Starting phenix.real_space_refine on Fri Mar 6 16:06:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k71_9840/03_2026/6k71_9840.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k71_9840/03_2026/6k71_9840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6k71_9840/03_2026/6k71_9840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k71_9840/03_2026/6k71_9840.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k71_9840/03_2026/6k71_9840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k71_9840/03_2026/6k71_9840.map" } resolution = 4.3 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= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20681 2.51 5 N 5685 2.21 5 O 6055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32589 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2055 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Chain: "B" Number of atoms: 2055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2055 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Chain: "C" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "D" Number of atoms: 2486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2486 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Chain: "E" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2306 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 11, 'TRANS': 324} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 7, 'ARG:plan': 6, 'GLU:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 143 Chain: "F" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2275 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 11, 'TRANS': 320} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 7, 'TRP:plan': 2, 'ASN:plan1': 7, 'ARG:plan': 6, 'GLU:plan': 8, 'GLN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 143 Chain: "G" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2779 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain: "H" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2779 Classifications: {'peptide': 357} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Chain: "I" Number of atoms: 3312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3312 Classifications: {'peptide': 421} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 402} Chain breaks: 1 Chain: "J" Number of atoms: 4675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4675 Classifications: {'peptide': 588} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 565} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2139 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain: "M" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 145 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "P" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3097 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 19, 'TRANS': 386} Chain breaks: 1 Time building chain proxies: 7.59, per 1000 atoms: 0.23 Number of scatterers: 32589 At special positions: 0 Unit cell: (160.23, 198.45, 173.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 6055 8.00 N 5685 7.00 C 20681 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: 2.37 Conformation dependent library (CDL) restraints added in 1.5 seconds 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8018 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 33.6% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 removed outlier: 4.269A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.109A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 92 through 106 removed outlier: 3.861A pdb=" N ARG A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.705A pdb=" N LEU A 135 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.559A pdb=" N MET A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.779A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.769A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 17 removed outlier: 3.948A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 33 through 36 removed outlier: 3.639A pdb=" N ARG B 36 " --> pdb=" O PHE B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 36' Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 62 through 76 removed outlier: 4.172A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 116 removed outlier: 3.945A pdb=" N ARG B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 141 removed outlier: 4.078A pdb=" N LEU B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'C' and resid 11 through 24 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.780A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 98 Processing helix chain 'C' and resid 128 through 154 removed outlier: 4.132A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 removed outlier: 3.674A pdb=" N HIS C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 221 through 228 removed outlier: 3.789A pdb=" N ALA C 224 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N MET C 226 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 228 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 345 through 350 removed outlier: 3.543A pdb=" N ASP C 348 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'D' and resid 11 through 22 Processing helix chain 'D' and resid 31 through 41 removed outlier: 3.992A pdb=" N ALA D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.649A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 98 Processing helix chain 'D' and resid 128 through 154 removed outlier: 3.877A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 185 Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.900A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.716A pdb=" N GLU D 293 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.836A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 321 " --> pdb=" O PRO D 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 317 through 321' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 345 through 349 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.664A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.937A pdb=" N GLU E 66 " --> pdb=" O LEU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 4.183A pdb=" N ILE E 93 " --> pdb=" O SER E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 123 removed outlier: 3.551A pdb=" N ALA E 123 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 183 through 190 removed outlier: 4.234A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.831A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 229 removed outlier: 3.781A pdb=" N LEU E 228 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 229 " --> pdb=" O SER E 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 225 through 229' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 62 through 66 removed outlier: 4.134A pdb=" N GLU F 66 " --> pdb=" O LEU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 91 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 216 removed outlier: 3.881A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.894A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 191 through 195' Processing helix chain 'G' and resid 204 through 215 removed outlier: 3.762A pdb=" N VAL G 208 " --> pdb=" O HIS G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 238 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 270 through 287 removed outlier: 3.522A pdb=" N HIS G 274 " --> pdb=" O SER G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 327 Processing helix chain 'G' and resid 341 through 351 Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 389 through 394 removed outlier: 6.177A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR G 393 " --> pdb=" O ALA G 390 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 394 " --> pdb=" O ALA G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 389 through 394' Processing helix chain 'G' and resid 421 through 427 removed outlier: 4.081A pdb=" N LEU G 425 " --> pdb=" O ALA G 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.863A pdb=" N PHE G 443 " --> pdb=" O THR G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 512 through 517 removed outlier: 3.646A pdb=" N LEU G 516 " --> pdb=" O VAL G 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.655A pdb=" N PHE H 195 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 215 Processing helix chain 'H' and resid 223 through 238 Processing helix chain 'H' and resid 252 through 267 removed outlier: 3.538A pdb=" N LYS H 257 " --> pdb=" O VAL H 253 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 287 Processing helix chain 'H' and resid 292 through 327 removed outlier: 3.521A pdb=" N ALA H 296 " --> pdb=" O ARG H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 351 Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 421 through 429 removed outlier: 3.974A pdb=" N LEU H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 518 removed outlier: 3.580A pdb=" N VAL H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 removed outlier: 3.561A pdb=" N LEU I 67 " --> pdb=" O PRO