Starting phenix.real_space_refine on Wed Jul 24 09:25:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/07_2024/7xkq_33264_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/07_2024/7xkq_33264.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/07_2024/7xkq_33264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/07_2024/7xkq_33264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/07_2024/7xkq_33264_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkq_33264/07_2024/7xkq_33264_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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 6 5.21 5 S 80 5.16 5 C 15921 2.51 5 N 4405 2.21 5 O 4867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 451": "OE1" <-> "OE2" Residue "D GLU 290": "OE1" <-> "OE2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "F PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 290": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25299 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3660 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 997 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.84, per 1000 atoms: 0.55 Number of scatterers: 25299 At special positions: 0 Unit cell: (126.72, 124.08, 156.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 80 16.00 P 20 15.00 Mg 6 11.99 O 4867 8.00 N 4405 7.00 C 15921 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 - 3.50 Amino acid : False - 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: 9.90 Conformation dependent library (CDL) restraints added in 4.8 seconds 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5956 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 23 sheets defined 47.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.661A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.569A pdb=" N ALA A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.691A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.991A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.711A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.554A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.685A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 398 removed outlier: 4.140A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.537A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.592A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.782A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 462 " --> pdb=" O LYS A 458 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.509A pdb=" N LYS A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 3.531A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.759A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.587A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 397 removed outlier: 3.994A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 421 removed outlier: 4.176A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.677A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.607A pdb=" N LEU B 487 " --> pdb=" O ASN B 483 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 4.215A pdb=" N GLY C 81 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.672A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.602A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.503A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.902A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 309 Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.753A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.666A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.881A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 465 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.565A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.586A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.806A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 4.141A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.575A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.671A pdb=" N ALA D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.596A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA D 385 " --> pdb=" O GLN D 381 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.524A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.576A pdb=" N PHE D 453 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 180 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 3.672A pdb=" N VAL E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.693A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.533A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 380 Processing helix chain 'E' and resid 380 through 388 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.578A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.786A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.678A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 180 removed outlier: 4.449A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.507A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.028A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.525A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.635A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 removed outlier: 3.764A pdb=" N LEU F 325 " --> pdb=" O PHE F 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 325' Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 removed outlier: 3.684A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 392 