydrogen bonds : bond 0.05937 ( 662) hydrogen bonds : angle 3.92942 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.32 seconds wall clock time: 80 minutes 15.31 seconds (4815.31 seconds total)