Starting phenix.real_space_refine on Tue Jul 23 12:49:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/07_2024/7px9_13694_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/07_2024/7px9_13694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/07_2024/7px9_13694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/07_2024/7px9_13694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/07_2024/7px9_13694_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px9_13694/07_2024/7px9_13694_neut.cif" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 5 5.21 5 S 67 5.16 5 C 13943 2.51 5 N 3823 2.21 5 O 4339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 494": "NH1" <-> "NH2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 427": "NH1" <-> "NH2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D GLU 280": "OE1" <-> "OE2" Residue "D ASP 441": "OD1" <-> "OD2" Residue "D TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "E GLU 336": "OE1" <-> "OE2" Residue "E ARG 378": "NH1" <-> "NH2" Residue "E ARG 380": "NH1" <-> "NH2" Residue "E ARG 494": "NH1" <-> "NH2" Residue "E GLU 497": "OE1" <-> "OE2" Residue "E GLU 559": "OE1" <-> "OE2" Residue "E ARG 580": "NH1" <-> "NH2" Residue "F GLU 262": "OE1" <-> "OE2" Residue "F GLU 344": "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: 22194 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3623 Classifications: {'peptide': 463} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain breaks: 3 Chain: "B" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3659 Classifications: {'peptide': 468} Link IDs: {'PTRANS': 22, 'TRANS': 445} Chain breaks: 2 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3629 Classifications: {'peptide': 464} Link IDs: {'PTRANS': 22, 'TRANS': 441} Chain breaks: 2 Chain: "D" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3542 Classifications: {'peptide': 452} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 428} Chain breaks: 3 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3719 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 22, 'TRANS': 453} Chain breaks: 1 Chain: "F" Number of atoms: 3723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3723 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 22, 'TRANS': 454} Chain breaks: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 112 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Time building chain proxies: 12.62, per 1000 atoms: 0.57 Number of scatterers: 22194 At special positions: 0 Unit cell: (136.864, 153.972, 127.088, 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 67 16.00 P 17 15.00 Mg 5 11.99 O 4339 8.00 N 3823 7.00 C 13943 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: 9.63 Conformation dependent library (CDL) restraints added in 3.8 seconds 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5236 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 16 sheets defined 40.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.671A pdb=" N PHE A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 281 removed outlier: 3.625A pdb=" N TYR A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 314 removed outlier: 3.648A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 338 removed outlier: 3.606A pdb=" N LEU A 338 " --> pdb=" O PRO A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 338' Processing helix chain 'A' and resid 346 through 362 Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 404 Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 460 through 466 removed outlier: 3.708A pdb=" N GLU A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 488 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 511 through 514 Processing helix chain 'A' and resid 515 through 538 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.561A pdb=" N LEU A 547 " --> pdb=" O ARG A 543 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 removed outlier: 4.364A pdb=" N THR A 564 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 578 Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 259 through 274 Proline residue: B 271 - end of helix Processing helix chain 'B' and resid 274 through 282 Processing helix chain 'B' and resid 298 through 317 Processing helix chain 'B' and resid 343 through 359 removed outlier: 3.553A pdb=" N LYS B 359 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 402 Processing helix chain 'B' and resid 441 through 453 removed outlier: 3.613A pdb=" N TYR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 466 removed outlier: 4.126A pdb=" N GLU B 466 " --> pdb=" O ASP B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 488 removed outlier: 3.545A pdb=" N CYS B 474 " --> pdb=" O ASP B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 511 through 514 Processing helix chain 'B' and resid 515 through 537 Processing helix chain 'B' and resid 543 through 559 removed outlier: 3.598A pdb=" N LEU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 578 removed outlier: 4.102A pdb=" N TRP B 570 " --> pdb=" O ASN B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 235 through 