I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 86 removed outlier: 3.731A pdb=" N TYR I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 107 Processing helix chain 'I' and resid 132 through 142 Processing helix chain 'I' and resid 161 through 176 removed outlier: 3.691A pdb=" N LYS I 176 " --> pdb=" O ARG I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 260 Processing helix chain 'I' and resid 269 through 275 removed outlier: 4.130A pdb=" N VAL I 273 " --> pdb=" O ARG I 269 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY I 275 " --> pdb=" O ASP I 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 269 through 275' Processing helix chain 'I' and resid 276 through 278 No H-bonds generated for 'chain 'I' and resid 276 through 278' Processing helix chain 'I' and resid 302 through 314 Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.524A pdb=" N ASN I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE I 342 " --> pdb=" O ARG I 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 342' Processing helix chain 'J' and resid 74 through 86 Processing helix chain 'J' and resid 98 through 106 removed outlier: 3.673A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 139 Processing helix chain 'J' and resid 161 through 175 removed outlier: 3.520A pdb=" N LEU J 165 " --> pdb=" O ILE J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 231 removed outlier: 3.677A pdb=" N LEU J 230 " --> pdb=" O PRO J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 262 removed outlier: 3.536A pdb=" N GLN J 258 " --> pdb=" O PRO J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 277 Processing helix chain 'J' and resid 302 through 311 Processing helix chain 'J' and resid 548 through 552 Processing helix chain 'J' and resid 552 through 561 removed outlier: 4.068A pdb=" N GLU J 556 " --> pdb=" O VAL J 552 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL J 557 " --> pdb=" O PHE J 553 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU J 561 " --> pdb=" O VAL J 557 " (cutoff:3.500A) Processing helix chain 'J' and resid 562 through 565 removed outlier: 3.507A pdb=" N LYS J 565 " --> pdb=" O GLN J 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 562 through 565' Processing helix chain 'J' and resid 571 through 584 removed outlier: 3.535A pdb=" N VAL J 575 " --> pdb=" O CYS J 571 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA J 584 " --> pdb=" O SER J 580 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 602 removed outlier: 5.465A pdb=" N GLN J 594 " --> pdb=" O LYS J 590 " (cutoff:3.500A) Processing helix chain 'J' and resid 614 through 622 Processing helix chain 'J' and resid 622 through 627 Processing helix chain 'J' and resid 638 through 656 Processing helix chain 'J' and resid 657 through 664 removed outlier: 5.135A pdb=" N ILE J 661 " --> pdb=" O ALA J 658 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER J 662 " --> pdb=" O LEU J 659 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET J 663 " --> pdb=" O GLY J 660 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA J 664 " --> pdb=" O ILE J 661 " (cutoff:3.500A) Processing helix chain 'J' and resid 666 through 670 Processing helix chain 'J' and resid 677 through 685 removed outlier: 4.681A pdb=" N ILE J 681 " --> pdb=" O ALA J 677 " (cutoff:3.500A) Processing helix chain 'J' and resid 693 through 699 Processing helix chain 'J' and resid 700 through 714 Processing helix chain 'K' and resid 96 through 114 removed outlier: 3.948A pdb=" N HIS K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.828A pdb=" N LEU K 130 " --> pdb=" O GLN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 135 No H-bonds generated for 'chain 'K' and resid 133 through 135' Processing helix chain 'K' and resid 143 through 156 removed outlier: 4.184A pdb=" N HIS K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 178 removed outlier: 4.527A pdb=" N ASN K 178 " --> pdb=" O GLU K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 183 removed outlier: 3.561A pdb=" N ARG K 183 " --> pdb=" O ASN K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 221 Processing helix chain 'K' and resid 245 through 261 removed outlier: 3.938A pdb=" N SER K 249 " --> pdb=" O THR K 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 174 through 187 removed outlier: 4.606A pdb=" N PHE M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 63 removed outlier: 4.130A pdb=" N VAL P 57 " --> pdb=" O GLY P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 149 Processing helix chain 'P' and resid 168 through 174 removed outlier: 3.710A pdb=" N GLU P 172 " --> pdb=" O PRO P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 209 removed outlier: 3.764A pdb=" N ALA P 200 " --> pdb=" O LYS P 196 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU P 205 " --> pdb=" O LYS P 201 " (cutoff:3.500A) Processing helix chain 'P' and resid 231 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 127 Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 3.610A pdb=" N GLY A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 208 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA4, first strand: chain 'B' and resid 151 through 152 removed outlier: 5.816A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 194 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 200 removed outlier: 3.936A pdb=" N GLY B 199 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 207 " --> pdb=" O GLY B 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 168 removed outlier: 5.940A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR C 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 313 through 316 removed outlier: 3.788A pdb=" N LEU C 245 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C 248 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR C 236 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS C 268 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR C 236 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 329 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.259A pdb=" N SER C 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N LEU G 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 499 " --> pdb=" O VAL G 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 215 through 216 removed outlier: 6.703A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLY D 235 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE D 168 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 266 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 267 " --> pdb=" O LEU D 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB3, first strand: chain 'E' and resid 51 through 52 removed outlier: 7.348A pdb=" N ALA E 5 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU E 128 " --> pdb=" O TYR E 264 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 170 through 171 Processing sheet with id=AB5, first strand: chain 'E' and resid 181 through 182 Processing sheet with id=AB6, first strand: chain 'E' and resid 357 through 358 removed outlier: 5.951A pdb=" N LEU E 357 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL E 374 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU E 391 " --> pdb=" O ILE E 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.386A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AB9, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.711A pdb=" N ILE F 193 " --> pdb=" O VAL I 240 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE F 195 " --> pdb=" O VAL I 238 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG I 241 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL I 203 " --> pdb=" O ARG I 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 181 through 183 removed outlier: 3.746A pdb=" N PHE I 224 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 363 through 364 removed outlier: 5.957A pdb=" N GLN F 363 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 380 " --> pdb=" O VAL F 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 402 through 404 removed outlier: 7.485A pdb=" N ASN F 403 " --> pdb=" O ILE F 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 414 through 417 removed outlier: 4.044A pdb=" N VAL G 414 " --> pdb=" O THR G 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 333 through 334 removed outlier: 3.697A pdb=" N LEU H 334 " --> pdb=" O LYS H 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 358 through 360 removed outlier: 6.536A pdb=" N VAL H 358 " --> pdb=" O SER H 384 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.931A pdb=" N VAL H 414 " --> pdb=" O THR H 492 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR H 492 " --> pdb=" O VAL H 414 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER H 416 " --> pdb=" O ASP H 490 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 436 through 437 Processing sheet with id=AC9, first strand: chain 'I' and resid 46 through 48 Processing sheet with id=AD1, first strand: chain 'I' and resid 94 through 95 removed outlier: 3.914A pdb=" N CYS I 95 " --> pdb=" O ILE I 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 179 through 185 removed outlier: 4.951A pdb=" N SER I 179 " --> pdb=" O GLN I 286 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N HIS I 288 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 390 through 392 removed outlier: 6.283A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 431 through 432 removed outlier: 3.595A pdb=" N THR I 432 " --> pdb=" O ILE I 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'J' and resid 119 through 121 removed outlier: 4.261A pdb=" N THR J 91 " --> pdb=" O VAL J 119 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA J 45 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL J 151 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 155 through 157 removed outlier: 4.018A pdb=" N ILE J 156 " --> pdb=" O ALA J 298 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA J 298 " --> pdb=" O ILE J 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.259A pdb=" N SER J 179 " --> pdb=" O GLN J 286 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS J 288 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N MET J 181 " --> pdb=" O HIS J 288 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS J 290 " --> pdb=" O MET J 181 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET J 183 " --> pdb=" O HIS J 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 212 through 214 removed outlier: 6.449A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL J 205 " --> pdb=" O GLU J 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 336 through 337 removed outlier: 3.525A pdb=" N ARG J 344 " --> pdb=" O THR J 336 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 355 through 356 removed outlier: 7.106A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 389 through 390 Processing sheet with id=AE3, first strand: chain 'J' and resid 411 through 412 removed outlier: 3.618A pdb=" N LEU J 412 " --> pdb=" O SER J 429 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'K' and resid 22 through 23 removed outlier: 3.606A pdb=" N VAL K 22 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 69 " --> pdb=" O VAL K 22 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'P' and resid 44 through 45 Processing sheet with id=AE6, first strand: chain 'P' and resid 159 through 160 removed outlier: 7.697A pdb=" N ILE P 159 " --> pdb=" O ASN P 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'P' and resid 277 through 278 removed outlier: 3.514A pdb=" N GLY P 277 " --> pdb=" O THR P 341 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLY P 340 " --> pdb=" O VAL P 319 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 419 through 420 removed outlier: 3.586A pdb=" N LYS P 426 " --> pdb=" O ALA P 419 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP P 456 " --> pdb=" O PHE P 376 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 414 through 415 removed outlier: 3.796A pdb=" N ALA P 442 " --> pdb=" O ASN P 407 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG P 452 " --> pdb=" O ARG P 445 " (cutoff:3.500A) 921 hydrogen bonds defined for protein. 2616 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: 6.20 Time building geometry restraints manager: 3.31 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: 10239 1.34 - 1.46: 6088 1.46 - 1.58: 16558 1.58 - 1.70: 0 1.70 - 1.82: 259 Bond restraints: 33144 Sorted by residual: bond pdb=" C ASP J 62 " pdb=" N GLN J 63 " ideal model delta sigma weight residual 1.329 1.256 0.073 1.86e-02 2.89e+03 1.54e+01 bond pdb=" C LEU H 499 " pdb=" N VAL H 500 " ideal model delta sigma weight residual 1.329 1.282 0.047 1.38e-02 5.25e+03 1.18e+01 bond pdb=" C LEU A 291 " pdb=" N THR A 292 " ideal model delta sigma weight residual 1.331 1.284 0.048 1.54e-02 4.22e+03 9.58e+00 bond pdb=" C LEU F 28 " pdb=" N PRO F 29 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.74e+00 bond pdb=" C TYR F 94 " pdb=" N PRO F 95 " ideal model delta sigma weight residual 1.336 1.364 -0.028 9.80e-03 1.04e+04 8.16e+00 ... (remaining 33139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 43991 4.02 - 8.04: 797 8.04 - 12.06: 101 12.06 - 16.08: 12 16.08 - 20.11: 2 Bond angle restraints: 44903 Sorted by residual: angle pdb=" N ILE F 36 " pdb=" CA ILE F 36 " pdb=" C ILE F 36 " ideal model delta sigma weight residual 112.17 105.72 6.45 9.50e-01 1.11e+00 4.61e+01 angle pdb=" N ILE P 192 " pdb=" CA ILE P 192 " pdb=" C ILE P 192 " ideal model delta sigma weight residual 113.20 106.77 6.43 9.60e-01 1.09e+00 4.48e+01 angle pdb=" N ASN K 179 " pdb=" CA ASN K 179 " pdb=" C ASN K 179 " ideal model delta sigma weight residual 111.07 118.23 -7.16 1.07e+00 8.73e-01 4.48e+01 angle pdb=" C CYS C 194 " pdb=" N ALA C 195 " pdb=" CA ALA C 195 " ideal model delta sigma weight residual 123.34 115.03 8.31 1.29e+00 6.01e-01 4.15e+01 angle pdb=" N LEU K 242 " pdb=" CA LEU K 242 " pdb=" C LEU K 242 " ideal model delta sigma weight residual 113.72 105.42 8.30 1.30e+00 5.92e-01 4.08e+01 ... (remaining 44898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 18114 15.91 - 31.82: 1679 31.82 - 47.73: 347 47.73 - 63.65: 16 63.65 - 79.56: 21 Dihedral angle restraints: 20177 sinusoidal: 7838 harmonic: 12339 Sorted by residual: dihedral pdb=" CA GLY E 47 " pdb=" C GLY E 47 " pdb=" N PHE E 48 " pdb=" CA PHE E 48 " ideal model delta harmonic sigma weight residual 180.00 126.78 53.22 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CA GLN A 156 " pdb=" C GLN A 156 " pdb=" N PRO A 157 " pdb=" CA PRO A 157 " ideal model delta harmonic sigma weight residual 180.00 132.75 47.25 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA MET P 180 " pdb=" C MET P 180 " pdb=" N LYS P 181 " pdb=" CA LYS P 181 " ideal model delta harmonic sigma weight residual 180.00 135.26 44.74 0 5.00e+00 4.00e-02 8.01e+01 ... (remaining 20174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4643 0.111 - 0.222: 586 0.222 - 0.332: 49 0.332 - 0.443: 3 0.443 - 0.554: 1 Chirality restraints: 5282 Sorted by residual: chirality pdb=" CB ILE G 198 " pdb=" CA ILE G 198 " pdb=" CG1 ILE G 198 " pdb=" CG2 ILE G 198 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILE K 65 " pdb=" CA ILE K 65 " pdb=" CG1 ILE K 65 " pdb=" CG2 ILE K 65 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CB ILE J 385 " pdb=" CA ILE J 385 " pdb=" CG1 ILE J 385 " pdb=" CG2 ILE J 385 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 5279 not shown) Planarity restraints: 5753 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 322 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.99e+01 pdb=" N PRO I 323 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO I 323 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO I 323 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 185 " 0.030 2.00e-02 2.50e+03 3.00e-02 1.57e+01 pdb=" CG PHE J 185 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE J 185 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE J 185 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE J 185 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE J 185 " 0.021 2.00e-02 2.50e+03 pdb=" CZ PHE J 185 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 156 " -0.064 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO A 157 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " -0.053 5.00e-02 4.00e+02 ... (remaining 5750 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 7 2.23 - 2.90: 12436 2.90 - 3.57: 46614 3.57 - 4.23: 72423 4.23 - 4.90: 117115 Nonbonded interactions: 248595 Sorted by model distance: nonbonded pdb=" CB VAL K 157 " pdb=" CD1 ILE K 180 " model vdw 1.563 3.890 nonbonded pdb=" CG1 VAL K 157 " pdb=" CD1 ILE K 180 " model vdw 1.700 3.880 nonbonded pdb=" CG2 VAL K 157 " pdb=" CD1 ILE K 180 " model vdw 1.859 3.880 nonbonded pdb=" ND2 ASN K 178 " pdb=" CD ARG K 182 " model vdw 2.148 3.520 nonbonded pdb=" O ASN K 178 " pdb=" CB ARG K 182 " model vdw 2.156 2.752 ... (remaining 248590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 1 through 267 or resid 276 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.380 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 33144 Z= 0.355 Angle : 1.398 20.105 44903 Z= 0.763 Chirality : 0.074 0.554 5282 Planarity : 0.009 0.111 5753 Dihedral : 12.846 79.557 12159 Min Nonbonded Distance : 1.563 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 15.32 % Favored : 84.63 % Rotamer: Outliers : 1.32 % Allowed : 7.87 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 4.73 % Twisted General : 0.79 % 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: -5.50 (0.10), residues: 4164 helix: -3.38 (0.10), residues: 1226 sheet: -3.90 (0.18), residues: 478 loop : -3.92 (0.10), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 136 TYR 0.060 0.004 TYR K 33 PHE 0.066 0.004 PHE J 185 TRP 0.037 0.003 TRP A 272 HIS 0.026 0.004 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00778 (33144) covalent geometry : angle 1.39775 (44903) hydrogen bonds : bond 0.18215 ( 921) hydrogen