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.897A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.594A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 470 Processing helix chain 'G' and resid 3 through 58 Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 59 through 63 removed outlier: 3.853A pdb=" N ALA G 63 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 4.243A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.618A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER G 124 " --> pdb=" O ARG G 120 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 162 removed outlier: 3.955A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 284 Proline residue: G 218 - end of helix removed outlier: 4.131A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 106 removed outlier: 3.995A pdb=" N ARG H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN H 105 " --> pdb=" O GLU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 129 removed outlier: 4.726A pdb=" N LEU H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS H 121 " --> pdb=" O GLU H 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 125 " --> pdb=" O LYS H 121 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.995A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.120A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.622A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 77 through 78 removed outlier: 6.741A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.574A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.405A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.534A pdb=" N ILE B 167 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.352A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.194A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 3.601A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 10 removed outlier: 6.348A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.320A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.360A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.488A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.518A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.508A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ASP F 252 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ALA F 186 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.326A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 136 through 137 removed outlier: 9.424A pdb=" N ILE G 137 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL G 117 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 204 through 205 removed outlier: 6.336A pdb=" N GLU G 204 " --> pdb=" O VAL H 42 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU H 41 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL H 6 " --> pdb=" O GLU H 17 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU H 17 " --> pdb=" O VAL H 6 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 30 through 33 removed outlier: 3.885A pdb=" N ALA H 27 " --> pdb=" O GLY H 30 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU H 32 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL H 25 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS H 26 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA H 49 " --> pdb=" O LYS H 26 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3444 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: 9.95 Time building geometry restraints manager: 10.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7659 1.33 - 1.45: 3166 1.45 - 1.57: 14702 1.57 - 1.69: 33 1.69 - 1.81: 160 Bond restraints: 25720 Sorted by residual: bond pdb=" N GLU A 54 " pdb=" CA GLU A 54 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.47e+00 bond pdb=" N PHE A 55 " pdb=" CA PHE A 55 " ideal model delta sigma weight residual 1.453 1.484 -0.031 1.22e-02 6.72e+03 6.39e+00 bond pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.35e-02 5.49e+03 4.51e+00 bond pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" CA ALA A 56 " pdb=" CB ALA A 56 " ideal model delta sigma weight residual 1.528 1.496 0.032 1.59e-02 3.96e+03 4.04e+00 ... (remaining 25715 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.85: 1011 107.85 - 115.85: 16206 115.85 - 123.85: 17171 123.85 - 131.85: 472 131.85 - 139.84: 20 Bond angle restraints: 34880 Sorted by residual: angle pdb=" C GLU A 54 " pdb=" CA GLU A 54 " pdb=" CB GLU A 54 " ideal model delta sigma weight residual 109.71 103.44 6.27 1.83e+00 2.99e-01 1.18e+01 angle pdb=" CA PHE A 55 " pdb=" CB PHE A 55 " pdb=" CG PHE A 55 " ideal model delta sigma weight residual 113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01 angle pdb=" C PHE A 55 " pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 120.29 124.89 -4.60 1.42e+00 4.96e-01 1.05e+01 angle pdb=" N GLY A 58 " pdb=" CA GLY A 58 " pdb=" C GLY A 58 " ideal model delta sigma weight residual 115.00 110.52 4.48 1.44e+00 4.82e-01 9.67e+00 angle pdb=" N VAL E 207 " pdb=" CA VAL E 207 " pdb=" C VAL E 207 " ideal model delta sigma weight residual 112.96 109.88 3.08 1.00e+00 1.00e+00 9.51e+00 ... (remaining 34875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14367 17.91 - 35.81: 1076 35.81 - 53.72: 226 53.72 - 71.63: 69 71.63 - 89.54: 29 Dihedral angle restraints: 15767 sinusoidal: 6467 harmonic: 9300 Sorted by residual: dihedral pdb=" CA GLN D 217 " pdb=" C GLN D 217 " pdb=" N MET D 218 " pdb=" CA MET D 