Starting phenix.real_space_refine on Mon May 19 21:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t9k_10414/05_2025/6t9k_10414_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t9k_10414/05_2025/6t9k_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6t9k_10414/05_2025/6t9k_10414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t9k_10414/05_2025/6t9k_10414.map" model { file = "/net/cci-nas-00/data/ceres_data/6t9k_10414/05_2025/6t9k_10414_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t9k_10414/05_2025/6t9k_10414_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.15, per 1000 atoms: 0.58 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: 5.06 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 1.88 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: 5.97 Time building geometry restraints manager: 5.95 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 43.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.090 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.990 ------------------------------------------------------------------------------- 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 : 5.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.018 0.002 TRP I 486 HIS 0.013 0.001 HIS D 524 PHE 0.030 0.002 PHE D 582 TYR 0.033 0.002 TYR B 130 ARG 0.005 0.000 ARG H 346 Details of bonding type rmsd hydrogen bonds : bond 0.14523 ( 819) hydrogen bonds : angle 6.56505 ( 2415) covalent geometry : bond 0.00467 (19597) covalent geometry : angle 0.92130 (26519) *********************** 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 : 2.168 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: 0.6394 (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: 0.3635 time to fit residues: 197.6551 Evaluate side-chains 243 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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 200 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 100 optimal weight: 0.0670 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.151274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124375 restraints weight = 30969.035| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.25 r_work: 0.3451 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19597 Z= 0.145 Angle : 0.641 9.119 26519 Z= 0.336 Chirality : 0.043 0.188 3014 Planarity : 0.005 0.062 3411 Dihedral : 6.002 51.395 2620 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 2.23 % Allowed : 14.49 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.15), residues: 2366 helix: -0.89 (0.14), residues: 1159 sheet: -1.06 (0.38), residues: 178 loop : -3.03 (0.16), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 247 HIS 0.005 0.001 HIS D 618 PHE 0.015 0.001 PHE E 96 TYR 0.024 0.001 TYR D 184 ARG 0.007 0.001 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 819) hydrogen bonds : angle 4.65584 ( 2415) covalent geometry : bond 0.00331 (19597) covalent geometry : angle 0.64114 (26519) *********************** 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 332 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 285 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7588 (pp) REVERT: D 704 LYS cc_start: 0.7978 (tmtt) cc_final: 0.7324 (mmmt) REVERT: E 216 LYS cc_start: 0.2078 (mttp) cc_final: 0.1492 (mtmt) REVERT: E 305 ASP cc_start: 0.7969 (t0) cc_final: 0.7616 (m-30) REVERT: E 348 ASP cc_start: 0.7894 (m-30) cc_final: 0.6974 (m-30) REVERT: E 386 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7883 (t) REVERT: E 407 PHE cc_start: 0.8177 (t80) cc_final: 0.7651 (t80) REVERT: H 186 MET cc_start: 0.7184 (tpp) cc_final: 0.6690 (tpp) REVERT: H 336 LYS cc_start: 0.6696 (pttt) cc_final: 0.6402 (pttm) REVERT: I 418 ARG cc_start: 0.7173 (ptt90) cc_final: 0.6789 (ptt-90) REVERT: I 433 ASP cc_start: 0.7905 (t0) cc_final: 0.7697 (t0) REVERT: I 458 THR cc_start: 0.8805 (t) cc_final: 0.8571 (p) REVERT: I 476 ARG cc_start: 0.7047 (ptm160) cc_final: 0.6742 (ptp-170) REVERT: I 497 GLU cc_start: 0.6595 (mt-10) cc_final: 0.6251 (mt-10) REVERT: K 747 GLU cc_start: 0.8500 (tp30) cc_final: 0.8275 (tp30) REVERT: K 856 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7455 (m-40) REVERT: K 927 MET cc_start: 0.8024 (mtt) cc_final: 0.7626 (mpp) REVERT: K 1039 MET cc_start: 0.8241 (mtm) cc_final: 0.8034 (mtp) REVERT: Q 409 TYR cc_start: 0.6210 (t80) cc_final: 