242 removed outlier: 3.704A pdb=" N GLU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 242 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 274 removed outlier: 4.339A pdb=" N LEU C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Proline residue: C 271 - end of helix Processing helix chain 'C' and resid 274 through 282 Processing helix chain 'C' and resid 298 through 314 removed outlier: 3.663A pdb=" N ILE C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 303 " --> pdb=" O LYS C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.892A pdb=" N ARG C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 391 Processing helix chain 'C' and resid 392 through 401 removed outlier: 3.531A pdb=" N LEU C 396 " --> pdb=" O VAL C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 441 through 453 Processing helix chain 'C' and resid 460 through 467 Processing helix chain 'C' and resid 470 through 487 Processing helix chain 'C' and resid 511 through 513 No H-bonds generated for 'chain 'C' and resid 511 through 513' Processing helix chain 'C' and resid 515 through 537 Processing helix chain 'C' and resid 543 through 555 removed outlier: 3.755A pdb=" N LEU C 547 " --> pdb=" O ARG C 543 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 257 through 274 removed outlier: 3.962A pdb=" N LEU D 270 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Proline residue: D 271 - end of helix Processing helix chain 'D' and resid 274 through 282 Processing helix chain 'D' and resid 298 through 314 removed outlier: 4.035A pdb=" N ALA D 303 " --> pdb=" O LYS D 299 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'D' and resid 343 through 362 removed outlier: 3.578A pdb=" N ARG D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 404 Processing helix chain 'D' and resid 442 through 453 Processing helix chain 'D' and resid 460 through 466 removed outlier: 3.716A pdb=" N GLU D 466 " --> pdb=" O ASP D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 487 Processing helix chain 'D' and resid 515 through 537 Processing helix chain 'D' and resid 543 through 559 removed outlier: 3.551A pdb=" N LEU D 547 " --> pdb=" O ARG D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 578 removed outlier: 4.506A pdb=" N LYS D 576 " --> pdb=" O ARG D 572 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.519A pdb=" N VAL E 242 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 243 " --> pdb=" O GLU E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 243' Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 258 through 274 removed outlier: 4.278A pdb=" N LEU E 270 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Proline residue: E 271 - end of helix Processing helix chain 'E' and resid 274 through 281 Processing helix chain 'E' and resid 298 through 318 removed outlier: 3.508A pdb=" N ALA E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 327 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.833A pdb=" N ARG E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 401 Proline residue: E 394 - end of helix Processing helix chain 'E' and resid 441 through 453 Processing helix chain 'E' and resid 460 through 467 removed outlier: 3.894A pdb=" N GLU E 466 " --> pdb=" O ASP E 462 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE E 467 " --> pdb=" O ASP E 463 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 487 Processing helix chain 'E' and resid 490 through 492 No H-bonds generated for 'chain 'E' and resid 490 through 492' Processing helix chain 'E' and resid 515 through 538 Processing helix chain 'E' and resid 543 through 558 removed outlier: 3.934A pdb=" N LEU E 547 " --> pdb=" O ARG E 543 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 578 removed outlier: 4.159A pdb=" N ILE E 573 " --> pdb=" O ASP E 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 193 Processing helix chain 'F' and resid 235 through 243 removed outlier: 3.567A pdb=" N GLU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N LEU F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 269 Processing helix chain 'F' and resid 269 through 274 Processing helix chain 'F' and resid 274 through 282 removed outlier: 3.541A pdb=" N TYR F 278 " --> pdb=" O HIS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 317 Processing helix chain 'F' and resid 323 through 328 removed outlier: 3.600A pdb=" N TYR F 328 " --> pdb=" O GLU F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 338 removed outlier: 3.961A pdb=" N LEU F 337 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 360 Processing helix chain 'F' and resid 372 through 376 removed outlier: 3.593A pdb=" N SER F 375 " --> pdb=" O GLU F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 400 Proline residue: F 394 - end of helix Processing helix chain 'F' and resid 417 through 421 Processing helix chain 'F' and resid 422 through 427 removed outlier: 3.571A pdb=" N LEU F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 453 removed outlier: 3.514A pdb=" N TYR F 452 " --> pdb=" O ILE F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 466 removed