218 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA VAL H 15 " pdb=" C VAL H 15 " pdb=" N TYR H 16 " pdb=" CA TYR H 16 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ARG E 454 " pdb=" C ARG E 454 " pdb=" N LEU E 455 " pdb=" CA LEU E 455 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 15764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3014 0.046 - 0.092: 738 0.092 - 0.138: 260 0.138 - 0.184: 4 0.184 - 0.231: 2 Chirality restraints: 4018 Sorted by residual: chirality pdb=" CA PHE A 55 " pdb=" N PHE A 55 " pdb=" C PHE A 55 " pdb=" CB PHE A 55 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU A 54 " pdb=" N GLU A 54 " pdb=" C GLU A 54 " pdb=" CB GLU A 54 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASN A 57 " pdb=" N ASN A 57 " pdb=" C ASN A 57 " pdb=" CB ASN A 57 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 4015 not shown) Planarity restraints: 4541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 53 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C VAL A 53 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL A 53 " 0.025 2.00e-02 2.50e+03 pdb=" N GLU A 54 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 428 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO F 429 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO F 429 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 429 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO E 316 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.026 5.00e-02 4.00e+02 ... (remaining 4538 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 173 2.55 - 3.14: 20029 3.14 - 3.73: 38325 3.73 - 4.31: 53238 4.31 - 4.90: 92004 Nonbonded interactions: 203769 Sorted by model distance: nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 502 " model vdw 1.967 2.170 nonbonded pdb=" O3G ATP F 501 " pdb="MG MG F 502 " model vdw 1.968 2.170 nonbonded pdb=" O3B ATP C 600 " pdb="MG MG C 601 " model vdw 1.979 2.170 nonbonded pdb=" O3G ATP C 600 " pdb="MG MG C 601 " model vdw 1.983 2.170 nonbonded pdb=" O3B ATP E 501 " pdb="MG MG E 502 " model vdw 2.002 2.170 ... (remaining 203764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 56 through 501)) selection = (chain 'C' and (resid 24 through 54 or (resid 55 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 56 through 501)) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } 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: 10.040 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 68.500 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 : 0.003 0.037 25720 Z= 0.216 Angle : 0.505 6.275 34880 Z= 0.276 Chirality : 0.044 0.231 4018 Planarity : 0.004 0.056 4541 Dihedral : 14.152 89.537 9811 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3243 helix: 1.66 (0.15), residues: 1249 sheet: 0.87 (0.22), residues: 540 loop : 0.13 (0.17), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.013 0.001 PHE B 494 TYR 0.016 0.001 TYR B 248 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.199 Fit side-chains REVERT: C 60 MET cc_start: 0.8503 (mmt) cc_final: 0.8278 (mmt) REVERT: D 253 ASN cc_start: 0.7710 (m-40) cc_final: 0.7227 (m-40) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3672 time to fit residues: 78.3098 Evaluate side-chains 101 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 272 optimal weight: 0.9980 chunk 244 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 293 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 GLN B 172 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN H 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25720 Z= 0.210 Angle : 0.508 5.575 34880 Z= 0.268 Chirality : 0.044 0.175 4018 Planarity : 0.004 0.053 4541 Dihedral : 7.809 83.868 3756 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 0.49 % Allowed : 4.86 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.15), residues: 3243 helix: 1.88 (0.15), residues: 1266 sheet: 0.99 (0.22), residues: 538 loop : 0.15 (0.17), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 38 PHE 0.022 0.001 PHE B 395 TYR 0.018 0.001 TYR B 248 ARG 0.006 0.000 ARG F 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 3.067 Fit side-chains REVERT: B 60 MET cc_start: 0.8633 (mmm) cc_final: 0.8277 (mmm) REVERT: D 253 ASN cc_start: 0.7855 (m-40) cc_final: 0.7291 (m-40) REVERT: E 395 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8191 (tp30) REVERT: H 38 HIS cc_start: 0.7489 (t70) cc_final: 0.7284 (t-90) outliers start: 13 outliers final: 4 residues processed: 113 average time/residue: 0.3425 time to fit residues: 65.9591 Evaluate side-chains 112 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 244 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 100 optimal weight: 0.0980 chunk 235 optimal weight: 8.