0.5960 (t80) outliers start: 47 outliers final: 25 residues processed: 314 average time/residue: 0.3152 time to fit residues: 149.5163 Evaluate side-chains 278 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 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 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 148 ILE Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 386 VAL 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 H residue 350 ILE Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 856 ASN 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 2 optimal weight: 0.0170 chunk 228 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 149 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 HIS C 209 ASN D 524 HIS D 566 HIS ** D 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN F 61 HIS ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN H 283 HIS H 396 ASN I 467 HIS ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1025 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.148334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.120954 restraints weight = 30953.660| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.44 r_work: 0.3376 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19597 Z= 0.225 Angle : 0.682 8.745 26519 Z= 0.357 Chirality : 0.046 0.225 3014 Planarity : 0.005 0.060 3411 Dihedral : 6.018 53.806 2619 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.65 % Favored : 92.31 % Rotamer: Outliers : 3.22 % Allowed : 16.05 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.16), residues: 2366 helix: -0.37 (0.15), residues: 1157 sheet: -1.16 (0.37), residues: 180 loop : -2.86 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 247 HIS 0.006 0.001 HIS E 217 PHE 0.018 0.002 PHE C 236 TYR 0.029 0.002 TYR D 581 ARG 0.007 0.001 ARG D 685 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 819) hydrogen bonds : angle 4.54866 ( 2415) covalent geometry : bond 0.00536 (19597) covalent geometry : angle 0.68234 (26519) *********************** 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 327 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7619 (pp) REVERT: C 196 TRP cc_start: 0.5934 (t-100) cc_final: 0.5429 (t-100) REVERT: C 207 ARG cc_start: 0.6559 (ptt-90) cc_final: 0.6291 (ptp90) REVERT: C 307 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8108 (mm-30) REVERT: D 472 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6811 (pt) REVERT: D 508 ASN cc_start: 0.2463 (OUTLIER) cc_final: 0.1514 (t0) REVERT: D 704 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7454 (mmmt) REVERT: E 386 VAL cc_start: 0.8154 (OUTLIER) cc_final: 0.7887 (t) REVERT: E 407 PHE cc_start: 0.8175 (t80) cc_final: 0.7620 (t80) REVERT: H 198 MET cc_start: 0.8255 (mtt) cc_final: 0.8040 (mtt) REVERT: I 418 ARG cc_start: 0.7439 (ptt90) cc_final: 0.6906 (ptt-90) REVERT: I 476 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6784 (ptp-170) REVERT: I 497 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6288 (mt-10) REVERT: K 927 MET cc_start: 0.8009 (mtt) cc_final: 0.7746 (mtt) REVERT: K 1039 MET cc_start: 0.8464 (mtm) cc_final: 0.8259 (mtp) outliers start: 68 outliers final: 49 residues processed: 303 average time/residue: 0.3314 time to fit residues: 150.3661 Evaluate side-chains 289 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 2.310 ------------------------------------------------------------------------------- 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 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 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 222 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain D residue 472 LEU 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 E residue 10 ILE Chi-restraints excluded: chain E residue 29 ILE 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 165 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 67 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 82 ASP 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 288 THR Chi-restraints excluded: chain H residue 315 THR Chi-restraints excluded: chain H residue 353 LEU Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 396 ASN Chi-restraints excluded: chain H residue 408 THR Chi-restraints excluded: chain I residue 512 GLN Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 