Starting phenix.real_space_refine on Thu Mar 5 04:06:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9k_10414/03_2026/6t9k_10414_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9k_10414/03_2026/6t9k_10414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t9k_10414/03_2026/6t9k_10414_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9k_10414/03_2026/6t9k_10414_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t9k_10414/03_2026/6t9k_10414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9k_10414/03_2026/6t9k_10414.map" } resolution = 3.3 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= 0.001 sd= 0.008 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 66 5.16 5 C 12168 2.51 5 N 3341 2.21 5 O 3666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 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: 19241 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1526 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain breaks: 2 Chain: "C" Number of atoms: 1774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1774 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 204} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4474 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 536} Chain breaks: 3 Chain: "E" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3441 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 19, 'TRANS': 413} Chain breaks: 3 Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 902 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 1 Chain: "G" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1108 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "H" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1803 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 2 Chain: "I" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "K" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2258 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 3 Chain: "Q" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 7, 'TRANS': 76} Chain: "U" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 415 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain breaks: 2 Time building chain proxies: 3.77, per 1000 atoms: 0.20 Number of scatterers: 19241 At special positions: 0 Unit cell: (106.05, 148.05, 168, 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 66 16.00 O 3666 8.00 N 3341 7.00 C 12168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 750.5 milliseconds 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4652 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 13 sheets defined 50.2% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 195 through 203 Processing helix chain 'B' and resid 288 through 300 removed outlier: 3.549A pdb=" N THR B 292 " --> pdb=" O ASN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.810A pdb=" N TYR B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.678A pdb=" N ALA B 344 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 345' Processing helix chain 'C' and resid 7 through 19 removed outlier: 3.782A pdb=" N VAL C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 18 " --> pdb=" O MET C 14 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 19 " --> pdb=" O MET C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 55 removed outlier: 3.552A pdb=" N THR C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 removed outlier: 4.009A pdb=" N VAL C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE C 65 " --> pdb=" O PRO C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 71 through 82 Processing helix chain 'C' and resid 192 through 202 removed outlier: 3.763A pdb=" N CYS C 199 " --> pdb=" O HIS C 195 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 200 " --> pdb=" O TRP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 217 removed outlier: 3.937A pdb=" N ASP C 214 " --> pdb=" O LYS C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.162A pdb=" N LEU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 229 through 264 removed outlier: 4.002A pdb=" N THR C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 313 Processing helix chain 'C' and resid 320 through 324 removed outlier: 3.828A pdb=" N ASN C 324 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 71 Processing helix chain 'D' and resid 74 through 87 removed outlier: 3.590A pdb=" N THR D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 3.591A pdb=" N ALA D 155 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 190 removed outlier: 3.777A pdb=" N LEU D 174 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TYR D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Proline residue: D 180 - end of helix Processing helix chain 'D' and resid 193 through 204 removed outlier: 3.534A pdb=" N ASP D 202 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 214 through 219 Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.522A pdb=" N ILE D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 229' Processing helix chain 'D' and resid 231 through 240 removed outlier: 3.945A pdb=" N GLN D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 265 through 276 removed outlier: 3.524A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'E' and resid 17 through 25 removed outlier: 3.778A pdb=" N SER E 23 " --> pdb=" O ASP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 59 removed outlier: 3.853A pdb=" N GLN E 51 " --> pdb=" O GLU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 removed outlier: 3.615A pdb=" N VAL E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 76 removed outlier: 4.078A pdb=" N ARG E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 76' Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.522A pdb=" N ASN E 122 " --> pdb=" O ASP E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 244 through 258 Processing helix chain 'E' and resid 264 through 278 removed outlier: 3.575A pdb=" N ILE E 269 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE E 271 " --> pdb=" O TYR E 267 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 305 through 309 removed outlier: 3.787A pdb=" N ILE E 308 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N HIS E 309 " --> pdb=" O PRO E 306 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 305 through 309' Processing helix chain 'E' and resid 311 through 320 removed outlier: 3.584A pdb=" N ILE E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU E 320 " --> pdb=" O LEU E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 