bonds : angle 8.44048 ( 2616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 602 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.6857 (ttm) cc_final: 0.6612 (ttt) REVERT: A 275 TYR cc_start: 0.7737 (t80) cc_final: 0.7128 (t80) REVERT: B 215 MET cc_start: 0.7383 (ptp) cc_final: 0.6279 (mmm) REVERT: B 220 LYS cc_start: 0.6959 (ptmt) cc_final: 0.6718 (tptt) REVERT: B 224 LYS cc_start: 0.6519 (ttpt) cc_final: 0.6172 (mtpt) REVERT: B 238 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6334 (pt) REVERT: C 58 MET cc_start: 0.7122 (ttp) cc_final: 0.6789 (ttm) REVERT: C 130 GLN cc_start: 0.6118 (pp30) cc_final: 0.5528 (pt0) REVERT: C 232 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7341 (p) REVERT: C 278 PHE cc_start: 0.6772 (t80) cc_final: 0.6102 (t80) REVERT: D 11 LEU cc_start: 0.5585 (pt) cc_final: 0.4690 (pt) REVERT: D 160 HIS cc_start: 0.7283 (m90) cc_final: 0.6883 (m90) REVERT: D 172 ARG cc_start: 0.6471 (mtm110) cc_final: 0.6261 (mtm-85) REVERT: D 229 VAL cc_start: 0.9358 (p) cc_final: 0.8981 (t) REVERT: E 8 MET cc_start: 0.6636 (mmt) cc_final: 0.6239 (mmt) REVERT: E 194 ARG cc_start: 0.7628 (tpt170) cc_final: 0.7373 (ttt180) REVERT: F 2 GLU cc_start: 0.4987 (pp20) cc_final: 0.4727 (pp20) REVERT: F 122 ARG cc_start: 0.6497 (mtp180) cc_final: 0.5181 (mmp-170) REVERT: F 131 LEU cc_start: 0.8874 (tt) cc_final: 0.8577 (tt) REVERT: F 214 PHE cc_start: 0.6197 (m-10) cc_final: 0.5981 (m-10) REVERT: G 452 PHE cc_start: 0.6943 (m-80) cc_final: 0.6490 (m-80) REVERT: H 506 MET cc_start: 0.7620 (pp-130) cc_final: 0.7370 (ppp) REVERT: I 57 PHE cc_start: 0.5673 (m-80) cc_final: 0.5459 (m-80) REVERT: I 147 ASP cc_start: 0.7733 (t0) cc_final: 0.7458 (t0) REVERT: I 149 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8079 (tt) REVERT: I 305 MET cc_start: 0.6840 (ttm) cc_final: 0.6638 (ttt) REVERT: I 339 ARG cc_start: 0.7255 (ptp-110) cc_final: 0.6959 (mtm-85) REVERT: J 61 LYS cc_start: 0.5894 (mmtm) cc_final: 0.5575 (mmtm) REVERT: J 92 PHE cc_start: 0.7508 (m-80) cc_final: 0.7003 (m-80) REVERT: J 270 ASP cc_start: 0.7936 (p0) cc_final: 0.7431 (m-30) REVERT: J 296 TYR cc_start: 0.6291 (p90) cc_final: 0.6017 (p90) REVERT: J 305 MET cc_start: 0.8251 (mmm) cc_final: 0.7843 (mmt) REVERT: J 328 THR cc_start: 0.7757 (m) cc_final: 0.7533 (m) REVERT: J 388 ASN cc_start: 0.7617 (t160) cc_final: 0.7376 (t0) REVERT: J 547 MET cc_start: 0.6075 (ttt) cc_final: 0.3346 (mpp) REVERT: J 608 MET cc_start: 0.3546 (mpp) cc_final: 0.3235 (mpp) REVERT: J 663 MET cc_start: 0.3632 (mtp) cc_final: 0.3391 (mtt) REVERT: K 30 MET cc_start: 0.6778 (tmt) cc_final: 0.5611 (tmt) REVERT: K 266 ARG cc_start: 0.6743 (mtt90) cc_final: 0.4406 (mmt180) REVERT: K 270 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6605 (t0) outliers start: 46 outliers final: 12 residues processed: 638 average time/residue: 0.2212 time to fit residues: 224.3193 Evaluate side-chains 382 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 366 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 8.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 214 GLN B 128 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN C 242 ASN ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN H 317 GLN H 455 ASN I 72 ASN I 192 HIS I 214 HIS I 216 GLN I 359 ASN I 409 HIS J 72 ASN J 105 HIS J 118 ASN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 279 ASN ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 HIS K 222 ASN P 184 HIS P 231 ASN P 329 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.135377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.120295 restraints weight = 91486.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.121462 restraints weight = 66583.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.121712 restraints weight = 51290.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122113 restraints weight = 46061.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.122296 restraints weight = 44328.238| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33144 Z= 0.168 Angle : 0.849 11.613 44903 Z= 0.441 Chirality : 0.052 0.269 5282 Planarity : 0.007 0.096 5753 Dihedral : 8.271 42.336 4557 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.51 % Favored : 87.44 % Rotamer: Outliers : 0.26 % Allowed : 6.07 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.30 % 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: -4.67 (0.11), residues: 4164 helix: -2.32 (0.12), residues: 1287 sheet: -3.58 (0.19), residues: 443 loop : -3.61 (0.11), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 169 TYR 0.028 0.002 TYR K 39 PHE 0.031 0.002 PHE J 185 TRP 0.014 0.002 TRP A 272 HIS 0.012 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00378 (33144) covalent geometry : angle 0.84908 (44903) hydrogen bonds : bond 0.05462 ( 921) hydrogen bonds : angle 6.46141 ( 2616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 484 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.8500 (mm) cc_final: 0.8297 (mm) REVERT: A 31 LEU cc_start: 0.7817 (tt) cc_final: 0.7616 (mm) REVERT: A 110 LYS cc_start: 0.7437 (mtmt) cc_final: 0.7163 (mtmt) REVERT: A 285 PHE cc_start: 0.7518 (m-80) cc_final: 0.7010 (m-80) REVERT: B 220 LYS cc_start: 0.7229 (ptmt) cc_final: 0.6781 (tptt) REVERT: B 223 ASN cc_start: 0.7801 (t0) cc_final: 0.7574 (t0) REVERT: C 58 MET cc_start: 0.7317 (ttp) cc_final: 0.6957 (ttm) REVERT: C 130 GLN cc_start: 0.6069 (pp30) cc_final: 0.5413 (pt0) REVERT: C 277 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7944 (tp-100) REVERT: C 278 PHE cc_start: 0.6184 (t80) cc_final: 0.5768 (t80) REVERT: C 340 MET cc_start: 0.5570 (mtt) cc_final: 0.4848 (mtt) REVERT: D 58 MET cc_start: 0.8316 (mtm) cc_final: 0.8103 (mtp) REVERT: D 172 ARG cc_start: 0.6267 (mtm110) cc_final: 0.6043 (mtm-85) REVERT: E 1 MET cc_start: 0.4050 (tmm) cc_final: 0.2188 (tpp) REVERT: E 194 ARG cc_start: 0.7640 (tpt170) cc_final: 0.7368 (ttp-170) REVERT: E 216 MET cc_start: 0.4395 (tmm) cc_final: 0.4130 (ppp) REVERT: F 84 MET cc_start: 0.2587 (mpp) cc_final: 0.2142 (mpp) REVERT: F 122 ARG cc_start: 0.6962 (mtp180) cc_final: 0.5091 (mmp-170) REVERT: F 131 LEU cc_start: 0.8722 (tt) cc_final: 0.8465 (tt) REVERT: F 133 ARG cc_start: 0.6207 (ttt180) cc_final: 0.5859 (ttt180) REVERT: G 188 ARG cc_start: 0.6957 (ptp90) cc_final: 0.6628 (ptp90) REVERT: H 506 MET cc_start: 0.7507 (ptt) cc_final: 0.6942 (ppp) REVERT: I 57 PHE cc_start: 0.5599 (m-80) cc_final: 0.5311 (m-10) REVERT: I 147 ASP cc_start: 0.7792 (t0) cc_final: 0.7502 (t0) REVERT: I 339 ARG cc_start: 0.6968 (ptp-110) cc_final: 0.6637 (mtp85) REVERT: I 414 CYS cc_start: 0.7042 (t) cc_final: 0.6102 (m) REVERT: J 270 ASP cc_start: 0.8222 (p0) cc_final: 0.7359 (m-30) REVERT: J 296 TYR cc_start: 0.6265 (p90) cc_final: 0.5863 (p90) REVERT: J 305 MET cc_start: 0.7703 (mmm) cc_final: 0.7380 (mmt) REVERT: J 547 MET cc_start: 0.5835 (ttt) cc_final: 0.3196 (mpp) REVERT: K 270 ASN cc_start: 0.8158 (t0) cc_final: 0.7778 (t0) REVERT: P 270 GLU cc_start: 0.6123 (pm20) cc_final: 0.5708 (pm20) outliers start: 9 outliers final: 1 residues processed: 487 average time/residue: 0.2059 time to fit residues: 163.0977 Evaluate side-chains 364 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 234 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 299 optimal weight: 0.4980 chunk 286 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 179 optimal weight: 40.0000 chunk 350 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 48 ASN B 128 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN G 281 ASN H 479 HIS I 216 GLN J 72 ASN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 GLN J 267 GLN J 376 ASN K 132 GLN P 173 HIS P 401 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.139078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123399 restraints weight = 88777.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.125255 restraints weight = 65795.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.125997 restraints weight = 47146.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.126333 restraints weight = 38647.