outlier: 4.374A pdb=" N GLU F 466 " --> pdb=" O ASP F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 487 Processing helix chain 'F' and resid 490 through 492 No H-bonds generated for 'chain 'F' and resid 490 through 492' Processing helix chain 'F' and resid 511 through 514 Processing helix chain 'F' and resid 515 through 537 Processing helix chain 'F' and resid 543 through 558 removed outlier: 3.723A pdb=" N ASN F 558 " --> pdb=" O GLU F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 578 removed outlier: 4.574A pdb=" N GLY F 575 " --> pdb=" O ALA F 571 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS F 576 " --> pdb=" O ARG F 572 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 125 removed outlier: 7.124A pdb=" N THR A 112 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N THR A 107 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A 114 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU A 151 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 167 removed outlier: 6.059A pdb=" N LEU A 164 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 177 " --> pdb=" O LEU A 164 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 188 current: chain 'A' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 228 through 232 current: chain 'B' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 183 through 188 current: chain 'B' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 228 through 233 current: chain 'C' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 188 current: chain 'C' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 228 through 233 current: chain 'D' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 183 through 188 current: chain 'D' and resid 228 through 233 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 228 through 233 current: chain 'E' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 183 through 188 current: chain 'E' and resid 228 through 232 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 228 through 232 current: chain 'F' and resid 173 through 177 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 183 through 188 current: chain 'F' and resid 228 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.824A pdb=" N ASP A 371 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 366 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 412 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N VAL A 368 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 414 " --> pdb=" O VAL A 368 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 370 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 289 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 415 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU A 291 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.852A pdb=" N TYR A 583 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 106 removed outlier: 6.451A pdb=" N ASP B 114 " --> pdb=" O LEU B 105 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 120 through 125 current: chain 'B' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 151 through 152 current: chain 'E' and resid 112 through 117 Processing sheet with id=AA6, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.635A pdb=" N LEU B 330 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B 371 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 332 " --> pdb=" O ASP B 371 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AA8, first strand: chain 'C' and resid 99 through 107 removed outlier: 6.731A pdb=" N ASP C 114 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N THR C 107 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR C 112 " --> pdb=" O THR C 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 120 through 125 current: chain 'C' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 151 through 152 current: chain 'D' and resid 112 through 117 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 120 through 125 current: chain 'D' and resid 151 through 152 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 151 through 152 current: chain 'F' and resid 112 through 117 Processing sheet with id=AA9, first strand: chain 'C' and resid 328 through 332 removed outlier: 6.782A pdb=" N TYR C 328 " --> pdb=" O ILE C 367 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N PHE C 369 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 330 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP C 371 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 332 " --> pdb=" O ASP C 371 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY C 288 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ILE C 435 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU C 290 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 505 through 509 Processing sheet with id=AB2, first strand: chain 'D' and resid 328 through 333 removed outlier: 6.944A pdb=" N TYR D 328 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE D 369 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU D 330 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ASP D 371 