361 removed outlier: 4.018A pdb=" N LEU E 346 " --> pdb=" O ARG E 342 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS E 359 " --> pdb=" O ASP E 355 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 361 " --> pdb=" O VAL E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 386 through 399 removed outlier: 3.570A pdb=" N TYR E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 407 Processing helix chain 'E' and resid 408 through 411 removed outlier: 4.313A pdb=" N ASN E 411 " --> pdb=" O PHE E 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 408 through 411' Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 429 through 433 removed outlier: 4.037A pdb=" N HIS E 433 " --> pdb=" O ILE E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 460 removed outlier: 3.766A pdb=" N ILE E 458 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 460 " --> pdb=" O THR E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 464 Processing helix chain 'F' and resid 31 through 43 Processing helix chain 'F' and resid 50 through 78 removed outlier: 4.353A pdb=" N LEU F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA F 78 " --> pdb=" O TYR F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 110 through 122 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'G' and resid 73 through 82 Processing helix chain 'G' and resid 89 through 101 removed outlier: 3.682A pdb=" N ILE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 135 removed outlier: 3.643A pdb=" N LYS G 110 " --> pdb=" O ASP G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 145 removed outlier: 3.581A pdb=" N VAL G 140 " --> pdb=" O SER G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.719A pdb=" N GLN G 152 " --> pdb=" O ALA G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 removed outlier: 3.765A pdb=" N GLN G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 194 removed outlier: 4.619A pdb=" N SER G 190 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 3.577A pdb=" N LEU H 188 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 199 Processing helix chain 'H' and resid 211 through 221 Processing helix chain 'H' and resid 229 through 239 removed outlier: 3.765A pdb=" N ASN H 239 " --> pdb=" O ARG H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 256 removed outlier: 3.860A pdb=" N TRP H 247 " --> pdb=" O THR H 243 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN H 249 " --> pdb=" O LEU H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 264 removed outlier: 3.781A pdb=" N SER H 263 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS H 264 " --> pdb=" O ALA H 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 259 through 264' Processing helix chain 'H' and resid 268 through 284 Processing helix chain 'H' and resid 292 through 317 removed outlier: 4.914A pdb=" N THR H 315 " --> pdb=" O PHE H 311 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL H 316 " --> pdb=" O THR H 312 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG H 317 " --> pdb=" O ILE H 313 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 349 removed outlier: 4.073A pdb=" N ARG H 346 " --> pdb=" O ALA H 342 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP H 347 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA H 348 " --> pdb=" O ASP H 344 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 349 " --> pdb=" O LYS H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 353 removed outlier: 3.844A pdb=" N LEU H 353 " --> pdb=" O ILE H 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 350 through 353' Processing helix chain 'H' and resid 356 through 365 Processing helix chain 'H' and resid 407 through 418 removed outlier: 3.688A pdb=" N ILE H 412 " --> pdb=" O THR H 408 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR H 413 " --> pdb=" O ASN H 409 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER H 417 " --> pdb=" O TYR H 413 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE H 418 " --> pdb=" O ASP H 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 428 Processing helix chain 'I' and resid 439 through 468 removed outlier: 3.919A pdb=" N THR I 455 " --> pdb=" O ASP I 451 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE I 460 " --> pdb=" O ASN I 456 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG I 463 " --> pdb=" O ALA I 459 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 485 removed outlier: 4.108A pdb=" N ILE I 478 " --> pdb=" O GLU I 474 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN I 485 " --> pdb=" O HIS I 481 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 524 removed outlier: 3.542A pdb=" N ASN I 511 " --> pdb=" O SER I 507 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 163 Processing helix chain 'K' and resid 167 through 185 Processing helix chain 'K' and resid 731 through 741 removed outlier: 3.559A pdb=" N SER K 735 " --> pdb=" O ASP K 731 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP K 737 " --> pdb=" O GLU K 733 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR K 741 " --> pdb=" O TRP K 737 " (cutoff:3.500A) Processing helix chain 'K' and resid 743 through 753 removed outlier: 3.513A pdb=" N GLU K 747 " --> pdb=" O LYS K 743 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR K 753 " --> pdb=" O CYS K 749 " (cutoff:3.500A) Processing helix chain 'K' and resid 868 through 884 removed outlier: 3.598A pdb=" N ASP K 872 " --> pdb=" O THR K 868 " (cutoff:3.500A) Processing helix chain 'K' and resid 901 through 916 Processing helix chain 'K' and resid 917 through 929 Processing helix chain 'K' and resid 975 through 989 removed outlier: 3.679A pdb=" N ILE K 979 " --> pdb=" O ASN K 975 " (cutoff:3.500A) Processing helix chain 'K' and resid 1000 through 1027 removed outlier: 3.707A pdb=" N ILE K1004 " --> pdb=" O HIS K1000 " (cutoff:3.500A) Processing helix chain 'K' and resid 1035 through 1046 removed outlier: 3.763A pdb=" N LEU K1040 " --> pdb=" O ASN K1036 " (cutoff:3.500A) Processing helix chain 'K' and resid 1053 through 1064 Processing helix chain 'K' and resid 1065 through 1085 Processing helix chain 'Q' and resid 354 through 366 Processing helix chain 'Q' and resid 381 through 398 removed outlier: 3.917A pdb=" N PHE Q 398 " --> pdb=" O PHE Q 394 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 29 removed outlier: 3.656A pdb=" N ALA U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA U 29 " --> pdb=" O ALA U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 