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.126511 restraints weight = 36048.651| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33144 Z= 0.132 Angle : 0.757 11.125 44903 Z= 0.387 Chirality : 0.049 0.257 5282 Planarity : 0.006 0.085 5753 Dihedral : 7.254 42.533 4557 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.98 % Favored : 89.00 % Rotamer: Outliers : 0.23 % Allowed : 6.93 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.17 % 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: -4.03 (0.12), residues: 4164 helix: -1.57 (0.13), residues: 1298 sheet: -3.24 (0.21), residues: 420 loop : -3.37 (0.11), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 225 TYR 0.028 0.002 TYR K 39 PHE 0.029 0.002 PHE J 185 TRP 0.010 0.001 TRP H 476 HIS 0.009 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00289 (33144) covalent geometry : angle 0.75692 (44903) hydrogen bonds : bond 0.04506 ( 921) hydrogen bonds : angle 5.79491 ( 2616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 494 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 PHE cc_start: 0.7277 (m-80) cc_final: 0.6688 (m-80) REVERT: B 93 MET cc_start: 0.5058 (mpp) cc_final: 0.3495 (mmt) REVERT: B 215 MET cc_start: 0.7542 (mtp) cc_final: 0.6829 (mmm) REVERT: C 58 MET cc_start: 0.7213 (ttp) cc_final: 0.6899 (ttm) REVERT: C 130 GLN cc_start: 0.5810 (pp30) cc_final: 0.5141 (pt0) REVERT: C 144 LEU cc_start: 0.3369 (mt) cc_final: 0.2429 (pp) REVERT: C 278 PHE cc_start: 0.6193 (t80) cc_final: 0.5890 (t80) REVERT: C 340 MET cc_start: 0.5308 (mtt) cc_final: 0.4662 (mtt) REVERT: D 236 THR cc_start: 0.8769 (t) cc_final: 0.8494 (p) REVERT: D 271 MET cc_start: 0.7253 (tpp) cc_final: 0.6985 (tmm) REVERT: E 1 MET cc_start: 0.3687 (tmm) cc_final: 0.1755 (tpp) REVERT: E 52 ILE cc_start: 0.7548 (mp) cc_final: 0.7232 (mm) REVERT: F 84 MET cc_start: 0.2803 (mpp) cc_final: 0.1564 (tpt) REVERT: G 195 PHE cc_start: 0.5740 (m-10) cc_final: 0.5505 (m-80) REVERT: G 285 THR cc_start: 0.7281 (m) cc_final: 0.7074 (m) REVERT: G 483 ARG cc_start: 0.8194 (mmt-90) cc_final: 0.7050 (ttm-80) REVERT: H 273 MET cc_start: 0.7520 (mmt) cc_final: 0.7056 (mmt) REVERT: I 57 PHE cc_start: 0.5619 (m-80) cc_final: 0.5359 (m-10) REVERT: I 147 ASP cc_start: 0.7623 (t0) cc_final: 0.7208 (t0) REVERT: I 414 CYS cc_start: 0.6837 (t) cc_final: 0.6472 (m) REVERT: J 57 PHE cc_start: 0.7082 (m-80) cc_final: 0.6247 (p90) REVERT: J 88 VAL cc_start: 0.8509 (t) cc_final: 0.8174 (m) REVERT: J 90 GLU cc_start: 0.5136 (mm-30) cc_final: 0.4640 (tp30) REVERT: J 181 MET cc_start: 0.6534 (mmp) cc_final: 0.5844 (mmt) REVERT: J 264 PHE cc_start: 0.5320 (m-80) cc_final: 0.4720 (m-80) REVERT: J 270 ASP cc_start: 0.8041 (p0) cc_final: 0.7259 (m-30) REVERT: J 547 MET cc_start: 0.5700 (ttt) cc_final: 0.3061 (mpp) REVERT: J 608 MET cc_start: 0.3153 (mpp) cc_final: 0.2278 (mpp) REVERT: J 646 LEU cc_start: 0.6741 (mt) cc_final: 0.6328 (mt) REVERT: K 103 THR cc_start: 0.8986 (m) cc_final: 0.8684 (p) REVERT: K 132 GLN cc_start: 0.7859 (tp40) cc_final: 0.7445 (tp40) REVERT: K 255 MET cc_start: 0.4374 (mmt) cc_final: 0.3296 (mtp) REVERT: K 270 ASN cc_start: 0.8009 (t0) cc_final: 0.7644 (t0) REVERT: P 270 GLU cc_start: 0.5942 (pm20) cc_final: 0.5604 (pm20) REVERT: P 272 ASP cc_start: 0.7402 (m-30) cc_final: 0.6909 (m-30) outliers start: 8 outliers final: 2 residues processed: 499 average time/residue: 0.1971 time to fit residues: 161.4027 Evaluate side-chains 361 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 88 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 31 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 414 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 48 ASN B 128 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN G 281 ASN H 479 HIS I 216 GLN ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 598 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.123435 restraints weight = 89341.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124493 restraints weight = 65494.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.124898 restraints weight = 50729.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.125215 restraints weight = 46986.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.125573 restraints weight = 42101.260| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33144 Z= 0.138 Angle : 0.753 10.182 44903 Z= 0.384 Chirality : 0.049 0.259 5282 Planarity : 0.006 0.099 5753 Dihedral : 6.939 40.476 4557 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.31 % Favored : 88.66 % Rotamer: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.15 % 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: -3.72 (0.12), residues: 4164 helix: -1.17 (0.14), residues: 1277 sheet: -3.12 (0.21), residues: 436 loop : -3.23 (0.11), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.000 ARG G 517 TYR 0.038 0.002 TYR K 39 PHE 0.035 0.002 PHE J 185 TRP 0.014 0.001 TRP J 628 HIS 0.013 0.001 HIS J 598 Details of bonding type rmsd covalent geometry : bond 0.00313 (33144) covalent geometry : angle 0.75333 (44903) hydrogen bonds : bond 0.04299 ( 921) hydrogen bonds : angle 5.60928 ( 2616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 474 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 PHE cc_start: 0.7191 (m-80) cc_final: 0.6900 (m-80) REVERT: B 215 MET cc_start: 0.7343 (mtp) cc_final: 0.6931 (mmm) REVERT: C 58 MET cc_start: 0.7000 (ttp) cc_final: 0.6745 (ttm) REVERT: C 91 GLU cc_start: 0.4100 (mm-30) cc_final: 0.3169 (tm-30) REVERT: C 130 GLN cc_start: 0.5844 (pp30) cc_final: 0.5050 (pt0) REVERT: C 144 LEU cc_start: 0.3438 (mt) cc_final: 0.2461 (pp) REVERT: C 278 PHE cc_start: 0.6834 (t80) cc_final: 0.6286 (t80) REVERT: C 292 GLU cc_start: 0.8000 (pp20) cc_final: 0.7664 (pm20) REVERT: C 340 MET cc_start: 0.5157 (mtt) cc_final: 0.4481 (mtt) REVERT: D 236 THR cc_start: 0.8888 (t) cc_final: 0.8614 (p) REVERT: D 271 MET cc_start: 0.7048 (tpp) cc_final: 0.6826 (tmm) REVERT: E 1 MET cc_start: 0.3491 (tmm) cc_final: 0.1765 (tpp) REVERT: E 52 ILE cc_start: 0.7524 (mp) cc_final: 0.7209 (mm) REVERT: F 84 MET cc_start: 0.2981 (mpp) cc_final: 0.1714 (tpt) REVERT: F 133 ARG cc_start: 0.6234 (ttt180) cc_final: 0.4255 (tpm170) REVERT: G 186 TYR cc_start: 0.6927 (m-10) cc_final: 0.5909 (m-10) REVERT: G 367 LEU cc_start: 0.8506 (tp) cc_final: 0.8162 (mm) REVERT: G 489 TYR cc_start: 0.6378 (m-80) cc_final: 0.5951 (m-80) REVERT: H 229 LEU cc_start: 0.7168 (tp) cc_final: 0.6687 (tp) REVERT: H 273 MET cc_start: 0.7324 (mmt) cc_final: 0.6648 (mmt) REVERT: H 394 VAL cc_start: 0.6187 (t) cc_final: 0.5958 (t) REVERT: I 57 PHE cc_start: 0.5655 (m-80) cc_final: 0.5371 (m-10) REVERT: I 147 ASP cc_start: 0.7458 (t0) cc_final: 0.7105 (t0) REVERT: I 372 CYS cc_start: 0.7878 (m) cc_final: 0.7469 (m) REVERT: I 414 CYS cc_start: 0.6996 (t) cc_final: 0.6565 (m) REVERT: J 57 PHE cc_start: 0.6947 (m-80) cc_final: 0.6072 (p90) REVERT: J 88 VAL cc_start: 0.8558 (t) cc_final: 0.8202 (m) REVERT: J 264 PHE cc_start: 0.5507 (m-80) cc_final: 0.4905 (m-80) REVERT: J 270 ASP cc_start: 0.8004 (p0) cc_final: 0.7248 (m-30) REVERT: J 398 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7395 (tp-100) REVERT: J 547 MET cc_start: 0.5741 (ttt) cc_final: 0.3083 (mpp) REVERT: J 608 MET cc_start: 0.3484 (mpp) cc_final: 0.2516 (mpp) REVERT: K 33 TYR cc_start: 0.5799 (p90) cc_final: 0.5357 (p90) REVERT: K 103 THR cc_start: 0.8931 (m) cc_final: 0.8626 (p) REVERT: K 132 GLN cc_start: 0.7611 (tp40) cc_final: 0.7387 (tp40) REVERT: K 255 MET cc_start: 0.4537 (mmt) cc_final: 0.3677 (mtp) REVERT: K 266 ARG cc_start: 0.5377 (mtt90) cc_final: 0.4575 (mmt180) REVERT: K 270 ASN cc_start: 0.7977 (t0) cc_final: 0.7619 (t0) REVERT: P 270 GLU cc_start: 0.6026 (pm20) cc_final: 0.5593 (pm20) REVERT: P 272 ASP cc_start: 0.7422 (m-30) cc_final: 0.6963 (m-30) outliers start: 2 outliers final: 1 residues processed: 476 average time/residue: 0.1948 time to fit residues: 155.3389 Evaluate side-chains 360 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 303 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 284 optimal weight: 10.0000 chunk 309 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 414 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 355 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 128 HIS ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 ASN G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN G 478 ASN ** I 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 286 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 598 HIS K 10 GLN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.131051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115839 restraints weight = 93065.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.117114 restraints weight = 67442.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.117308 restraints weight = 52158.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.117471 restraints weight = 47349.