Starting phenix.real_space_refine on Fri Apr 12 01:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh6_34753/04_2024/8hh6_34753_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh6_34753/04_2024/8hh6_34753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh6_34753/04_2024/8hh6_34753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh6_34753/04_2024/8hh6_34753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh6_34753/04_2024/8hh6_34753_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh6_34753/04_2024/8hh6_34753_updated.pdb" } resolution = 2.9 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= 0.001 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 18 5.49 5 Mg 6 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 325": "OD1" <-> "OD2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 57": "OD1" <-> "OD2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 337": "OE1" <-> "OE2" Residue "D ASP 390": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 45": "OD1" <-> "OD2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 197": "OD1" <-> "OD2" Residue "E TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 396": "OD1" <-> "OD2" Residue "F ASP 451": "OD1" <-> "OD2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 136": "OD1" <-> "OD2" Residue "G GLU 182": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24277 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, '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: {'PTRANS': 10, 'TRANS': 272} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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} Time building chain proxies: 13.39, per 1000 atoms: 0.55 Number of scatterers: 24277 At special positions: 0 Unit cell: (124.08, 124.08, 153.12, 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 77 16.00 P 18 15.00 Mg 6 11.99 O 4670 8.00 N 4219 7.00 C 15287 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: 9.93 Conformation dependent library (CDL) restraints added in 4.7 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 122 helices and 22 sheets defined 42.2% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.588A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 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 232 through 251 Proline residue: A 239 - end of helix removed outlier: 3.706A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 276 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 290 through 300 removed outlier: 3.530A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 329 through 337 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 392 removed outlier: 3.910A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 397 removed outlier: 4.126A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 394 through 397' Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 450 through 467 removed outlier: 4.704A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 removed outlier: 3.723A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 154 No H-bonds generated for 'chain 'B' and resid 151 through 154' Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.735A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 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 232 through 251 Proline residue: B 239 - end of helix removed outlier: 3.720A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.407A pdb=" N PHE B 291 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 296 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU B 299 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 346 through 352 removed outlier: 4.737A pdb=" N SER B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.887A pdb=" N GLN B 397 " --> pdb=" O GLU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.529A pdb=" N LEU B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 430 through 441 removed outlier: 3.788A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 467 removed outlier: 4.560A pdb=" N ARG B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 486 through 497 removed outlier: 3.580A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.558A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 217 through 220 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.575A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 276 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 290 through 300 removed outlier: 4.189A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 373 through 395 removed outlier: 3.742A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 441 removed outlier: 3.952A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 466 removed outlier: 4.875A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 179 Processing helix chain 'D' and resid 192 through 205 Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 222 through 241 removed outlier: 5.195A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 281 through 289 Processing helix chain 'D' and resid 309 through 311 No H-bonds generated for 'chain 'D' and resid 309 through 311' Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 356 through 359 No H-bonds generated for 'chain 'D' and resid 356 through 359' Processing helix chain 'D' and resid 361 through 386 removed outlier: 3.658A pdb=" N GLU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 391 No