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE D 332 " --> pdb=" O ASP D 371 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL D 366 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE D 412 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 368 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ALA D 414 " --> pdb=" O VAL D 368 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE D 370 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLY D 288 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE D 435 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 290 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 506 through 508 removed outlier: 3.781A pdb=" N LEU D 496 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR D 583 " --> pdb=" O THR D 499 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 329 through 331 removed outlier: 6.405A pdb=" N LEU E 330 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP E 371 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL E 289 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N SER E 415 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 291 " --> pdb=" O SER E 415 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY E 288 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE E 435 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU E 290 " --> pdb=" O ILE E 435 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 505 through 509 Processing sheet with id=AB6, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.889A pdb=" N LEU F 330 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL F 366 " --> pdb=" O ILE F 410 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE F 412 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 368 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA F 414 " --> pdb=" O VAL F 368 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N PHE F 370 " --> pdb=" O ALA F 414 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 506 through 509 858 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 10.42 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: 6720 1.33 - 1.45: 2891 1.45 - 1.57: 12807 1.57 - 1.69: 28 1.69 - 1.81: 116 Bond restraints: 22562 Sorted by residual: bond pdb=" C4 ATP F 701 " pdb=" C5 ATP F 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.67e+01 bond pdb=" C4 ATP C 701 " pdb=" C5 ATP C 701 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.65e+01 bond pdb=" C4 ATP E 701 " pdb=" C5 ATP E 701 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.57e+01 ... (remaining 22557 not shown) Histogram of bond angle deviations from ideal: 100.21 - 107.39: 808 107.39 - 114.56: 13380 114.56 - 121.73: 11357 121.73 - 128.91: 4902 128.91 - 136.08: 106 Bond angle restraints: 30553 Sorted by residual: angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 118.55 21.32 1.00e+00 1.00e+00 4.55e+02 angle pdb=" PB ATP E 701 " pdb=" O3B ATP E 701 " pdb=" PG ATP E 701 " ideal model delta sigma weight residual 139.87 119.11 20.76 1.00e+00 1.00e+00 4.31e+02 angle pdb=" PB ATP C 701 " pdb=" O3B ATP C 701 " pdb=" PG ATP C 701 " ideal model delta sigma weight residual 139.87 119.12 20.75 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 119.58 20.29 1.00e+00 1.00e+00 4.12e+02 angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 119.89 19.98 1.00e+00 1.00e+00 3.99e+02 ... (remaining 30548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 13488 23.28 - 46.56: 355 46.56 - 69.85: 53 69.85 - 93.13: 19 93.13 - 116.41: 2 Dihedral angle restraints: 13917 sinusoidal: 5805 harmonic: 8112 Sorted by residual: dihedral pdb=" CA ARG D 439 " pdb=" C ARG D 439 " pdb=" N PRO D 440 " pdb=" CA PRO D 440 " ideal model delta harmonic sigma weight residual -180.00 -78.26 -101.74 0 5.00e+00 4.00e-02 4.14e+02 dihedral pdb=" O1B ADP D 701 " pdb=" O3A ADP D 701 " pdb=" PB ADP D 701 " pdb=" PA ADP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 56.41 -116.41 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" CA ASN D 563 " pdb=" C ASN D 563 " pdb=" N THR D 564 " pdb=" CA THR D 564 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 13914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2492 0.037 - 0.074: 648 0.074 - 0.111: 287 0.111 - 0.149: 48 0.149 - 0.186: 3 Chirality restraints: 3478 Sorted by residual: chirality pdb=" CA ILE D 437 " pdb=" N ILE D 437 " pdb=" C ILE D 437 " pdb=" CB ILE D 437 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA CYS D 297 " pdb=" N CYS D 297 " pdb=" C CYS D 297 " pdb=" CB CYS D 297 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA MET D 486 " pdb=" N MET D 486 " pdb=" C MET D 486 " pdb=" CB MET D 486 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.78e-01 ... (remaining 3475 not shown) Planarity restraints: 3969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 334 " 0.026 5.00e-02 4.00e+02 4.00e-02 2.55e+00 pdb=" N PRO F 335 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 335 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 335 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 561 