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.117642 restraints weight = 47664.391| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 33144 Z= 0.240 Angle : 0.882 11.347 44903 Z= 0.456 Chirality : 0.053 0.265 5282 Planarity : 0.006 0.084 5753 Dihedral : 7.456 39.665 4557 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.03 % Favored : 84.97 % Rotamer: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.22 % 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: -3.93 (0.12), residues: 4164 helix: -1.45 (0.13), residues: 1285 sheet: -3.21 (0.21), residues: 433 loop : -3.31 (0.11), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 237 TYR 0.038 0.003 TYR C 93 PHE 0.035 0.003 PHE J 185 TRP 0.025 0.002 TRP J 628 HIS 0.011 0.002 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00558 (33144) covalent geometry : angle 0.88207 (44903) hydrogen bonds : bond 0.05073 ( 921) hydrogen bonds : angle 5.99312 ( 2616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 426 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.6913 (t80) cc_final: 0.6682 (m-80) REVERT: A 285 PHE cc_start: 0.7628 (m-80) cc_final: 0.7124 (m-80) REVERT: C 58 MET cc_start: 0.6886 (ttp) cc_final: 0.6662 (ttm) REVERT: C 130 GLN cc_start: 0.5897 (pp30) cc_final: 0.5121 (pt0) REVERT: C 278 PHE cc_start: 0.7219 (t80) cc_final: 0.6560 (t80) REVERT: C 304 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7559 (mm-30) REVERT: C 340 MET cc_start: 0.5106 (mtt) cc_final: 0.4267 (mtt) REVERT: D 203 MET cc_start: 0.7197 (tmm) cc_final: 0.6959 (tmm) REVERT: D 271 MET cc_start: 0.6779 (tpp) cc_final: 0.6330 (tmm) REVERT: E 1 MET cc_start: 0.3748 (tmm) cc_final: 0.2196 (tpp) REVERT: E 8 MET cc_start: 0.7221 (mmt) cc_final: 0.7012 (mmt) REVERT: E 52 ILE cc_start: 0.7420 (mp) cc_final: 0.7102 (mm) REVERT: F 50 GLU cc_start: 0.7539 (pm20) cc_final: 0.7262 (mp0) REVERT: F 84 MET cc_start: 0.3807 (mpp) cc_final: 0.1886 (tpt) REVERT: G 195 PHE cc_start: 0.5688 (m-10) cc_final: 0.5480 (m-80) REVERT: G 326 LYS cc_start: 0.8464 (tppt) cc_final: 0.7913 (tptm) REVERT: G 366 TRP cc_start: 0.7604 (m-90) cc_final: 0.6855 (m100) REVERT: G 489 TYR cc_start: 0.6364 (m-80) cc_final: 0.6023 (m-80) REVERT: H 273 MET cc_start: 0.7368 (mmt) cc_final: 0.6854 (mmt) REVERT: I 57 PHE cc_start: 0.5847 (m-80) cc_final: 0.5549 (m-80) REVERT: I 147 ASP cc_start: 0.7613 (t0) cc_final: 0.7222 (t0) REVERT: I 372 CYS cc_start: 0.7997 (m) cc_final: 0.7517 (m) REVERT: I 414 CYS cc_start: 0.6851 (t) cc_final: 0.6415 (m) REVERT: J 81 GLU cc_start: 0.6542 (mm-30) cc_final: 0.4521 (tm-30) REVERT: J 88 VAL cc_start: 0.8507 (t) cc_final: 0.8211 (m) REVERT: J 158 ASN cc_start: 0.6711 (p0) cc_final: 0.6464 (p0) REVERT: J 265 ASP cc_start: 0.7010 (p0) cc_final: 0.5778 (t0) REVERT: J 270 ASP cc_start: 0.8426 (p0) cc_final: 0.7854 (m-30) REVERT: J 296 TYR cc_start: 0.5669 (p90) cc_final: 0.5338 (p90) REVERT: J 305 MET cc_start: 0.6795 (mmp) cc_final: 0.6548 (mmt) REVERT: J 398 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7471 (tm-30) REVERT: J 547 MET cc_start: 0.5480 (ttt) cc_final: 0.2919 (mpp) REVERT: J 608 MET cc_start: 0.3692 (mpp) cc_final: 0.2834 (mpp) REVERT: K 255 MET cc_start: 0.4132 (mmt) cc_final: 0.3361 (mtm) REVERT: K 266 ARG cc_start: 0.5850 (mtt90) cc_final: 0.4530 (mmt180) REVERT: K 270 ASN cc_start: 0.8242 (t0) cc_final: 0.7768 (t0) REVERT: P 77 ILE cc_start: 0.6783 (mm) cc_final: 0.6508 (mm) REVERT: P 270 GLU cc_start: 0.6127 (pm20) cc_final: 0.5651 (pm20) outliers start: 6 outliers final: 2 residues processed: 431 average time/residue: 0.1923 time to fit residues: 138.6416 Evaluate side-chains 338 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 131 optimal weight: 4.9990 chunk 220 optimal weight: 0.9980 chunk 325 optimal weight: 6.9990 chunk 198 optimal weight: 0.0570 chunk 379 optimal weight: 4.9990 chunk 318 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 273 optimal weight: 0.1980 chunk 408 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.2500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN A 243 GLN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 GLN G 478 ASN G 486 ASN H 479 HIS I 216 GLN ** I 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 359 ASN J 376 ASN P 85 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.136212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.121423 restraints weight = 89690.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122442 restraints weight = 66564.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.122534 restraints weight = 53173.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.123032 restraints weight = 50103.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.123311 restraints weight = 42834.693| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33144 Z= 0.136 Angle : 0.772 10.806 44903 Z= 0.387 Chirality : 0.050 0.316 5282 Planarity : 0.005 0.079 5753 Dihedral : 6.823 39.978 4557 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.09 % Allowed : 3.66 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.12 % 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: -3.55 (0.12), residues: 4164 helix: -1.05 (0.14), residues: 1287 sheet: -3.08 (0.21), residues: 411 loop : -3.11 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 14 TYR 0.032 0.002 TYR K 39 PHE 0.026 0.002 PHE A 118 TRP 0.010 0.001 TRP J 684 HIS 0.008 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00310 (33144) covalent geometry : angle 0.77160 (44903) hydrogen bonds : bond 0.04266 ( 921) hydrogen bonds : angle 5.52531 ( 2616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 469 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TYR cc_start: 0.6827 (t80) cc_final: 0.6603 (m-80) REVERT: A 275 TYR cc_start: 0.7356 (t80) cc_final: 0.7058 (t80) REVERT: A 285 PHE cc_start: 0.7207 (m-80) cc_final: 0.6968 (m-80) REVERT: C 58 MET cc_start: 0.7290 (ttp) cc_final: 0.6978 (ttm) REVERT: C 91 GLU cc_start: 0.4383 (mm-30) cc_final: 0.3400 (tm-30) REVERT: C 277 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7840 (mm-40) REVERT: C 278 PHE cc_start: 0.6978 (t80) cc_final: 0.6395 (t80) REVERT: C 340 MET cc_start: 0.4972 (mtt) cc_final: 0.4122 (mtt) REVERT: D 236 THR cc_start: 0.8629 (t) cc_final: 0.8378 (p) REVERT: D 237 LYS cc_start: 0.8449 (tmtt) cc_final: 0.7780 (tptt) REVERT: D 271 MET cc_start: 0.6731 (tpp) cc_final: 0.6310 (tmm) REVERT: E 1 MET cc_start: 0.3257 (tmm) cc_final: 0.1829 (tpp) REVERT: E 52 ILE cc_start: 0.7455 (mp) cc_final: 0.7165 (mm) REVERT: F 84 MET cc_start: 0.3714 (mpp) cc_final: 0.1806 (tpt) REVERT: F 133 ARG cc_start: 0.6215 (ttt180) cc_final: 0.4305 (tpm170) REVERT: G 483 ARG cc_start: 0.8130 (mmt-90) cc_final: 0.6677 (mtt-85) REVERT: G 489 TYR cc_start: 0.5931 (m-80) cc_final: 0.5665 (m-80) REVERT: H 183 LEU cc_start: 0.7319 (tt) cc_final: 0.6824 (tt) REVERT: H 273 MET cc_start: 0.7210 (mmt) cc_final: 0.6790 (mmt) REVERT: I 147 ASP cc_start: 0.7601 (t0) cc_final: 0.7172 (t0) REVERT: I 414 CYS cc_start: 0.6671 (t) cc_final: 0.6322 (m) REVERT: J 57 PHE cc_start: 0.7027 (m-80) cc_final: 0.6058 (p90) REVERT: J 88 VAL cc_start: 0.8735 (t) cc_final: 0.8521 (m) REVERT: J 181 MET cc_start: 0.6936 (mmp) cc_final: 0.5923 (mmt) REVERT: J 265 ASP cc_start: 0.6601 (p0) cc_final: 0.5914 (t0) REVERT: J 270 ASP cc_start: 0.8463 (p0) cc_final: 0.7674 (m-30) REVERT: J 422 ARG cc_start: 0.8745 (mtp180) cc_final: 0.8228 (mmm-85) REVERT: J 547 MET cc_start: 0.5314 (ttt) cc_final: 0.2706 (mpp) REVERT: J 608 MET cc_start: 0.3893 (mpp) cc_final: 0.2896 (mpp) REVERT: K 103 THR cc_start: 0.9100 (m) cc_final: 0.8712 (p) REVERT: K 132 GLN cc_start: 0.7985 (tp40) cc_final: 0.7267 (tp-100) REVERT: K 255 MET cc_start: 0.4432 (mmt) cc_final: 0.3830 (mtp) REVERT: K 266 ARG cc_start: 0.5872 (mtt90) cc_final: 0.4519 (mmt180) REVERT: K 270 ASN cc_start: 0.8096 (t0) cc_final: 0.7573 (t0) REVERT: P 270 GLU cc_start: 0.5956 (pm20) cc_final: 0.5578 (pm20) REVERT: P 272 ASP cc_start: 0.7631 (m-30) cc_final: 0.7321 (m-30) outliers start: 3 outliers final: 0 residues processed: 471 average time/residue: 0.1946 time to fit residues: 153.0899 Evaluate side-chains 364 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 243 optimal weight: 0.4980 chunk 277 optimal weight: 0.7980 chunk 359 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 195 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 177 optimal weight: 50.0000 chunk 334 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 150 ASN D 349 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN H 455 ASN I 197 HIS I 216 GLN J 267 GLN J 398 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.136775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.121716 restraints weight = 90280.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.122889 restraints weight = 70295.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.123346 restraints weight = 53413.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123766 restraints weight = 46912.