H-bonds generated for 'chain 'D' and resid 389 through 391' Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.818A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.811A pdb=" N GLN D 419 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 442 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 242 removed outlier: 4.945A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.568A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 removed outlier: 4.385A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 311 No H-bonds generated for 'chain 'E' and resid 309 through 311' Processing helix chain 'E' and resid 316 through 323 removed outlier: 3.625A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 387 removed outlier: 3.973A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.724A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 3.560A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 125 through 127 No H-bonds generated for 'chain 'F' and resid 125 through 127' Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 164 through 178 removed outlier: 4.372A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 207 through 210 Processing helix chain 'F' and resid 222 through 241 removed outlier: 4.866A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 268 removed outlier: 4.122A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU F 268 " --> pdb=" O VAL F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 291 removed outlier: 4.206A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 311 No H-bonds generated for 'chain 'F' and resid 309 through 311' Processing helix chain 'F' and resid 316 through 320 Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 387 removed outlier: 3.586A pdb=" N VAL F 366 " --> pdb=" O GLU F 362 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN F 381 " --> pdb=" O TYR F 377 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 391 No H-bonds generated for 'chain 'F' and resid 389 through 391' Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.707A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 419 removed outlier: 3.913A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 416 through 419' Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 removed outlier: 3.664A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 56 removed outlier: 3.830A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) Proline residue: G 44 - end of helix removed outlier: 5.415A pdb=" N ASN G 55 " --> pdb=" O GLU G 51 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 106 removed outlier: 3.902A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 112 No H-bonds generated for 'chain 'G' and resid 110 through 112' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 146 through 163 removed outlier: 3.655A pdb=" N LYS G 150 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLU G 151 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP G 162 " --> pdb=" O LEU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 283 removed outlier: 3.532A pdb=" N LEU G 213 " --> pdb=" O GLN G 209 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.690A pdb=" N GLN G 267 " --> pdb=" O ASN G 263 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.663A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 removed outlier: 3.939A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.761A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.696A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.584A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS B 42 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL B 31 " --> pdb=" O HIS B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.723A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.677A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 8.642A pdb=" N ILE B 222 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS B 255 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ILE B 194 " --> pdb=" O HIS B 255 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 257 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL B 196 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 259 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE B 198 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 316 " --> pdb=" O TYR B 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.512A pdb=" N GLU C 54 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N HIS C 42 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL C 31 " --> pdb=" O HIS C 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.786A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 107 through 109 removed outlier: 8.597A pdb=" N VAL C 108 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 223 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N ILE C 222 " --> pdb=" O MET C 191 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER C 193 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL C 224 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA C 226 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA C 197 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS C 255 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE C 194 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU C 257 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL C 196 