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25720 Z= 0.374 Angle : 0.572 5.631 34880 Z= 0.301 Chirality : 0.046 0.159 4018 Planarity : 0.004 0.056 4541 Dihedral : 8.007 86.395 3756 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.19 % Rotamer: Outliers : 0.71 % Allowed : 7.37 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3243 helix: 1.63 (0.15), residues: 1281 sheet: 0.87 (0.23), residues: 529 loop : 0.00 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 200 PHE 0.019 0.002 PHE F 257 TYR 0.017 0.001 TYR B 248 ARG 0.006 0.000 ARG H 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 2.863 Fit side-chains REVERT: B 60 MET cc_start: 0.8892 (mmm) cc_final: 0.8490 (mmm) REVERT: D 253 ASN cc_start: 0.8180 (m-40) cc_final: 0.7502 (m-40) REVERT: H 71 ARG cc_start: 0.6624 (ttp80) cc_final: 0.6351 (ttp80) outliers start: 19 outliers final: 8 residues processed: 116 average time/residue: 0.3371 time to fit residues: 67.1941 Evaluate side-chains 105 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 290 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 294 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 279 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25720 Z= 0.265 Angle : 0.506 6.256 34880 Z= 0.266 Chirality : 0.044 0.142 4018 Planarity : 0.004 0.055 4541 Dihedral : 7.693 82.948 3756 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 0.75 % Allowed : 9.58 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.15), residues: 3243 helix: 1.76 (0.15), residues: 1285 sheet: 0.85 (0.22), residues: 532 loop : 0.03 (0.17), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.013 0.001 PHE F 257 TYR 0.015 0.001 TYR B 248 ARG 0.002 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 2.911 Fit side-chains REVERT: B 60 MET cc_start: 0.8863 (mmm) cc_final: 0.8515 (mmm) REVERT: D 253 ASN cc_start: 0.8149 (m-40) cc_final: 0.7465 (m-40) REVERT: H 71 ARG cc_start: 0.6507 (ttp80) cc_final: 0.6258 (ttp80) outliers start: 20 outliers final: 12 residues processed: 115 average time/residue: 0.3416 time to fit residues: 67.5519 Evaluate side-chains 108 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 323 random chunks: chunk 260 optimal weight: 0.7980 chunk 177 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** G 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25720 Z= 0.189 Angle : 0.478 9.805 34880 Z= 0.250 Chirality : 0.043 0.158 4018 Planarity : 0.004 0.053 4541 Dihedral : 7.454 83.621 3756 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 0.67 % Allowed : 10.40 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.15), residues: 3243 helix: 1.92 (0.15), residues: 1290 sheet: 0.87 (0.22), residues: 542 loop : 0.08 (0.17), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.014 0.001 PHE C 398 TYR 0.015 0.001 TYR B 248 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 3.004 Fit side-chains REVERT: B 60 MET cc_start: 0.8791 (mmm) cc_final: 0.8456 (mmm) REVERT: C 129 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9304 (mt) REVERT: D 253 ASN cc_start: 0.8083 (m-40) cc_final: 0.7449 (m-40) outliers start: 18 outliers final: 11 residues processed: 112 average time/residue: 0.3340 time to fit residues: 64.3525 Evaluate side-chains 109 residues out of total 2673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 485 ASP Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/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-5388/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-5388/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-5388/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-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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-5388/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-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.488 > 50: distance: 69 - 99: 24.362 distance: 74 - 106: 9.567 distance: 82 - 88: 27.580 distance: 88 - 89: 10.061 distance: 89 - 90: 19.906 distance: 89 - 92: 47.452 distance: 90 - 91: 36.788 distance: 90 - 99: 40.373 distance: 92 - 93: 26.656 distance: 93 - 94: 24.871 distance: 93 - 95: 17.626 distance: 94 - 96: 51.013 distance: 95 - 97: 22.082 distance: 96 - 98: 31.446 distance: 97 - 98: 40.538 distance: 99 - 100: 15.663 distance: 100 - 101: 23.429 distance: 100 - 103: 40.705 distance: 101 - 102: 32.519 distance: 101 - 106: 13.223 distance: 103 - 104: 31.729 distance: 103 - 105: 15.541 distance: 106 - 107: 18.381 distance: 107 - 108: 36.177 distance: 108 - 109: 55.005 distance: 108 - 110: 40.536 distance: 110 - 111: 54.095 distance: 111 - 112: 19.559 distance: 111 - 114: 31.954 distance: 112 - 113: 29.262 distance: 112 - 119: 50.782 distance: 114 - 115: 47.529 distance: 115 - 116: 42.440 distance: 116 - 117: 18.165 distance: 116 - 118: 23.905 distance: 119 - 120: 10.990 distance: 119 - 125: 22.211 distance: 120 - 121: 26.284 distance: 120 - 123: 58.943 distance: 121 - 122: 55.623 distance: 121 - 126: 11.695 distance: 123 - 124: 49.720 distance: 124 - 125: 52.435 distance: 126 - 127: 29.440 distance: 127 - 128: 41.732 distance: 128 - 129: 50.761 distance: 128 - 130: 40.255 distance: 130 - 131: 39.330 distance: 131 - 132: 23.628 distance: 131 - 134: 14.549 distance: 132 - 133: 17.249 distance: 132 - 136: 40.095 distance: 134 - 135: 35.794 distance: 136 - 137: 33.564 distance: 137 - 138: 15.955 distance: 137 - 140: 44.049 distance: 138 - 139: 26.939 distance: 138 - 148: 43.337 distance: 140 - 141: 19.317 distance: 141 - 142: 13.954 distance: 141 - 143: 13.008 distance: 142 - 144: 9.565 distance: 143 - 145: 5.928 distance: 144 - 146: 3.721 distance: 145 - 146: 3.885 distance: 148 - 149: 29.930 distance: 149 - 150: 14.451 distance: 149 - 152: 13.592 distance: 150 - 151: 25.076 distance: 150 - 155: 16.313 distance: 152 - 153: 24.152 distance: 152 - 154: 7.018 distance: 155 - 156: 18.769 distance: 155 - 161: 33.665 distance: 156 - 157: 15.485 distance: 156 - 159: 18.831 distance: 157 - 158: 8.910 distance: 157 - 162: 6.170 distance: 158 - 180: 16.478 distance: 159 - 160: 18.814 distance: 160 - 161: 34.884