113 Processing helix chain 'U' and resid 125 through 137 removed outlier: 3.759A pdb=" N ALA U 137 " --> pdb=" O ALA U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 141 through 152 removed outlier: 3.850A pdb=" N ALA U 145 " --> pdb=" O ALA U 141 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.817A pdb=" N LEU B 211 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.691A pdb=" N HIS B 349 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 242 through 245 removed outlier: 6.428A pdb=" N TYR D 242 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASN D 280 " --> pdb=" O TYR D 242 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 244 " --> pdb=" O ASN D 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'D' and resid 781 through 784 removed outlier: 5.937A pdb=" N SER D 456 " --> pdb=" O ALA D 790 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ALA D 792 " --> pdb=" O SER D 456 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N CYS D 458 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY D 794 " --> pdb=" O CYS D 458 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR D 460 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 469 through 474 removed outlier: 4.834A pdb=" N GLY D 484 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU D 472 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA D 482 " --> pdb=" O LEU D 472 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE D 474 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 480 " --> pdb=" O PHE D 474 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 528 through 533 removed outlier: 6.456A pdb=" N VAL D 549 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER D 562 " --> pdb=" O VAL D 549 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU D 551 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 570 through 574 removed outlier: 6.451A pdb=" N ALA D 585 " --> pdb=" O TRP D 571 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 573 " --> pdb=" O ALA D 583 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA D 583 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 586 " --> pdb=" O THR D 590 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR D 590 " --> pdb=" O SER D 586 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER D 595 " --> pdb=" O PRO D 601 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 612 through 617 removed outlier: 3.832A pdb=" N THR D 632 " --> pdb=" O SER D 628 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS D 633 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU D 646 " --> pdb=" O CYS D 633 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N MET D 635 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 654 through 659 removed outlier: 3.626A pdb=" N LYS D 687 " --> pdb=" O VAL D 677 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP D 679 " --> pdb=" O ARG D 685 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ARG D 685 " --> pdb=" O ASP D 679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 701 through 702 removed outlier: 3.924A pdb=" N ALA D 770 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP D 722 " --> pdb=" O LEU D 768 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU D 768 " --> pdb=" O ASP D 722 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 101 Processing sheet with id=AB3, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AB4, first strand: chain 'H' and resid 335 through 337 removed outlier: 6.561A pdb=" N TYR H 335 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 819 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 2.13 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: 6241 1.34 - 1.46: 3683 1.46 - 1.58: 9563 1.58 - 1.70: 1 1.70 - 1.82: 109 Bond restraints: 19597 Sorted by residual: bond pdb=" C PRO E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.334 1.359 -0.025 8.40e-03 1.42e+04 9.11e+00 bond pdb=" C ASN D 123 " pdb=" N PRO D 124 " ideal model delta sigma weight residual 1.326 1.362 -0.035 1.44e-02 4.82e+03 6.06e+00 bond pdb=" C TYR D 600 " pdb=" N PRO D 601 " ideal model delta sigma weight residual 1.331 1.358 -0.026 1.21e-02 6.83e+03 4.78e+00 bond pdb=" C LYS E 204 " pdb=" N PRO E 205 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.87e+00 bond pdb=" CA THR K 953 " pdb=" CB THR K 953 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.69e-02 3.50e+03 2.94e+00 ... (remaining 19592 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 25883 2.52 - 5.04: 527 5.04 - 7.56: 80 7.56 - 10.08: 21 10.08 - 12.59: 8 Bond angle restraints: 26519 Sorted by residual: angle pdb=" C ASN H 239 " pdb=" N ASN H 240 " pdb=" CA ASN H 240 " ideal model delta sigma weight residual 122.61 131.69 -9.08 1.56e+00 4.11e-01 3.39e+01 angle pdb=" C ASN D 504 " pdb=" N ILE D 505 " pdb=" CA ILE D 505 " ideal model delta sigma weight residual 121.97 132.17 -10.20 1.80e+00 3.09e-01 3.21e+01 angle pdb=" CA LYS D 775 " pdb=" CB LYS D 775 " pdb=" CG LYS D 775 " ideal model delta sigma weight residual 114.10 125.11 -11.01 2.00e+00 2.50e-01 3.03e+01 angle pdb=" C ASP D 476 " pdb=" N ASP D 477 " pdb=" CA ASP D 477 " ideal model delta sigma weight residual 125.66 135.19 -9.53 1.85e+00 2.92e-01 2.65e+01 angle pdb=" C ARG H 403 " pdb=" N THR H 404 " pdb=" CA THR H 404 " ideal model delta sigma weight residual 122.08 129.35 -7.27 1.47e+00 4.63e-01 2.44e+01 ... (remaining 26514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 10537 17.89 - 35.77: 1154 35.77 - 53.66: 195 53.66 - 71.54: 43 71.54 - 89.43: 22 Dihedral angle restraints: 11951 sinusoidal: 4814 harmonic: 7137 Sorted by residual: dihedral pdb=" CA ASN D 504 " pdb=" C ASN D 504 " pdb=" N ILE D 505 " pdb=" CA ILE D 505 " ideal model delta harmonic sigma weight residual -180.00 -139.36 -40.64 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA ASP D 476 " pdb=" C ASP D 476 " pdb=" N ASP D 477 " pdb=" CA ASP D 477 " ideal model delta harmonic sigma weight residual -180.00 -148.32 -31.68 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ASP D 546 " pdb=" C ASP D 546 " pdb=" N LYS D 547 " pdb=" CA LYS D 547 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 11948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2745 0.092 - 0.185: 255 0.185 - 0.277: 11 0.277 - 0.369: 2 0.369 - 0.462: 1 Chirality restraints: 3014 Sorted by residual: chirality pdb=" CB ILE H 350 " pdb=" CA ILE H 350 " pdb=" CG1 ILE H 350 " pdb=" CG2 ILE H 350 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CB