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** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.150249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.123269 restraints weight = 31023.271| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.55 r_work: 0.3411 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19597 Z= 0.144 Angle : 0.604 8.320 26519 Z= 0.316 Chirality : 0.043 0.207 3014 Planarity : 0.004 0.058 3411 Dihedral : 5.712 57.895 2619 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.55 % Favored : 93.41 % Rotamer: Outliers : 3.27 % Allowed : 17.99 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2366 helix: 0.10 (0.15), residues: 1158 sheet: -1.09 (0.37), residues: 180 loop : -2.69 (0.18), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 678 HIS 0.005 0.001 HIS E 217 PHE 0.022 0.002 PHE D 186 TYR 0.016 0.001 TYR D 581 ARG 0.005 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 819) hydrogen bonds : angle 4.29488 ( 2415) covalent geometry : bond 0.00338 (19597) covalent geometry : angle 0.60402 (26519) *********************** 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 336 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7591 (pp) REVERT: C 15 MET cc_start: 0.8550 (mtt) cc_final: 0.8324 (mtt) REVERT: C 196 TRP cc_start: 0.5934 (t-100) cc_final: 0.5384 (t-100) REVERT: C 221 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6325 (pt) REVERT: C 307 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8037 (mm-30) REVERT: D 508 ASN cc_start: 0.2362 (OUTLIER) cc_final: 0.1372 (t0) REVERT: D 689 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.7138 (mmt) REVERT: D 704 LYS cc_start: 0.7994 (tmtt) cc_final: 0.7497 (mmmt) REVERT: D 777 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8187 (p) REVERT: E 247 MET cc_start: 0.7723 (mmm) cc_final: 0.7495 (tpp) REVERT: E 355 ASP cc_start: 0.8396 (t0) cc_final: 0.8188 (m-30) REVERT: E 386 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7908 (t) REVERT: E 407 PHE cc_start: 0.8127 (t80) cc_final: 0.7558 (t80) REVERT: H 250 ASP cc_start: 0.7428 (t0) cc_final: 0.7200 (t0) REVERT: I 418 ARG cc_start: 0.7384 (ptt90) cc_final: 0.6825 (ptt-90) REVERT: I 476 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6802 (ptp-170) REVERT: I 497 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6242 (mt-10) REVERT: K 747 GLU cc_start: 0.8443 (tp30) cc_final: 0.8218 (tp30) REVERT: K 927 MET cc_start: 0.8014 (mtt) cc_final: 0.7720 (mtt) REVERT: K 1039 MET cc_start: 0.8403 (mtm) cc_final: 0.8183 (mtp) outliers start: 69 outliers final: 47 residues processed: 310 average time/residue: 0.3164 time to fit residues: 149.5176 Evaluate side-chains 299 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 2.190 ------------------------------------------------------------------------------- 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 207 ARG Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 107 GLN Chi-restraints excluded: chain D residue 170 TYR 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 659 VAL 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 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 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 386 VAL 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 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 290 ASP 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 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU 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 141 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 217 optimal weight: 0.0070 chunk 36 optimal weight: 2.9990 chunk 211 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN H 396 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 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 = 0.4043 r_free = 0.4043 target = 0.150329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123910 restraints weight = 31190.064| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.63 r_work: 0.3403 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 19597 Z= 0.145 Angle : 0.600 8.087 26519 Z= 0.314 Chirality : 0.043 0.193 3014 Planarity : 0.004 0.061 3411 Dihedral : 5.505 46.896 2619 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 3.50 % Allowed : 19.22 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.17), residues: 2366 