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.124056 restraints weight = 41234.487| |-----------------------------------------------------------------------------| r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33144 Z= 0.134 Angle : 0.753 10.105 44903 Z= 0.379 Chirality : 0.049 0.262 5282 Planarity : 0.005 0.070 5753 Dihedral : 6.596 39.374 4557 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 0.06 % Allowed : 2.86 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.10 % 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: -3.31 (0.12), residues: 4164 helix: -0.81 (0.14), residues: 1277 sheet: -2.88 (0.22), residues: 409 loop : -2.99 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG J 563 TYR 0.031 0.002 TYR K 39 PHE 0.025 0.002 PHE K 102 TRP 0.023 0.001 TRP J 628 HIS 0.009 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00305 (33144) covalent geometry : angle 0.75349 (44903) hydrogen bonds : bond 0.04102 ( 921) hydrogen bonds : angle 5.42213 ( 2616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ILE cc_start: 0.6419 (tt) cc_final: 0.6195 (tt) REVERT: A 275 TYR cc_start: 0.7220 (t80) cc_final: 0.6788 (t80) REVERT: A 285 PHE cc_start: 0.7166 (m-80) cc_final: 0.6611 (m-80) REVERT: B 215 MET cc_start: 0.7995 (ttm) cc_final: 0.7739 (ttm) REVERT: C 144 LEU cc_start: 0.3700 (mt) cc_final: 0.2847 (pp) REVERT: C 278 PHE cc_start: 0.6940 (t80) cc_final: 0.6667 (t80) REVERT: D 41 LEU cc_start: 0.7737 (mt) cc_final: 0.7513 (mt) REVERT: D 236 THR cc_start: 0.8665 (t) cc_final: 0.8415 (p) REVERT: D 262 SER cc_start: 0.7526 (t) cc_final: 0.7292 (t) REVERT: D 271 MET cc_start: 0.6694 (tpp) cc_final: 0.6223 (tmm) REVERT: E 1 MET cc_start: 0.3310 (tmm) cc_final: 0.2001 (tpp) REVERT: F 84 MET cc_start: 0.3653 (mpp) cc_final: 0.1825 (tpt) REVERT: F 133 ARG cc_start: 0.6238 (ttt180) cc_final: 0.4304 (tpm170) REVERT: G 186 TYR cc_start: 0.7145 (m-10) cc_final: 0.6365 (m-10) REVERT: G 209 ARG cc_start: 0.8243 (ttt90) cc_final: 0.7479 (ttp-170) REVERT: G 456 GLU cc_start: 0.7844 (mp0) cc_final: 0.7609 (mp0) REVERT: G 483 ARG cc_start: 0.8059 (mmt-90) cc_final: 0.6688 (mtt-85) REVERT: G 489 TYR cc_start: 0.6128 (m-80) cc_final: 0.5898 (m-80) REVERT: H 273 MET cc_start: 0.7048 (mmt) cc_final: 0.6637 (mmt) REVERT: H 324 TYR cc_start: 0.6613 (t80) cc_final: 0.6410 (t80) REVERT: H 364 ARG cc_start: 0.7395 (mtt180) cc_final: 0.7058 (ttm-80) REVERT: I 147 ASP cc_start: 0.7618 (t0) cc_final: 0.7183 (t0) REVERT: I 414 CYS cc_start: 0.6729 (t) cc_final: 0.6363 (m) REVERT: J 57 PHE cc_start: 0.6915 (m-80) cc_final: 0.6101 (p90) REVERT: J 81 GLU cc_start: 0.5769 (mp0) cc_final: 0.5330 (tp30) REVERT: J 88 VAL cc_start: 0.8715 (t) cc_final: 0.8455 (m) REVERT: J 265 ASP cc_start: 0.5983 (p0) cc_final: 0.5526 (t0) REVERT: J 270 ASP cc_start: 0.8455 (p0) cc_final: 0.7638 (m-30) REVERT: J 422 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8228 (mmm-85) REVERT: J 547 MET cc_start: 0.5298 (ttt) cc_final: 0.2698 (mpp) REVERT: J 608 MET cc_start: 0.3916 (mpp) cc_final: 0.2882 (mpp) REVERT: K 103 THR cc_start: 0.9020 (m) cc_final: 0.8704 (p) REVERT: K 132 GLN cc_start: 0.7906 (tp40) cc_final: 0.7215 (tp-100) REVERT: K 255 MET cc_start: 0.4279 (mmt) cc_final: 0.3876 (mtp) REVERT: K 266 ARG cc_start: 0.5955 (mtt90) cc_final: 0.4455 (mmt180) REVERT: K 270 ASN cc_start: 0.8017 (t0) cc_final: 0.7520 (t0) REVERT: P 270 GLU cc_start: 0.5961 (pm20) cc_final: 0.5487 (pm20) REVERT: P 272 ASP cc_start: 0.7696 (m-30) cc_final: 0.7411 (m-30) outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.1819 time to fit residues: 140.7364 Evaluate side-chains 348 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 369 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 168 optimal weight: 0.0470 chunk 367 optimal weight: 0.0050 chunk 389 optimal weight: 20.0000 chunk 371 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 overall best weight: 1.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN H 479 HIS I 168 HIS I 216 GLN ** J 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 286 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.136551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.121686 restraints weight = 90333.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122560 restraints weight = 68997.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.123099 restraints weight = 54659.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.123644 restraints weight = 46093.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123812 restraints weight = 42550.930| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33144 Z= 0.140 Angle : 0.766 14.235 44903 Z= 0.384 Chirality : 0.049 0.241 5282 Planarity : 0.005 0.070 5753 Dihedral : 6.507 39.269 4557 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 0.11 % Allowed : 2.00 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.10 % 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: -3.24 (0.12), residues: 4164 helix: -0.78 (0.14), residues: 1289 sheet: -2.62 (0.23), residues: 426 loop : -2.98 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 563 TYR 0.031 0.002 TYR K 39 PHE 0.027 0.002 PHE K 102 TRP 0.014 0.001 TRP C 51 HIS 0.009 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00324 (33144) covalent geometry : angle 0.76559 (44903) hydrogen bonds : bond 0.04113 ( 921) hydrogen bonds : angle 5.38700 ( 2616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 450 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ILE cc_start: 0.6561 (tt) cc_final: 0.6239 (tt) REVERT: A 275 TYR cc_start: 0.7330 (t80) cc_final: 0.6807 (t80) REVERT: A 285 PHE cc_start: 0.7216 (m-80) cc_final: 0.6704 (m-80) REVERT: B 93 MET cc_start: 0.5289 (pmm) cc_final: 0.4237 (ptm) REVERT: B 215 MET cc_start: 0.8084 (ttm) cc_final: 0.7845 (ttm) REVERT: C 144 LEU cc_start: 0.3648 (mt) cc_final: 0.2897 (pp) REVERT: C 278 PHE cc_start: 0.6948 (t80) cc_final: 0.6644 (t80) REVERT: D 236 THR cc_start: 0.8686 (t) cc_final: 0.8396 (p) REVERT: D 271 MET cc_start: 0.6857 (tpp) cc_final: 0.6236 (tmm) REVERT: E 1 MET cc_start: 0.3440 (tmm) cc_final: 0.2723 (tpp) REVERT: F 84 MET cc_start: 0.3373 (mpp) cc_final: 0.1576 (tpt) REVERT: F 133 ARG cc_start: 0.6159 (ttt180) cc_final: 0.4283 (tpm170) REVERT: G 186 TYR cc_start: 0.7272 (m-10) cc_final: 0.6647 (m-10) REVERT: G 196 MET cc_start: 0.7724 (tpt) cc_final: 0.7333 (tpt) REVERT: G 209 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7435 (ttp-170) REVERT: G 285 THR cc_start: 0.7595 (m) cc_final: 0.7388 (m) REVERT: G 483 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.7353 (mtp85) REVERT: G 489 TYR cc_start: 0.6165 (m-80) cc_final: 0.5709 (m-80) REVERT: H 324 TYR cc_start: 0.6570 (t80) cc_final: 0.6298 (t80) REVERT: H 364 ARG cc_start: 0.7218 (mtt180) cc_final: 0.6906 (ttm-80) REVERT: I 147 ASP cc_start: 0.7609 (t0) cc_final: 0.7182 (t0) REVERT: I 414 CYS cc_start: 0.6786 (t) cc_final: 0.6407 (m) REVERT: J 57 PHE cc_start: 0.6956 (m-80) cc_final: 0.6099 (p90) REVERT: J 88 VAL cc_start: 0.8596 (t) cc_final: 0.8332 (m) REVERT: J 265 ASP cc_start: 0.6020 (p0) cc_final: 0.5630 (t0) REVERT: J 270 ASP cc_start: 0.8480 (p0) cc_final: 0.7667 (m-30) REVERT: J 422 ARG cc_start: 0.8699 (mtp180) cc_final: 0.8167 (mmm-85) REVERT: J 547 MET cc_start: 0.5246 (ttt) cc_final: 0.2704 (mpp) REVERT: J 608 MET cc_start: 0.3874 (mpp) cc_final: 0.2864 (mpp) REVERT: K 30 MET cc_start: 0.6427 (tmm) cc_final: 0.5946 (tmm) REVERT: K 103 THR cc_start: 0.9032 (m) cc_final: 0.8743 (p) REVERT: K 132 GLN cc_start: 0.7850 (tp40) cc_final: 0.7240 (tp-100) REVERT: K 266 ARG cc_start: 0.6111 (mtt90) cc_final: 0.4378 (mmt180) REVERT: K 270 ASN cc_start: 0.7884 (t0) cc_final: 0.7393 (t0) REVERT: P 270 GLU cc_start: 0.5747 (pm20) cc_final: 0.5493 (pm20) REVERT: P 272 ASP cc_start: 0.7685 (m-30) cc_final: 0.7407 (m-30) outliers start: 4 outliers final: 0 residues processed: 453 average time/residue: 0.1949 time to fit residues: 147.0546 Evaluate side-chains 351 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 138 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 238 optimal weight: 0.3980 chunk 415 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 405 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 213 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 HIS ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 280 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 HIS I 216 GLN J 267 GLN J 286 GLN J 568 ASN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.134030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.119217 restraints weight = 91139.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120125 restraints weight = 71182.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.120363 restraints weight = 56632.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.120628 restraints weight = 51659.