VAL E 265 " pdb=" CA VAL E 265 " pdb=" CG1 VAL E 265 " pdb=" CG2 VAL E 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE C 21 " pdb=" CA ILE C 21 " pdb=" CG1 ILE C 21 " pdb=" CG2 ILE C 21 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3011 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 243 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO H 244 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO H 244 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 244 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 775 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C LYS D 775 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS D 775 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS D 776 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 568 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO D 569 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 569 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 569 " -0.038 5.00e-02 4.00e+02 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3997 2.78 - 3.31: 17481 3.31 - 3.84: 31777 3.84 - 4.37: 36874 4.37 - 4.90: 63455 Nonbonded interactions: 153584 Sorted by model distance: nonbonded pdb=" OH TYR D 256 " pdb=" OG SER D 441 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR E 16 " pdb=" OD2 ASP F 32 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR K1042 " pdb=" OE2 GLU K1046 " model vdw 2.288 3.040 nonbonded pdb=" O SER D 656 " pdb=" OG1 THR D 668 " model vdw 2.288 3.040 nonbonded pdb=" O LEU Q 373 " pdb=" OH TYR Q 427 " model vdw 2.295 3.040 ... (remaining 153579 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.570 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: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19597 Z= 0.220 Angle : 0.921 12.595 26519 Z= 0.506 Chirality : 0.055 0.462 3014 Planarity : 0.007 0.084 3411 Dihedral : 15.565 89.429 7299 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 0.43 % Allowed : 8.14 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.36 (0.13), residues: 2366 helix: -2.69 (0.11), residues: 1137 sheet: -1.55 (0.35), residues: 186 loop : -3.33 (0.15), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 346 TYR 0.033 0.002 TYR B 130 PHE 0.030 0.002 PHE D 582 TRP 0.018 0.002 TRP I 486 HIS 0.013 0.001 HIS D 524 Details of bonding type rmsd covalent geometry : bond 0.00467 (19597) covalent geometry : angle 0.92130 (26519) hydrogen bonds : bond 0.14523 ( 819) hydrogen bonds : angle 6.56505 ( 2415) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 367 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 307 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7771 (mm-30) REVERT: D 704 LYS cc_start: 0.7762 (tmtt) cc_final: 0.7153 (mmmt) REVERT: E 216 LYS cc_start: 0.1935 (mttp) cc_final: 0.1546 (mtmt) REVERT: E 348 ASP cc_start: 0.7099 (m-30) cc_final: 0.6406 (m-30) REVERT: H 186 MET cc_start: 0.6920 (tpp) cc_final: 0.6396 (tpp) REVERT: H 364 ASP cc_start: 0.6691 (m-30) cc_final: 0.6376 (m-30) REVERT: I 418 ARG cc_start: 0.7023 (ptt90) cc_final: 0.6708 (ptt-90) REVERT: I 422 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5955 (mm-30) REVERT: I 476 ARG cc_start: 0.6689 (ptm160) cc_final: 0.6317 (ptp-170) REVERT: I 481 HIS cc_start: 0.8109 (t70) cc_final: 0.7791 (t-170) REVERT: I 497 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5706 (mt-10) REVERT: K 1039 MET cc_start: 0.7901 (mtm) cc_final: 0.7654 (mtp) REVERT: Q 409 TYR cc_start: 0.5755 (t80) cc_final: 0.5551 (t80) outliers start: 9 outliers final: 2 residues processed: 373 average time/residue: 0.1577 time to fit residues: 86.1034 Evaluate side-chains 245 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 243 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 0.2980 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 235 optimal weight: 5.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN B 336 HIS C 46 GLN C 209 ASN C 227 HIS C 319 HIS D 274 ASN D 275 GLN D 276 HIS D 463 GLN D 486 GLN D 537 ASN D 587 HIS D 618 HIS D 676 ASN D 751 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN E 217 HIS F 51 GLN G 118 GLN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 ASN H 240 ASN H 303 GLN H 373 ASN H 396 ASN I 472 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 505 ASN K 856 ASN K 890 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.152927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125851 restraints weight = 30950.141| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.24 r_work: 0.3465 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19597 Z= 0.129 Angle : 0.631 9.135 26519 Z= 0.331 Chirality : 0.043 0.178 3014 Planarity : 0.005 0.061 3411 Dihedral : 5.950 50.970 2620 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.38 % Favored : 93.58 % Rotamer: Outliers : 2.13 % Allowed : 14.16 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.15), residues: 2366 helix: -0.93 (0.14), residues: 1165 sheet: -0.96 (0.38), residues: 176 loop : -3.01 (0.16), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 415 TYR 0.022 0.001 TYR D 184 PHE 0.016 0.001 PHE E 96 TRP 0.022 0.002 TRP H 247 HIS 0.005 0.001 HIS D 618 Details of bonding type rmsd covalent geometry : bond 0.00289 (19597) covalent geometry : angle 0.63094 (26519) hydrogen bonds : bond 0.04075 ( 819) hydrogen bonds : angle 4.65854 ( 2415) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 288 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7606 (pp) REVERT: D 704 LYS cc_start: 0.7940 (tmtt) cc_final: 0.7353 (mmmt) REVERT: E 216 LYS cc_start: 0.2071 (mttp) cc_final: 0.1529 (mtmt) REVERT: E 305 ASP cc_start: 0.7906 (t0) cc_final: 0.7584 (m-30) REVERT: E 348 ASP cc_start: 0.7884 (m-30) cc_final: 0.6966 (m-30) REVERT: E 407 PHE cc_start: 0.8152 (t80) cc_final: 0.7646 (t80) REVERT: H 336 LYS cc_start: 0.6616 (pttt) cc_final: 0.6310 (pttm) REVERT: H 364 ASP cc_start: 0.7387 (m-30) cc_final: 0.6880 (m-30) REVERT: I 418 ARG cc_start: 0.7174 (ptt90) cc_final: 0.6805 (ptt-90) REVERT: I 433 ASP cc_start: 0.7872 (t0) cc_final: 0.7671 (t0) REVERT: I 458 THR cc_start: 0.8784 (t) cc_final: 0.8538 (p) REVERT: I 476 ARG cc_start: 0.7034 (ptm160) cc_final: 0.6761 (ptp-170) REVERT: I 497 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6232 (mt-10) REVERT: K 856 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7413 (m-40) REVERT: K 875 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: K 927 MET cc_start: 0.8022 (mtt) cc_final: 0.7620 (mpp) REVERT: K 1039 MET cc_start: 0.8225 (mtm) cc_final: 0.7998 (mtp) REVERT: Q 409 TYR cc_start: 0.6134 (t80) cc_final: 0.5899 (t80) outliers start: 45 outliers final: 22 residues processed: 317 average time/residue: 0.1471 time to fit residues: 70.8662 Evaluate side-chains 280 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 10 optimal weight: 1.9990 chunk 185 optimal weight: 0.0060 chunk 103 optimal weight: 0.5980 chunk 136 optimal weight: 8.9990 chunk 31 optimal weight: 0.0270 chunk 181 optimal weight: 0.0020 chunk 95 optimal weight: 0.0770 chunk 163 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 overall best weight: 0.