helix: 0.30 (0.15), residues: 1164 sheet: -1.02 (0.37), residues: 180 loop : -2.56 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 678 HIS 0.005 0.001 HIS E 217 PHE 0.024 0.001 PHE D 186 TYR 0.022 0.001 TYR D 179 ARG 0.006 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 819) hydrogen bonds : angle 4.17721 ( 2415) covalent geometry : bond 0.00344 (19597) covalent geometry : angle 0.60034 (26519) *********************** 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 331 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 257 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7587 (pp) REVERT: C 307 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8063 (mm-30) REVERT: D 479 ARG cc_start: 0.8475 (ttm110) cc_final: 0.8141 (ttp80) REVERT: D 508 ASN cc_start: 0.2473 (OUTLIER) cc_final: 0.1537 (t0) REVERT: D 689 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7135 (mmt) REVERT: D 704 LYS cc_start: 0.7991 (tmtt) cc_final: 0.7502 (mmmt) REVERT: D 777 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8102 (p) REVERT: E 247 MET cc_start: 0.7764 (mmm) cc_final: 0.7554 (tpp) REVERT: E 305 ASP cc_start: 0.7923 (t0) cc_final: 0.7695 (m-30) REVERT: E 355 ASP cc_start: 0.8424 (t0) cc_final: 0.8218 (m-30) REVERT: E 386 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7899 (t) REVERT: E 407 PHE cc_start: 0.8021 (t80) cc_final: 0.7480 (t80) REVERT: H 250 ASP cc_start: 0.7557 (t0) cc_final: 0.7348 (t0) REVERT: H 347 ASP cc_start: 0.8372 (p0) cc_final: 0.8022 (p0) REVERT: I 418 ARG cc_start: 0.7427 (ptt90) cc_final: 0.6883 (ptt-90) REVERT: I 476 ARG cc_start: 0.6978 (ptm160) cc_final: 0.6734 (ptp-170) REVERT: I 497 GLU cc_start: 0.6719 (mt-10) cc_final: 0.6290 (mt-10) REVERT: K 747 GLU cc_start: 0.8476 (tp30) cc_final: 0.8237 (tp30) REVERT: K 927 MET cc_start: 0.7952 (mtt) cc_final: 0.7611 (mtt) REVERT: K 1039 MET cc_start: 0.8416 (mtm) cc_final: 0.8201 (mtp) REVERT: K 1076 LYS cc_start: 0.8076 (mmtm) cc_final: 0.7732 (mmmt) REVERT: Q 435 GLN cc_start: 0.8734 (mp10) cc_final: 0.8352 (mp10) outliers start: 74 outliers final: 57 residues processed: 305 average time/residue: 0.3302 time to fit residues: 154.6721 Evaluate side-chains 302 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 240 time to evaluate : 2.090 ------------------------------------------------------------------------------- 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 207 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 336 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 470 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 45 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 165 ILE Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 67 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 288 THR Chi-restraints excluded: chain H residue 315 THR 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 408 THR Chi-restraints excluded: chain I residue 519 SER Chi-restraints excluded: chain K residue 160 LEU Chi-restraints excluded: chain K residue 862 VAL Chi-restraints excluded: chain K residue 961 ILE Chi-restraints excluded: chain Q residue 420 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 82 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 168 optimal weight: 0.2980 chunk 187 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN C 152 HIS C 209 ASN D 676 ASN E 14 GLN ** G 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.150829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.124301 restraints weight = 31081.445| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.40 r_work: 0.3417 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 19597 Z= 0.143 Angle : 0.597 8.126 26519 Z= 0.312 Chirality : 0.043 0.185 3014 Planarity : 0.004 0.068 3411 Dihedral : 5.361 43.641 2619 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 3.88 % Allowed : 19.89 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.17), residues: 2366 helix: 0.49 (0.15), residues: 1160 sheet: -0.97 (0.37), residues: 179 loop : -2.47 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 678 HIS 0.004 0.001 HIS E 217 PHE 0.026 0.002 PHE D 186 TYR 0.024 0.001 TYR D 179 ARG 0.005 0.000 ARG Q 415 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 819) hydrogen bonds : angle 4.12370 ( 2415) covalent geometry : bond 0.00337 (19597) covalent geometry : angle 0.59657 (26519) *********************** 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 336 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 254 time to evaluate : 2.