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL C 259 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE C 198 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N SER C 312 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL C 258 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR C 314 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N TYR C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU C 316 " --> pdb=" O TYR C 260 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 340 through 344 Processing sheet with id= M, first strand: chain 'D' and resid 5 through 9 removed outlier: 6.424A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 327 through 330 removed outlier: 3.525A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.698A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 327 through 331 removed outlier: 8.552A pdb=" N ILE E 154 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER E 302 " --> pdb=" O ILE E 154 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU E 156 " --> pdb=" O SER E 302 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN E 304 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLY E 158 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 75 through 77 removed outlier: 6.536A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 327 through 330 removed outlier: 7.776A pdb=" N ILE F 154 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE F 182 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE F 250 " --> pdb=" O ILE F 182 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL F 184 " --> pdb=" O PHE F 250 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 115 through 118 removed outlier: 5.600A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2577 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: 8.54 Time building geometry restraints manager: 10.68 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: 8230 1.34 - 1.46: 4668 1.46 - 1.58: 11609 1.58 - 1.70: 23 1.70 - 1.82: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" O3 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.31e+00 bond pdb=" O4 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" O2 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O1 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C VAL G 43 " pdb=" N PRO G 44 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.12e+00 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 99.51 - 107.58: 931 107.58 - 115.64: 15348 115.64 - 123.71: 16694 123.71 - 131.77: 489 131.77 - 139.84: 17 Bond angle restraints: 33479 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 112.83 107.40 5.43 9.90e-01 1.02e+00 3.00e+01 angle pdb=" C ARG A 390 " pdb=" N GLU A 391 " pdb=" CA GLU A 391 " ideal model delta sigma weight residual 121.92 114.70 7.22 1.73e+00 3.34e-01 1.74e+01 angle pdb=" CA LEU G 68 " pdb=" CB LEU G 68 " pdb=" CG LEU G 68 " ideal model delta sigma weight residual 116.30 130.30 -14.00 3.50e+00 8.16e-02 1.60e+01 angle pdb=" N ILE F 340 " pdb=" CA ILE F 340 " pdb=" C ILE F 340 " ideal model delta sigma weight residual 106.21 110.49 -4.28 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N VAL A 378 " pdb=" CA VAL A 378 " pdb=" C VAL A 378 " ideal model delta sigma weight residual 113.71 110.11 3.60 9.50e-01 1.11e+00 1.44e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 14803 35.42 - 70.84: 262 70.84 - 106.27: 26 106.27 - 141.69: 0 141.69 - 177.11: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" C5' ADP D 602 " pdb=" O5' ADP D 602 " pdb=" PA ADP D 602 " pdb=" O2A ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 117.11 -177.11 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PA ADP D 602 " pdb=" PB ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 102.65 -162.65 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" CA LYS G 187 " pdb=" C LYS G 187 " pdb=" N LEU G 188 " pdb=" CA LEU G 188 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2514 0.035 - 0.069: 897 0.069 - 0.104: 285 0.104 - 0.139: 153 0.139 - 0.174: 7 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CB THR F 130 " pdb=" CA THR F 130 " pdb=" OG1 THR F 130 " pdb=" CG2 THR F 130 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CG LEU G 68 " pdb=" CB LEU G 68 " pdb=" CD1 LEU G 68 " pdb=" CD2 LEU G 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA LYS G 74 " pdb=" N LYS G 74 " pdb=" C LYS G 74 " pdb=" CB LYS G 74 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU G 140 " -0.049 5.00e-02 4.00e+02 7.53e-02 9.06e+00 pdb=" N PRO G 141 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 141 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 141 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 354 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.50e+00 pdb=" N PRO A 355 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO C 110 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " 0.026 5.00e-02 4.00e+02 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 145 2.58 - 3.16: 20156 3.16 - 3.74: 37183 3.74 - 4.32: 52494 4.32 - 4.90: 88799 Nonbonded interactions: 198777 Sorted by model distance: nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.002 2.170 nonbonded pdb="MG MG B 601 " pdb=" O2G ATP B 602 " model vdw 2.020 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 603 " model vdw 2.021 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.032 