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 598 HIS D 676 ASN E 14 GLN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 396 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 914 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.127925 restraints weight = 31049.367| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.02 r_work: 0.3525 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 19597 Z= 0.107 Angle : 0.570 8.570 26519 Z= 0.298 Chirality : 0.041 0.168 3014 Planarity : 0.004 0.061 3411 Dihedral : 5.468 59.506 2620 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 2.23 % Allowed : 16.19 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2366 helix: -0.01 (0.15), residues: 1155 sheet: -0.91 (0.38), residues: 170 loop : -2.68 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 745 TYR 0.018 0.001 TYR C 81 PHE 0.017 0.001 PHE C 236 TRP 0.029 0.001 TRP H 247 HIS 0.004 0.001 HIS I 481 Details of bonding type rmsd covalent geometry : bond 0.00233 (19597) covalent geometry : angle 0.56977 (26519) hydrogen bonds : bond 0.03318 ( 819) hydrogen bonds : angle 4.22865 ( 2415) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 288 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7673 (pp) REVERT: C 42 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 196 TRP cc_start: 0.6121 (t-100) cc_final: 0.5568 (t-100) REVERT: C 307 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 508 ASN cc_start: 0.2079 (OUTLIER) cc_final: 0.1237 (t0) REVERT: D 704 LYS cc_start: 0.7968 (tmtt) cc_final: 0.7382 (mmmt) REVERT: E 216 LYS cc_start: 0.2551 (mttp) cc_final: 0.1884 (mtmt) REVERT: E 247 MET cc_start: 0.7795 (mmm) cc_final: 0.7580 (tpp) REVERT: E 305 ASP cc_start: 0.7910 (t0) cc_final: 0.7557 (m-30) REVERT: E 348 ASP cc_start: 0.7959 (m-30) cc_final: 0.7035 (m-30) REVERT: E 407 PHE cc_start: 0.8151 (t80) cc_final: 0.7569 (t80) REVERT: G 82 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: H 198 MET cc_start: 0.8294 (mtp) cc_final: 0.7964 (mtt) REVERT: H 250 ASP cc_start: 0.7871 (t0) cc_final: 0.7633 (t0) REVERT: H 336 LYS cc_start: 0.6470 (pttt) cc_final: 0.6163 (pttm) REVERT: H 364 ASP cc_start: 0.7520 (m-30) cc_final: 0.6933 (m-30) REVERT: I 418 ARG cc_start: 0.7300 (ptt90) cc_final: 0.6724 (ptt-90) REVERT: I 458 THR cc_start: 0.8803 (t) cc_final: 0.8466 (m) REVERT: I 476 ARG cc_start: 0.7027 (ptm160) cc_final: 0.6818 (ptp-170) REVERT: I 497 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6475 (mt-10) REVERT: K 875 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: K 927 MET cc_start: 0.8040 (mtt) cc_final: 0.7762 (mtt) REVERT: K 1039 MET cc_start: 0.8314 (mtm) cc_final: 0.8112 (mtp) outliers start: 47 outliers final: 23 residues processed: 313 average time/residue: 0.1434 time to fit residues: 68.5670 Evaluate side-chains 281 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 82 ASP Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 512 GLN Chi-restraints excluded: chain K residue 875 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 125 optimal weight: 0.0060 chunk 59 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 138 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 205 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN E 14 GLN E 337 HIS ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.152706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125621 restraints weight = 30905.649| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.30 r_work: 0.3471 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 19597 Z= 0.133 Angle : 0.577 8.128 26519 Z= 0.301 Chirality : 0.042 0.199 3014 Planarity : 0.004 0.060 3411 Dihedral : 5.292 49.950 2620 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 3.12 % Allowed : 16.62 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2366 helix: 0.34 (0.15), residues: 1159 sheet: -0.97 (0.37), residues: 181 loop : -2.52 (0.18), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 415 TYR 0.021 0.001 TYR D 179 PHE 0.013 0.001 PHE C 236 TRP 0.029 0.002 TRP H 247 HIS 0.004 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00310 (19597) covalent geometry : angle 0.57735 (26519) hydrogen bonds : bond 0.03383 ( 819) hydrogen bonds : angle 4.10513 ( 2415) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7591 (pp) REVERT: C 42 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7071 (mm-30) REVERT: C 196 TRP cc_start: 0.5934 (t-100) cc_final: 0.5477 (t-100) REVERT: D 504 ASN cc_start: 0.5036 (m-40) cc_final: 0.4647 (m110) REVERT: D 508 ASN cc_start: 0.2164 (OUTLIER) cc_final: 0.1299 (t0) REVERT: D 704 LYS cc_start: 0.7916 (tmtt) cc_final: 0.7445 (mmmt) REVERT: E 247 MET cc_start: 0.7725 (mmm) cc_final: 0.7513 (tpp) REVERT: E 305 ASP cc_start: 0.7878 (t0) cc_final: 0.7528 (m-30) REVERT: E 348 ASP cc_start: 0.7811 (m-30) cc_final: 0.6966 (m-30) REVERT: E 355 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: E 407 PHE cc_start: 0.8085 (t80) cc_final: 0.7484 (t80) REVERT: G 82 ASP cc_start: 0.7954 (t70) cc_final: 0.7729 (m-30) REVERT: H 246 GLU cc_start: 0.7803 (mp0) cc_final: 0.7513 (mp0) REVERT: H 336 LYS cc_start: 0.6382 (pttt) cc_final: 0.5955 (pttm) REVERT: H 361 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: I 418 ARG cc_start: 0.7328 (ptt90) cc_final: 0.6787 (ptt-90) REVERT: I 458 THR cc_start: 0.8741 (t) cc_final: 0.8421 (m) REVERT: I 497 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6347 (mt-10) REVERT: K 875 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: K 927 MET cc_start: 0.7954 (mtt) cc_final: 0.7658 (mtt) REVERT: K 1076 LYS cc_start: 0.8062 (mmtm) cc_final: 0.7731 (mmmt) outliers start: 66 outliers final: 44 residues processed: 306 average time/residue: 0.1418 time to fit residues: 66.5228 Evaluate side-chains 297 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 248 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 