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 177 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7401 (pt0) REVERT: B 327 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7662 (pp) REVERT: C 233 ILE cc_start: 0.8152 (mm) cc_final: 0.7802 (tp) REVERT: D 489 TYR cc_start: 0.6772 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: D 508 ASN cc_start: 0.2429 (OUTLIER) cc_final: 0.1490 (t0) REVERT: D 689 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.7079 (mmt) REVERT: D 704 LYS cc_start: 0.7974 (tmtt) cc_final: 0.7493 (mmmt) REVERT: D 777 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8096 (p) REVERT: E 62 ASP cc_start: 0.7027 (p0) cc_final: 0.6799 (p0) REVERT: E 305 ASP cc_start: 0.8087 (t0) cc_final: 0.7702 (m-30) REVERT: E 386 VAL cc_start: 0.8129 (OUTLIER) cc_final: 0.7860 (t) REVERT: E 407 PHE cc_start: 0.7933 (t80) cc_final: 0.7391 (t80) REVERT: H 413 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6796 (m-80) REVERT: I 418 ARG cc_start: 0.7426 (ptt90) cc_final: 0.6885 (ptt-90) REVERT: I 476 ARG cc_start: 0.7046 (ptm160) cc_final: 0.6823 (ptp-170) REVERT: I 497 GLU cc_start: 0.6666 (mt-10) cc_final: 0.6253 (mt-10) REVERT: K 747 GLU cc_start: 0.8499 (tp30) cc_final: 0.8292 (tp30) REVERT: K 927 MET cc_start: 0.7981 (mtt) cc_final: 0.7625 (mtt) REVERT: K 1039 MET cc_start: 0.8418 (mtm) cc_final: 0.8200 (mtp) REVERT: K 1076 LYS cc_start: 0.8069 (mmtm) cc_final: 0.7742 (mmmt) REVERT: Q 435 GLN cc_start: 0.8802 (mp10) cc_final: 0.8454 (mp10) outliers start: 82 outliers final: 62 residues processed: 313 average time/residue: 0.3102 time to fit residues: 148.3359 Evaluate side-chains 305 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 236 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 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 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 470 SER Chi-restraints excluded: chain D residue 489 TYR Chi-restraints excluded: chain D residue 508 ASN Chi-restraints excluded: chain D residue 638 VAL Chi-restraints excluded: chain D residue 644 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 D residue 784 PHE 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 45 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 165 ILE Chi-restraints excluded: chain E residue 170 VAL 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 348 ASP Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 384 ASN Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain F residue 67 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 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 357 LYS Chi-restraints excluded: chain H residue 361 GLU Chi-restraints excluded: chain H residue 369 ILE 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 862 VAL 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 38 optimal weight: 0.0270 chunk 107 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 227 optimal weight: 8.9990 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 598 HIS D 676 ASN E 14 GLN H 240 ASN ** I 485 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 856 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.151191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.124413 restraints weight = 30925.434| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.40 r_work: 0.3432 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 19597 Z= 0.123 Angle : 0.588 8.764 26519 Z= 0.306 Chirality : 0.042 0.185 3014 Planarity : 0.004 0.071 3411 Dihedral : 5.171 41.460 2619 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.47 % Favored : 93.49 % Rotamer: Outliers : 3.46 % Allowed : 20.83 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2366 helix: 0.67 (0.16), residues: 1160 sheet: -0.72 (0.38), residues: 173 loop : -2.39 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 678 HIS 0.004 0.001 HIS E 217 PHE 0.028 0.001 PHE D 186 TYR 0.025 0.001 TYR D 179 ARG 0.007 0.000 ARG D 479 Details of bonding type rmsd hydrogen bonds : bond 0.03284 ( 819) hydrogen bonds : angle 4.02602 ( 2415) covalent geometry : bond 0.00290 (19597) covalent geometry : angle 0.58775 (26519) *********************** 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 