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.121009 restraints weight = 46605.916| |-----------------------------------------------------------------------------| r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33144 Z= 0.177 Angle : 0.804 10.003 44903 Z= 0.407 Chirality : 0.051 0.281 5282 Planarity : 0.006 0.074 5753 Dihedral : 6.696 39.794 4557 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 0.14 % Allowed : 1.43 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.12 % 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: -3.32 (0.12), residues: 4164 helix: -0.90 (0.14), residues: 1284 sheet: -2.77 (0.22), residues: 413 loop : -2.98 (0.12), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 297 TYR 0.032 0.002 TYR K 39 PHE 0.031 0.002 PHE J 185 TRP 0.030 0.002 TRP J 628 HIS 0.010 0.001 HIS C 188 Details of bonding type rmsd covalent geometry : bond 0.00415 (33144) covalent geometry : angle 0.80398 (44903) hydrogen bonds : bond 0.04310 ( 921) hydrogen bonds : angle 5.57533 ( 2616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 434 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7543 (mtmt) REVERT: A 206 ILE cc_start: 0.6979 (tt) cc_final: 0.6593 (tt) REVERT: A 275 TYR cc_start: 0.7431 (t80) cc_final: 0.6911 (t80) REVERT: B 93 MET cc_start: 0.5160 (pmm) cc_final: 0.4700 (ppp) REVERT: B 215 MET cc_start: 0.8156 (ttm) cc_final: 0.7917 (ttm) REVERT: C 157 GLU cc_start: 0.7564 (mp0) cc_final: 0.7103 (tp30) REVERT: C 278 PHE cc_start: 0.7083 (t80) cc_final: 0.6665 (t80) REVERT: D 236 THR cc_start: 0.8819 (t) cc_final: 0.8466 (p) REVERT: D 271 MET cc_start: 0.6686 (tpp) cc_final: 0.6450 (tmm) REVERT: D 292 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6640 (mm-30) REVERT: E 1 MET cc_start: 0.3682 (tmm) cc_final: 0.2260 (tpp) REVERT: F 84 MET cc_start: 0.3497 (mpp) cc_final: 0.1665 (tpt) REVERT: F 133 ARG cc_start: 0.6305 (ttt180) cc_final: 0.4307 (tpm170) REVERT: F 167 LEU cc_start: 0.7918 (pp) cc_final: 0.7642 (pt) REVERT: G 196 MET cc_start: 0.7801 (tpt) cc_final: 0.7503 (tpt) REVERT: G 209 ARG cc_start: 0.8081 (ttt90) cc_final: 0.7424 (ttp-170) REVERT: G 213 GLN cc_start: 0.7903 (tt0) cc_final: 0.7623 (tt0) REVERT: G 483 ARG cc_start: 0.8195 (mmt-90) cc_final: 0.7273 (mtt90) REVERT: G 489 TYR cc_start: 0.6238 (m-80) cc_final: 0.5827 (m-80) REVERT: H 364 ARG cc_start: 0.7108 (mtt180) cc_final: 0.6813 (mtt90) REVERT: I 147 ASP cc_start: 0.7609 (t0) cc_final: 0.7228 (t0) REVERT: I 414 CYS cc_start: 0.6796 (t) cc_final: 0.6427 (m) REVERT: J 88 VAL cc_start: 0.8640 (t) cc_final: 0.8346 (m) REVERT: J 92 PHE cc_start: 0.6755 (m-80) cc_final: 0.6206 (m-10) REVERT: J 181 MET cc_start: 0.5335 (mmp) cc_final: 0.4943 (ttp) REVERT: J 265 ASP cc_start: 0.5517 (p0) cc_final: 0.5271 (t0) REVERT: J 270 ASP cc_start: 0.8377 (p0) cc_final: 0.7648 (m-30) REVERT: J 398 GLN cc_start: 0.7232 (tp40) cc_final: 0.7000 (tm-30) REVERT: J 422 ARG cc_start: 0.8706 (mtp180) cc_final: 0.8170 (mmm-85) REVERT: J 547 MET cc_start: 0.5338 (ttt) cc_final: 0.2752 (mpp) REVERT: J 608 MET cc_start: 0.3914 (mpp) cc_final: 0.2892 (mpp) REVERT: K 30 MET cc_start: 0.6526 (tmm) cc_final: 0.6079 (tmm) REVERT: K 103 THR cc_start: 0.9059 (m) cc_final: 0.8746 (p) REVERT: K 132 GLN cc_start: 0.7612 (tp40) cc_final: 0.7354 (tp-100) REVERT: K 266 ARG cc_start: 0.6282 (mtt90) cc_final: 0.4509 (mmt180) REVERT: K 270 ASN cc_start: 0.7767 (t0) cc_final: 0.7265 (t0) REVERT: P 77 ILE cc_start: 0.6736 (mm) cc_final: 0.6466 (mm) REVERT: P 270 GLU cc_start: 0.5804 (pm20) cc_final: 0.5577 (pm20) REVERT: P 272 ASP cc_start: 0.7600 (m-30) cc_final: 0.7280 (m-30) outliers start: 5 outliers final: 0 residues processed: 438 average time/residue: 0.1917 time to fit residues: 140.9185 Evaluate side-chains 347 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 35 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 141 optimal weight: 50.0000 chunk 285 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 301 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 13 optimal weight: 0.1980 chunk 384 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 479 HIS I 216 GLN J 267 GLN J 568 ASN K 179 ASN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.134332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.119745 restraints weight = 91210.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120289 restraints weight = 65673.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.120641 restraints weight = 54529.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.120994 restraints weight = 48089.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.121191 restraints weight = 46648.185| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33144 Z= 0.167 Angle : 0.798 10.499 44903 Z= 0.403 Chirality : 0.051 0.259 5282 Planarity : 0.006 0.082 5753 Dihedral : 6.668 39.164 4557 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 0.11 % Allowed : 0.89 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.96 % Twisted General : 0.12 % 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: -3.35 (0.12), residues: 4164 helix: -0.93 (0.14), residues: 1286 sheet: -2.75 (0.22), residues: 427 loop : -3.00 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 297 TYR 0.034 0.002 TYR K 39 PHE 0.029 0.002 PHE A 285 TRP 0.012 0.001 TRP J 111 HIS 0.010 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00394 (33144) covalent geometry : angle 0.79835 (44903) hydrogen bonds : bond 0.04292 ( 921) hydrogen bonds : angle 5.57128 ( 2616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8328 Ramachandran restraints generated. 4164 Oldfield, 0 Emsley, 4164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 433 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ILE cc_start: 0.6988 (tt) cc_final: 0.6596 (tt) REVERT: A 275 TYR cc_start: 0.7399 (t80) cc_final: 0.6877 (t80) REVERT: B 93 MET cc_start: 0.5280 (pmm) cc_final: 0.4718 (ppp) REVERT: B 215 MET cc_start: 0.8160 (ttm) cc_final: 0.7929 (ttm) REVERT: C 58 MET cc_start: 0.7333 (ttm) cc_final: 0.7127 (ttm) REVERT: C 157 GLU cc_start: 0.7254 (mp0) cc_final: 0.6728 (tp30) REVERT: C 226 MET cc_start: 0.8336 (pmm) cc_final: 0.8019 (pmm) REVERT: C 278 PHE cc_start: 0.7037 (t80) cc_final: 0.6673 (t80) REVERT: D 144 LEU cc_start: 0.8148 (pt) cc_final: 0.7942 (pt) REVERT: D 160 HIS cc_start: 0.6910 (m90) cc_final: 0.6390 (m90) REVERT: D 236 THR cc_start: 0.8797 (t) cc_final: 0.8428 (p) REVERT: D 271 MET cc_start: 0.6447 (tpp) cc_final: 0.6199 (tmm) REVERT: E 132 MET cc_start: 0.6049 (ttm) cc_final: 0.5262 (ptm) REVERT: F 84 MET cc_start: 0.3775 (mpp) cc_final: 0.1987 (tpt) REVERT: F 133 ARG cc_start: 0.6080 (ttt180) cc_final: 0.4079 (tpm170) REVERT: G 196 MET cc_start: 0.7883 (tpt) cc_final: 0.7583 (tpt) REVERT: G 209 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7469 (ttp-170) REVERT: I 147 ASP cc_start: 0.7621 (t0) cc_final: 0.7263 (t0) REVERT: I 414 CYS cc_start: 0.6903 (t) cc_final: 0.6416 (m) REVERT: J 88 VAL cc_start: 0.8617 (t) cc_final: 0.8309 (m) REVERT: J 181 MET cc_start: 0.5684 (mmp) cc_final: 0.5439 (ttp) REVERT: J 265 ASP cc_start: 0.6050 (p0) cc_final: 0.5669 (t0) REVERT: J 270 ASP cc_start: 0.8360 (p0) cc_final: 0.7558 (m-30) REVERT: J 398 GLN cc_start: 0.7199 (tp40) cc_final: 0.6920 (tm-30) REVERT: J 422 ARG cc_start: 0.8687 (mtp180) cc_final: 0.8159 (mmm-85) REVERT: J 547 MET cc_start: 0.5336 (ttt) cc_final: 0.2738 (mpp) REVERT: J 608 MET cc_start: 0.4066 (mpp) cc_final: 0.2911 (mpp) REVERT: K 30 MET cc_start: 0.6574 (tmm) cc_final: 0.6217 (tmm) REVERT: K 103 THR cc_start: 0.9179 (m) cc_final: 0.8911 (p) REVERT: K 158 SER cc_start: 0.8111 (m) cc_final: 0.7632 (p) REVERT: K 266 ARG cc_start: 0.6235 (mtt90) cc_final: 0.4511 (mmt180) REVERT: K 270 ASN cc_start: 0.7776 (t0) cc_final: 0.7364 (t0) REVERT: P 77 ILE cc_start: 0.6712 (mm) cc_final: 0.6435 (mm) REVERT: P 270 GLU cc_start: 0.5591 (pm20) cc_final: 0.5346 (pm20) REVERT: P 272 ASP cc_start: 0.7600 (m-30) cc_final: 0.7286 (m-30) outliers start: 4 outliers final: 0 residues processed: 436 average time/residue: 0.1915 time to fit residues: 141.4296 Evaluate side-chains 346 residues out of total 3694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 308 optimal weight: 2.9990 chunk 351 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 83 optimal weight: 0.0170 chunk 171 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 124 optimal weight: 0.0060 chunk 119 optimal weight: 4.9990 chunk 282 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 345 optimal weight: 0.8980 overall best weight: 1.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN B 48 ASN ** B 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN G 486 ASN H 479 HIS I 216 GLN J 267 GLN ** P 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.135476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.120727 restraints weight = 90575.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.121453 restraints weight = 69658.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.121768 restraints weight = 56599.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121930 restraints weight = 50487.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.122234 restraints weight = 47261.794| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33144 Z= 0.146 Angle : 0.783 10.050 44903 Z= 0.392 Chirality : 0.050 0.299 5282 Planarity : 0.005 0.080 5753 Dihedral : 6.534 39.309 4557 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.73 % Cis-general : 0.00 % Twisted Proline : 2.37 % Twisted General : 0.10 % 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: -3.21 (0.12), residues: 4164 helix: -0.78 (0.14), residues: 1279 sheet: -2.73 (0.23), residues: 413 loop : -2.91 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 316 TYR 0.033 0.002 TYR K 39 PHE 0.033 0.002 PHE A 285 TRP 0.031 0.002 TRP J 628 HIS 0.009 0.001 HIS D 160 Details of bonding type rmsd covalent geometry : bond 0.00344 (33144) covalent geometry : angle 0.78250 (44903) hydrogen bonds : bond 0.04142 ( 921) hydrogen bonds : angle 5.44296 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4837.94 seconds wall clock time: 85 minutes 21.12 seconds (5121.12 seconds total)