14 GLN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 187 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 203 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 147 optimal weight: 0.0980 chunk 119 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 59 optimal weight: 0.0770 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 HIS C 209 ASN D 275 GLN E 14 GLN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1036 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.153423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126171 restraints weight = 30752.100| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.23 r_work: 0.3485 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 19597 Z= 0.110 Angle : 0.568 7.940 26519 Z= 0.294 Chirality : 0.042 0.173 3014 Planarity : 0.004 0.059 3411 Dihedral : 5.076 40.744 2620 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 2.94 % Allowed : 17.76 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.17), residues: 2366 helix: 0.57 (0.16), residues: 1167 sheet: -0.60 (0.40), residues: 154 loop : -2.44 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 417 TYR 0.023 0.001 TYR D 179 PHE 0.011 0.001 PHE C 239 TRP 0.026 0.001 TRP H 247 HIS 0.003 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00253 (19597) covalent geometry : angle 0.56760 (26519) hydrogen bonds : bond 0.03178 ( 819) hydrogen bonds : angle 3.97780 ( 2415) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 264 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7594 (pp) REVERT: C 196 TRP cc_start: 0.5903 (t-100) cc_final: 0.5458 (t-100) REVERT: D 508 ASN cc_start: 0.2062 (OUTLIER) cc_final: 0.1213 (t0) REVERT: D 704 LYS cc_start: 0.7906 (tmtt) cc_final: 0.7417 (mmmt) REVERT: D 777 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8091 (p) REVERT: E 305 ASP cc_start: 0.7841 (t0) cc_final: 0.7521 (m-30) REVERT: E 348 ASP cc_start: 0.7763 (m-30) cc_final: 0.6857 (m-30) REVERT: E 407 PHE cc_start: 0.8062 (t80) cc_final: 0.7411 (t80) REVERT: G 82 ASP cc_start: 0.7918 (t70) cc_final: 0.7703 (m-30) REVERT: H 246 GLU cc_start: 0.7737 (mp0) cc_final: 0.7508 (mp0) REVERT: H 361 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7753 (mm-30) REVERT: I 418 ARG cc_start: 0.7293 (ptt90) cc_final: 0.6753 (ptt-90) REVERT: I 458 THR cc_start: 0.8729 (t) cc_final: 0.8410 (m) REVERT: K 927 MET cc_start: 0.7850 (mtt) cc_final: 0.7511 (mtt) REVERT: K 1076 LYS cc_start: 0.8055 (mmtm) cc_final: 0.7725 (mmmt) outliers start: 62 outliers final: 41 residues processed: 303 average time/residue: 0.1398 time to fit residues: 65.4098 Evaluate side-chains 292 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 73 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 191 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 524 HIS D 676 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1025 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.150393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123263 restraints weight = 30966.412| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.44 r_work: 0.3401 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19597 Z= 0.178 Angle : 0.622 8.583 26519 Z= 0.323 Chirality : 0.044 0.184 3014 Planarity : 0.004 0.061 3411 Dihedral : 5.229 41.744 2620 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.20 % Rotamer: Outliers : 3.17 % Allowed : 18.75 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2366 helix: 0.54 (0.15), residues: 1165 sheet: -0.87 (0.38), residues: 179 loop : -2.44 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 121 TYR 0.025 0.002 TYR D 581 PHE 0.027 0.002 PHE D 186 TRP 0.024 0.002 TRP H 247 HIS 0.004 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00423 (19597) covalent geometry : angle 0.62173 (26519) hydrogen bonds : bond 0.03631 ( 819) hydrogen bonds : angle 4.10011 ( 2415) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7543 (pp) REVERT: C 42 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6808 (mm-30) REVERT: C 196 TRP cc_start: 0.5928 (t-100) cc_final: 0.5467 (t-100) REVERT: C 307 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8051 (mm-30) REVERT: D 508 ASN cc_start: 0.2141 (OUTLIER) cc_final: 0.1268 (t0) REVERT: D 704 LYS cc_start: 0.7987 (tmtt) cc_final: 0.7478 (mmmt) REVERT: D 751 GLN cc_start: 0.6835 (mm110) cc_final: 0.6518 (mm-40) REVERT: D 777 THR cc_start: 0.8338 (OUTLIER) cc_final: 0.8002 (p) REVERT: E 42 GLU cc_start: 0.7434 (pp20) cc_final: 0.6587 (pt0) REVERT: E 348 ASP cc_start: 0.7919 (m-30) cc_final: 0.7038 (m-30) REVERT: E 407 PHE cc_start: 0.8067 (t80) cc_final: 0.7467 (t80) REVERT: G 81 MET cc_start: 0.7269 (ttm) cc_final: 0.6629 (ttm) REVERT: H 246 GLU cc_start: 0.7946 (mp0) cc_final: 0.7523 (mp0) REVERT: H 361 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7994 (mm-30) REVERT: I 418 ARG cc_start: 0.7435 (ptt90) cc_final: 0.6896 (ptt-90) REVERT: I 458 THR cc_start: 0.8743 (t) cc_final: 0.8417 (m) REVERT: I 476 ARG cc_start: 0.7408 (ptp-170) cc_final: 0.7173 (ptp-170) REVERT: I 497 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6178 (mt-10) REVERT: K 927 MET cc_start: 0.7895 (mtt) cc_final: 0.7537 (mtt) REVERT: K 1076 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7750 (mmmt) REVERT: Q 435 GLN cc_start: 0.8874 (mp10) cc_final: 0.8662 (mp10) outliers start: 67 outliers final: 51 residues processed: 300 average time/residue: 0.1392 time to fit residues: 64.5524 Evaluate side-chains 302 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 131 TYR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 195 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 184 optimal weight: 0.0020 chunk 114 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 140 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** D 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.151970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124739 restraints weight = 30719.967| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.22 r_work: 0.3450 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 19597 Z= 0.124 Angle : 0.583 8.728 26519 Z= 0.303 Chirality : 0.042 0.193 3014 Planarity : 0.004 0.066 3411 Dihedral : 5.063 39.969 2620 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.21 % Favored : 93.74 % Rotamer: Outliers : 3.08 % Allowed : 18.84 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.17), residues: 2366 helix: 0.70 (0.16), residues: 1166 sheet: -0.56 (0.39), residues: 163 loop : -2.38 