322 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 249 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 327 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7646 (pp) REVERT: D 479 ARG cc_start: 0.8459 (ttm110) cc_final: 0.8147 (ttp80) REVERT: D 489 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: D 508 ASN cc_start: 0.2128 (OUTLIER) cc_final: 0.1208 (t0) REVERT: D 689 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7004 (mmt) REVERT: D 704 LYS cc_start: 0.7933 (tmtt) cc_final: 0.7459 (mmmt) REVERT: D 777 THR cc_start: 0.8333 (OUTLIER) cc_final: 0.8036 (p) REVERT: E 305 ASP cc_start: 0.8134 (t0) cc_final: 0.7672 (m-30) REVERT: E 407 PHE cc_start: 0.7756 (t80) cc_final: 0.7215 (t80) REVERT: H 347 ASP cc_start: 0.8293 (p0) cc_final: 0.8077 (p0) REVERT: H 413 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6891 (m-80) REVERT: I 418 ARG cc_start: 0.7391 (ptt90) cc_final: 0.6847 (ptt-90) REVERT: I 476 ARG cc_start: 0.7022 (ptm160) cc_final: 0.6815 (ptp-170) REVERT: I 497 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6098 (mt-10) REVERT: K 747 GLU cc_start: 0.8561 (tp30) cc_final: 0.8293 (tp30) REVERT: K 856 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7505 (m-40) REVERT: K 927 MET cc_start: 0.7961 (mtt) cc_final: 0.7585 (mtt) REVERT: K 1039 MET cc_start: 0.8405 (mtm) cc_final: 0.8189 (mtp) REVERT: K 1076 LYS cc_start: 0.8068 (mmtm) cc_final: 0.7738 (mmmt) REVERT: Q 435 GLN cc_start: 0.8833 (mp10) cc_final: 0.8483 (mp10) outliers start: 73 outliers final: 51 residues processed: 299 average time/residue: 0.3185 time to fit residues: 145.8166 Evaluate side-chains 292 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 2.341 ------------------------------------------------------------------------------- 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 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 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 489 TYR 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 14 GLN Chi-restraints excluded: chain E residue 29 ILE 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 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 91 GLU 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 288 THR 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 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 856 ASN Chi-restraints excluded: chain K residue 961 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.661 > 50: distance: 7 - 114: 31.846 distance: 10 - 111: 26.440 distance: 27 - 97: 22.885 distance: 29 - 37: 11.340 distance: 30 - 94: 11.895 distance: 37 - 38: 11.680 distance: 37 - 172: 11.220 distance: 38 - 39: 30.179 distance: 38 - 41: 38.098 distance: 39 - 45: 21.921 distance: 41 - 42: 41.041 distance: 45 - 46: 20.880 distance: 46 - 47: 25.801 distance: 46 - 49: 34.555 distance: 47 - 57: 12.156 distance: 50 - 51: 16.276 distance: 51 - 53: 13.661 distance: 53 - 55: 23.487 distance: 54 - 55: 8.886 distance: 55 - 56: 21.847 distance: 57 - 58: 11.787 distance: 59 - 60: 5.948 distance: 59 - 66: 9.049 distance: 62 - 63: 8.253 distance: 63 - 64: 12.006 distance: 63 - 65: 37.870 distance: 66 - 67: 30.929 distance: 67 - 68: 14.824 distance: 68 - 69: 7.248 distance: 68 - 74: 29.878 distance: 70 - 71: 40.203 distance: 71 - 72: 26.642 distance: 74 - 75: 23.235 distance: 75 - 78: 17.700 distance: 78 - 79: 45.658 distance: 82 - 151: 35.190 distance: 83 - 84: 19.753 distance: 83 - 86: 26.920 distance: 84 - 85: 11.119 distance: 84 - 94: 21.750 distance: 85 - 148: 23.735 distance: 86 - 87: 10.840 distance: 87 - 88: 3.437 distance: 87 - 89: 13.057 distance: 88 - 90: 16.196 distance: 89 - 91: 5.202 distance: 91 - 92: 4.666 distance: 94 - 95: 16.205 distance: 95 - 96: 13.875 distance: 95 - 98: 9.264 distance: 96 - 97: 8.932 distance: 96 - 103: 24.839 distance: 98 - 99: 21.530 distance: 99 - 100: 5.577 distance: 100 - 101: 15.992 distance: 103 - 104: 26.490 distance: 104 - 105: 21.467 distance: 104 - 107: 7.511 distance: 105 - 106: 14.107 distance: 105 - 111: 26.008 distance: 107 - 108: 46.169 distance: 107 - 109: 6.708 distance: 108 - 110: 23.211 distance: 111 - 112: 7.781 distance: 112 - 113: 5.717 distance: 112 - 115: 35.589 distance: 113 - 114: 41.002 distance: 113 - 117: 38.514 distance: 117 - 118: 41.209 distance: 118 - 119: 56.921 distance: 119 - 122: 34.507