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.037 2.170 ... (remaining 198772 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 501) selection = (chain 'C' and resid 24 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: 24.430 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: 36.140 Check model and map are aligned: 0.340 Set scattering table: 0.220 Process input model: 67.320 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.140 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:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 0.061 24684 Z= 0.176 Angle : 0.580 14.000 33479 Z= 0.329 Chirality : 0.044 0.174 3856 Planarity : 0.004 0.075 4363 Dihedral : 13.715 177.112 9381 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 1.53 (0.15), residues: 3115 helix: 1.71 (0.15), residues: 1261 sheet: 1.12 (0.23), residues: 533 loop : 0.42 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 65 PHE 0.011 0.001 PHE D 125 TYR 0.013 0.001 TYR B 248 ARG 0.004 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 2.808 Fit side-chains revert: symmetry clash REVERT: A 67 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7598 (mt-10) REVERT: A 401 ASP cc_start: 0.8318 (m-30) cc_final: 0.7960 (t0) REVERT: D 201 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 311 ASP cc_start: 0.8072 (t0) cc_final: 0.7657 (t0) REVERT: E 149 ILE cc_start: 0.9021 (mt) cc_final: 0.8715 (mm) REVERT: F 389 MET cc_start: 0.8857 (tpp) cc_final: 0.8560 (tpp) REVERT: G 40 LYS cc_start: 0.6963 (mmpt) cc_final: 0.6522 (mmpt) REVERT: G 187 LYS cc_start: 0.4656 (tmtt) cc_final: 0.4067 (tptp) REVERT: G 189 LEU cc_start: 0.7614 (mm) cc_final: 0.7313 (tp) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 1.5156 time to fit residues: 411.1523 Evaluate side-chains 152 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 0.0770 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 281 optimal weight: 7.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 200 GLN A 371 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN D 40 ASN E 8 GLN E 423 GLN ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 282 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24684 Z= 0.275 Angle : 0.544 10.686 33479 Z= 0.284 Chirality : 0.046 0.157 3856 Planarity : 0.005 0.061 4363 Dihedral : 8.732 154.436 3580 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.36 % Allowed : 7.48 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 3115 helix: 1.68 (0.15), residues: 1253 sheet: 0.97 (0.22), residues: 536 loop : 0.27 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 363 PHE 0.017 0.001 PHE D 125 TYR 0.010 0.001 TYR G 262 ARG 0.006 0.000 ARG D 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 3.027 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8142 (mmt180) cc_final: 0.7793 (mmm160) REVERT: A 401 ASP cc_start: 0.8400 (m-30) cc_final: 0.7961 (t0) REVERT: B 181 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: B 407 GLN cc_start: 0.8213 (tp-100) cc_final: 0.7942 (mm-40) REVERT: D 201 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7954 (tp30) REVERT: D 311 ASP cc_start: 0.8307 (t70) cc_final: 0.7763 (t0) REVERT: E 397 LYS cc_start: 0.8361 (tptp) cc_final: 0.8054 (mmpt) REVERT: E 469 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7358 (ttm) REVERT: F 389 MET cc_start: 0.8919 (tpp) cc_final: 0.8652 (tpp) REVERT: G 187 LYS cc_start: 0.4913 (tmtt) cc_final: 0.4416 (tptp) REVERT: G 189 LEU cc_start: 0.7828 (mm) cc_final: 0.7624 (tp) outliers start: 35 outliers final: 7 residues processed: 180 average time/residue: 1.5150 time to fit residues: 312.3704 Evaluate side-chains 161 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 130 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4297 > 50: distance: 29 - 31: 7.344 distance: 31 - 32: 6.891 distance: 32 - 33: 10.205 distance: 32 - 35: 11.223 distance: 33 - 34: 20.727 distance: 33 - 36: 13.771 distance: 36 - 37: 10.304 distance: 37 - 38: 28.809 distance: 38 - 39: 14.980 distance: 38 - 40: 15.102 distance: 40 - 41: 15.750 distance: 41 - 42: 6.335 distance: 41 - 44: 12.015 distance: 42 - 43: 6.341 distance: 42 - 47: 12.522 distance: 44 - 45: 29.579 distance: 44 - 46: 26.498 distance: 47 - 48: 15.552 distance: 48 - 49: 4.015 distance: 49 - 50: 4.332 distance: 49 - 51: 7.099 distance: 51 - 52: 4.776 distance: 52 - 55: 5.336 distance: 53 - 60: 4.729 distance: 54 - 82: 10.682 distance: 55 - 56: 3.381 distance: 56 - 57: 7.282 distance: 60 - 61: 3.804 distance: 61 - 62: 3.918 distance: 61 - 64: 7.137 distance: 62 - 63: 3.667 distance: 63 - 90: 4.603 distance: 64 - 65: 4.655 distance: 68 - 71: 4.439 distance: 69 - 74: 4.957 distance: 70 - 99: 8.459 distance: 71 - 72: 7.000 distance: 71 - 73: 3.835 distance: 74 - 75: 6.479 distance: 75 - 76: 4.934 distance: 75 - 78: 6.167 distance: 76 - 77: 5.296 distance: 76 - 82: 3.693 distance: 77 - 105: 8.868 distance: 78 - 79: 6.870 distance: 79 - 81: 9.300 distance: 82 - 83: 5.450 distance: 83 - 84: 3.663 distance: 83 - 86: 6.506 distance: 84 - 85: 3.727 distance: 84 - 90: 3.778 distance: 86 - 87: 4.007 distance: 86 - 88: 9.108 distance: 87 - 89: 9.760 distance: 91 - 92: 4.909 distance: 91 - 94: 6.849 distance: 92 - 93: 7.979 distance: 92 - 99: 3.028 distance: 94 - 95: 3.424 distance: 95 - 96: 5.027 distance: 96 - 98: 5.668