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 415 TYR 0.026 0.001 TYR D 179 PHE 0.029 0.001 PHE D 186 TRP 0.023 0.001 TRP D 678 HIS 0.005 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00290 (19597) covalent geometry : angle 0.58272 (26519) hydrogen bonds : bond 0.03297 ( 819) hydrogen bonds : angle 3.97733 ( 2415) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7592 (pp) REVERT: C 14 MET cc_start: 0.8260 (mtm) cc_final: 0.7871 (mtm) REVERT: C 42 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6737 (mm-30) REVERT: C 196 TRP cc_start: 0.5729 (t-100) cc_final: 0.5316 (t-100) REVERT: D 508 ASN cc_start: 0.2059 (OUTLIER) cc_final: 0.1194 (t0) REVERT: D 689 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.6997 (mmt) REVERT: D 704 LYS cc_start: 0.7936 (tmtt) cc_final: 0.7458 (mmmt) REVERT: D 751 GLN cc_start: 0.6763 (mm110) cc_final: 0.6450 (mm-40) REVERT: D 767 ASP cc_start: 0.7676 (m-30) cc_final: 0.7282 (m-30) REVERT: D 777 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7952 (p) REVERT: E 42 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: E 305 ASP cc_start: 0.7858 (t0) cc_final: 0.7444 (m-30) REVERT: E 348 ASP cc_start: 0.7829 (m-30) cc_final: 0.6944 (m-30) REVERT: E 407 PHE cc_start: 0.7758 (t80) cc_final: 0.7180 (t80) REVERT: G 81 MET cc_start: 0.7289 (ttm) cc_final: 0.6665 (ttm) REVERT: H 336 LYS cc_start: 0.6558 (pttm) cc_final: 0.6174 (pttt) REVERT: H 347 ASP cc_start: 0.8326 (p0) cc_final: 0.8024 (p0) REVERT: H 361 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7846 (mm-30) REVERT: I 418 ARG cc_start: 0.7377 (ptt90) cc_final: 0.6860 (ptt-90) REVERT: I 458 THR cc_start: 0.8726 (t) cc_final: 0.8399 (m) REVERT: I 476 ARG cc_start: 0.7372 (ptp-170) cc_final: 0.7120 (ptp-170) REVERT: I 497 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6269 (mt-10) REVERT: K 927 MET cc_start: 0.7891 (mtt) cc_final: 0.7077 (mmm) REVERT: K 1076 LYS cc_start: 0.8079 (mmtm) cc_final: 0.7740 (mmmt) REVERT: Q 435 GLN cc_start: 0.8882 (mp10) cc_final: 0.8431 (mp10) outliers start: 65 outliers final: 49 residues processed: 303 average time/residue: 0.1272 time to fit residues: 59.3147 Evaluate side-chains 298 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 165 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 223 optimal weight: 1.9990 chunk 150 optimal weight: 0.0570 chunk 55 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 676 ASN H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.149297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.122047 restraints weight = 31125.983| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.73 r_work: 0.3375 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19597 Z= 0.196 Angle : 0.642 8.535 26519 Z= 0.333 Chirality : 0.045 0.199 3014 Planarity : 0.005 0.072 3411 Dihedral : 5.246 41.313 2620 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.17 % Allowed : 19.65 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.17), residues: 2366 helix: 0.58 (0.15), residues: 1166 sheet: -0.76 (0.39), residues: 169 loop : -2.43 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 415 TYR 0.027 0.002 TYR D 179 PHE 0.029 0.002 PHE D 186 TRP 0.018 0.002 TRP K 737 HIS 0.007 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00470 (19597) covalent geometry : angle 0.64160 (26519) hydrogen bonds : bond 0.03766 ( 819) hydrogen bonds : angle 4.11432 ( 2415) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7631 (pp) REVERT: C 42 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6748 (mm-30) REVERT: C 196 TRP cc_start: 0.5729 (t-100) cc_final: 0.5270 (t-100) REVERT: C 307 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 508 ASN cc_start: 0.2115 (OUTLIER) cc_final: 0.1211 (t0) REVERT: D 689 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7254 (mmt) REVERT: D 704 LYS cc_start: 0.8054 (tmtt) cc_final: 0.7561 (mmmt) REVERT: D 751 GLN cc_start: 0.6778 (mm110) cc_final: 0.6435 (mm-40) REVERT: D 777 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7987 (p) REVERT: E 42 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6823 (pt0) REVERT: E 348 ASP cc_start: 0.7971 (m-30) cc_final: 0.7029 (m-30) REVERT: E 407 PHE cc_start: 0.7867 (t80) cc_final: 0.7317 (t80) REVERT: G 81 MET cc_start: 0.7315 (ttm) cc_final: 0.6640 (ttm) REVERT: H 246 GLU cc_start: 0.8050 (mp0) cc_final: 0.7837 (mp0) REVERT: H 336 LYS cc_start: 0.6544 (pttm) cc_final: 0.6271 (pttt) REVERT: H 361 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8040 (mm-30) REVERT: H 413 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: I 418 ARG cc_start: 0.7493 (ptt90) cc_final: 0.6960 (ptt-90) REVERT: I 476 ARG cc_start: 0.7481 (ptp-170) cc_final: 0.7223 (ptp-170) REVERT: I 497 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6317 (mt-10) REVERT: K 747 GLU cc_start: 0.8500 (tp30) cc_final: 0.8264 (tp30) REVERT: K 927 MET cc_start: 0.7966 (mtt) cc_final: 0.7115 (mmm) REVERT: K 1076 LYS cc_start: 0.8087 (mmtm) cc_final: 0.7747 (mmmt) outliers start: 67 outliers final: 53 residues processed: 290 average time/residue: 0.1267 time to fit residues: 56.9729 Evaluate side-chains 301 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 241 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 ASP Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 198 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 206 optimal weight: 0.0270 chunk 166 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 141 optimal weight: 0.4980 chunk 137 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 676 ASN H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.151641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.124047 restraints weight = 30686.656| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.11 r_work: 0.3456 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 19597 Z= 0.125 Angle : 0.596 10.934 26519 Z= 0.308 Chirality : 0.042 0.219 3014 Planarity : 0.004 0.075 3411 Dihedral : 5.037 38.147 2620 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.89 % Allowed : 20.22 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2366 helix: 0.78 (0.16), residues: 1164 sheet: -0.51 (0.40), residues: 163 loop : -2.34 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 415 TYR 0.028 0.001 TYR D 179 PHE 0.032 0.001 PHE D 186 TRP 0.022 0.001 TRP H 247 HIS 0.004 0.001 HIS E 217 Details of bonding type rmsd covalent geometry : bond 0.00293 (19597) covalent geometry : angle 0.59562 (26519) hydrogen bonds : bond 0.03300 ( 819) hydrogen bonds : angle 3.98967 ( 2415) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7552 (pp) REVERT: C 42 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6670 (mm-30) REVERT: C 196 TRP cc_start: 0.5754 (t-100) cc_final: 0.5377 (t-100) REVERT: C 307 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7974 (mm-30) REVERT: D 508 ASN cc_start: 0.1928 (OUTLIER) cc_final: 0.1063 (t0) REVERT: D 689 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.6981 (mmt) REVERT: D 704 LYS cc_start: 0.7931 (tmtt) cc_final: 0.7482 (mmmt) REVERT: D 751 GLN cc_start: 0.6703 (mm110) cc_final: 0.6345 (mm-40) REVERT: D 777 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.8007 (p) REVERT: E 305 ASP cc_start: 0.7864 (t0) cc_final: 0.7428 (m-30) REVERT: E 348 ASP cc_start: 0.7837 (m-30) cc_final: 0.6939 (m-30) REVERT: E 407 PHE cc_start: 0.7846 (t80) cc_final: 0.7243 (t80) REVERT: G 81 MET cc_start: 0.7174 (ttm) cc_final: 0.6956 (ttm) REVERT: H 252 MET cc_start: 0.8081 (ttm) cc_final: 0.7810 (mtp) REVERT: H 336 LYS cc_start: 0.6622 (pttm) cc_final: 0.6318 (pttt) REVERT: H 347 ASP cc_start: 0.8246 (p0) cc_final: 0.8023 (p0) REVERT: I 418 ARG cc_start: 0.7369 (ptt90) cc_final: 0.6863 (ptt-90) REVERT: I 476 ARG cc_start: 0.7385 (ptp-170) cc_final: 0.7107 (ptp-170) REVERT: I 497 GLU cc_start: 0.6826 (mt-10) cc_final: 0.6217 (mt-10) REVERT: K 747 GLU cc_start: 0.8426 (tp30) cc_final: 0.8188 (tp30) REVERT: K 927 MET cc_start: 0.7888 (mtt) cc_final: 0.7056 (mmm) REVERT: K 1076 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7735 (mmmt) outliers start: 61 outliers final: 46 residues processed: 286 average time/residue: 0.1314 time to fit residues: 58.3610 Evaluate side-chains 284 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 193 TYR Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.0020 chunk 195 optimal weight: 9.9990 chunk 210 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 149 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 676 ASN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.152571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.125317 restraints weight = 30858.919| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.15 r_work: 0.3459 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 19597 Z= 0.125 Angle : 0.594 10.734 26519 Z= 0.307 Chirality : 0.042 0.221 3014 Planarity : 0.004 0.077 3411 Dihedral : 4.938 36.647 2620 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.75 % Allowed : 20.45 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2366 helix: 0.88 (0.16), residues: 1164 sheet: -0.48 (0.40), residues: 163 loop : -2.26 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 415 TYR 0.029 0.001 TYR D 179 PHE 0.033 0.001 PHE D 186 TRP 0.025 0.001 TRP H 247 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00294 (19597) covalent geometry : angle 0.59411 (26519) hydrogen bonds : bond 0.03253 ( 819) hydrogen bonds : angle 3.96268 ( 2415) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4732 Ramachandran restraints generated. 2366 Oldfield, 0 Emsley, 2366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7572 (pp) REVERT: C 42 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6685 (mm-30) REVERT: C 196 TRP cc_start: 0.5681 (t-100) cc_final: 0.5372 (t-100) REVERT: C 307 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7956 (mm-30) REVERT: D 508 ASN cc_start: 0.2025 (OUTLIER) cc_final: 0.1200 (t0) REVERT: D 689 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7022 (mmt) REVERT: D 704 LYS cc_start: 0.7924 (tmtt) cc_final: 0.7462 (mmmt) REVERT: D 751 GLN cc_start: 0.6708 (mm110) cc_final: 0.6365 (mm-40) REVERT: D 777 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8149 (p) REVERT: E 305 ASP cc_start: 0.7871 (t0) cc_final: 0.7428 (m-30) REVERT: E 348 ASP cc_start: 0.7802 (m-30) cc_final: 0.6898 (m-30) REVERT: E 407 PHE cc_start: 0.7893 (t80) cc_final: 0.7292 (t80) REVERT: H 252 MET cc_start: 0.8065 (ttm) cc_final: 0.7806 (mtp) REVERT: H 336 LYS cc_start: 0.6580 (pttm) cc_final: 0.6282 (pttt) REVERT: H 347 ASP cc_start: 0.8223 (p0) cc_final: 0.7997 (p0) REVERT: H 413 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: I 418 ARG cc_start: 0.7352 (ptt90) cc_final: 0.6822 (ptt-90) REVERT: I 431 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7176 (tt0) REVERT: I 476 ARG cc_start: 0.7335 (ptp-170) cc_final: 0.7072 (ptp-170) REVERT: I 497 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6215 (mt-10) REVERT: K 747 GLU cc_start: 0.8362 (tp30) cc_final: 0.8130 (tp30) REVERT: K 927 MET cc_start: 0.7831 (mtt) cc_final: 0.7037 (mmm) REVERT: K 1076 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7752 (mmmt) outliers start: 58 outliers final: 46 residues processed: 286 average time/residue: 0.1357 time to fit residues: 59.9892 Evaluate side-chains 288 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 237 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 676 ASN Chi-restraints excluded: chain D residue 689 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 371 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 875 GLU Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 160 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 63 optimal weight: 0.0010 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 198 optimal weight: 0.6980 chunk 202 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 676 ASN E 217 HIS H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.151829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124478 restraints weight = 30771.836| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.15 r_work: 0.3455 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 19597 Z= 0.129 Angle : 0.598 10.953 26519 Z= 0.309 Chirality : 0.043 0.216 3014 Planarity : 0.004 0.073 3411 Dihedral : 4.918 35.944 2620 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.84 % Allowed : 20.64 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 2366 helix: 0.90 (0.16), residues: 1164 sheet: -0.43 (0.40), residues: 163 loop : -2.24 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG Q 415 TYR 0.028 0.001 TYR D 179 PHE 0.033 0.001 PHE D 186 TRP 0.026 0.001 TRP H 247 HIS 0.004 0.001 HIS B 359 Details of bonding type rmsd covalent geometry : bond 0.00306 (19597) covalent geometry : angle 0.59770 (26519) hydrogen bonds : bond 0.03266 ( 819) hydrogen bonds : angle 3.96198 ( 2415) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.69 seconds wall clock time: 74 minutes 4.91 seconds (4444.91 seconds total)