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO D 562 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO D 562 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 562 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 246 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 247 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.019 5.00e-02 4.00e+02 ... (remaining 3966 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 220 2.58 - 3.16: 18511 3.16 - 3.74: 34499 3.74 - 4.32: 46222 4.32 - 4.90: 77471 Nonbonded interactions: 176923 Sorted by model distance: nonbonded pdb=" O2B ATP B 701 " pdb="MG MG B 702 " model vdw 2.005 2.170 nonbonded pdb=" O1B ATP A 701 " pdb="MG MG A 702 " model vdw 2.047 2.170 nonbonded pdb=" O2B ATP C 701 " pdb="MG MG C 702 " model vdw 2.054 2.170 nonbonded pdb=" O1B ATP F 701 " pdb="MG MG F 702 " model vdw 2.076 2.170 nonbonded pdb=" O2B ATP E 701 " pdb="MG MG E 702 " model vdw 2.123 2.170 ... (remaining 176918 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 97 through 377 or resid 390 through 587)) selection = (chain 'B' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'C' and (resid 97 through 377 or resid 390 through 587)) selection = (chain 'D' and resid 97 through 587) selection = (chain 'E' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) selection = (chain 'F' and (resid 97 through 315 or resid 326 through 377 or resid 390 throu \ gh 587)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 59.170 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.100 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 0.082 22562 Z= 0.216 Angle : 0.676 21.322 30553 Z= 0.503 Chirality : 0.041 0.186 3478 Planarity : 0.003 0.040 3969 Dihedral : 11.058 116.411 8681 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 1.89 % Allowed : 5.32 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % 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: 1.46 (0.17), residues: 2779 helix: 2.19 (0.18), residues: 949 sheet: 0.55 (0.23), residues: 549 loop : 0.32 (0.19), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 570 HIS 0.002 0.000 HIS C 460 PHE 0.008 0.001 PHE E 353 TYR 0.008 0.001 TYR A 449 ARG 0.003 0.000 ARG E 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 251 time to evaluate : 2.766 Fit side-chains revert: symmetry clash REVERT: A 310 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6588 (mm) REVERT: A 492 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.6975 (t0) REVERT: B 172 HIS cc_start: 0.6917 (t70) cc_final: 0.6574 (t70) REVERT: C 281 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: C 496 LEU cc_start: 0.6591 (tp) cc_final: 0.6118 (tp) REVERT: C 536 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: C 570 TRP cc_start: 0.5759 (m-90) cc_final: 0.3921 (m-90) REVERT: D 420 MET cc_start: 0.5305 (ttt) cc_final: 0.4950 (tpp) REVERT: D 486 MET cc_start: 0.5812 (tmm) cc_final: 0.5465 (tmm) REVERT: E 314 MET cc_start: 0.8026 (mmm) cc_final: 0.7803 (mmm) REVERT: E 520 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7247 (tm-30) REVERT: F 244 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5744 (pp20) REVERT: F 330 LEU cc_start: 0.8913 (mp) cc_final: 0.8705 (mp) REVERT: F 407 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6425 (mm-30) outliers start: 45 outliers final: 14 residues processed: 290 average time/residue: 0.3603 time to fit residues: 158.6256 Evaluate side-chains 141 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 22562 Z= 0.427 Angle : 0.689 6.883 30553 Z= 0.360 Chirality : 0.047 0.199 3478 Planarity : 0.005 0.079 3969 Dihedral : 9.033 110.120 3280 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.15 % Favored : 94.78 % Rotamer: Outliers : 3.35 % Allowed : 8.18 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % 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: 0.79 (0.17), residues: 2779 helix: 1.46 (0.17), residues: 978 sheet: 0.18 (0.23), residues: 543 loop : 0.05 (0.19), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 570 HIS 0.006 0.001 HIS F 323 PHE 0.034 0.003 PHE C 272 TYR 0.018 0.002 TYR A 328 ARG 0.007 0.001 ARG E 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 122 time to evaluate : 2.648 Fit side-chains REVERT: A 491 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: B 172 HIS cc_start: 0.7124 (t70) cc_final: 0.6855 (t70) REVERT: B 346 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: B 352 ILE cc_start: 0.8644 (mt) cc_final: 0.8442 (mm) REVERT: B 463 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6380 (t0) REVERT: C 122 MET cc_start: 0.6810 (mpp) cc_final: 0.6609 (mpp) REVERT: C 160 GLU cc_start: 0.7567 (pm20) cc_final: 0.7108 (pm20) REVERT: C 281 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7699 (m-80) REVERT: C 536 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: D 167 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.6073 (tp) REVERT: D 486 MET cc_start: 0.6525 (tmm) cc_final: 0.6182 (tmm) REVERT: E 508 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7765 (mtp) REVERT: F 244 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5884 (pp20) outliers start: 80 outliers final: 44 residues processed: 191 average time/residue: 0.2943 time to fit residues: 92.7644 Evaluate side-chains 156 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 104 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 GLU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 443 GLU Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 171 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 273 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22562 Z= 0.185 Angle : 0.535 7.563 30553 Z= 0.276 Chirality : 0.042 0.170 3478 Planarity : 0.004 0.063 3969 Dihedral : 8.689 113.874 3277 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 2.98 % Allowed : 9.52 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % 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: 0.99 (0.17), residues: 2779 helix: 1.73 (0.17), residues: 977 sheet: 0.17 (0.23), residues: 525 loop : 0.14 (0.19), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 187 HIS 0.007 0.001 HIS E 274 PHE 0.023 0.001 PHE C 377 TYR 0.011 0.001 TYR F 500 ARG 0.003 0.000 ARG E 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 116 time to evaluate : 2.627 Fit side-chains REVERT: A 491 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: B 172 HIS cc_start: 0.6928 (t70) cc_final: 0.6654 (t70) REVERT: B 352 ILE cc_start: 0.8647 (mt) cc_final: 0.8380 (mt) REVERT: B 463 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6460 (t0) REVERT: C 160 GLU cc_start: 0.7489 (pm20) cc_final: 0.7017 (pm20) REVERT: C 281 TYR cc_start: 0.8078 (OUTLIER) cc_final: 0.7614 (m-80) REVERT: C 570 TRP cc_start: 0.6588 (m-90) cc_final: 0.4675 (m-90) REVERT: D 167 ILE cc_start: 0.6654 (OUTLIER) cc_final: 0.6413 (tp) REVERT: D 420 MET cc_start: 0.4922 (tpp) cc_final: 0.4572 (tpp) REVERT: D 486 MET cc_start: 0.6762 (tmm) cc_final: 0.6534 (tmm) REVERT: E 508 MET cc_start: 0.8099 (mtp) cc_final: 0.7680 (mtp) REVERT: F 244 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5992 (pp20) outliers start: 71 outliers final: 43 residues processed: 179 average time/residue: 0.2974 time to fit residues: 88.6202 Evaluate side-chains 158 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 110 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain E residue 129 ASN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 GLN ** C 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN E 493 ASN E 566 ASN ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22562 Z= 0.282 Angle : 0.573 6.808 30553 Z= 0.298 Chirality : 0.044 0.189 3478 Planarity : 0.005 0.059 3969 Dihedral : 8.716 113.201 3277 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 3.06 % Allowed : 10.82 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % 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: 0.77 (0.17), residues: 2779 helix: 1.56 (0.17), residues: 982 sheet: 0.04 (0.23), residues: 529 loop : 0.00 (0.19), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 187 HIS 0.006 0.001 HIS E 274 PHE 0.020 0.002 PHE C 377 TYR 0.013 0.001 TYR E 583 ARG 0.003 0.000 ARG B 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 109 time to evaluate : 2.621 Fit side-chains REVERT: A 491 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: B 172 HIS cc_start: 0.6988 (t70) cc_final: 0.6721 (t70) REVERT: B 352 ILE cc_start: 0.8692 (mt) cc_final: 0.8424 (mt) REVERT: B 463 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6631 (t0) REVERT: C 160 GLU cc_start: 0.7727 (pm20) cc_final: 0.7225 (pm20) REVERT: C 281 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: D 122 MET cc_start: 0.7081 (mmt) cc_final: 0.6784 (mmm) REVERT: D 167 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6360 (tp) REVERT: D 486 MET cc_start: 0.6609 (tmm) cc_final: 0.6385 (tmm) REVERT: D 497 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: E 508 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7751 (mtp) REVERT: F 244 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.6128 (pp20) outliers start: 73 outliers final: 51 residues processed: 171 average time/residue: 0.2920 time to fit residues: 83.5461 Evaluate side-chains 164 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 106 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 566 ASN Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 200 optimal weight: 0.0040 chunk 110 optimal weight: 0.6980 chunk 229 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 137 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 3.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 HIS C 514 ASN D 348 HIS ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22562 Z= 0.322 Angle : 0.603 9.126 30553 Z= 0.314 Chirality : 0.045 0.195 3478 Planarity : 0.005 0.063 3969 Dihedral : 8.833 111.203 3277 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.04 % Favored : 94.93 % Rotamer: Outliers : 3.35 % Allowed : 11.87 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.07 % Twisted Proline : 0.79 % 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: 0.52 (0.17), residues: 2779 helix: 1.40 (0.17), residues: 979 sheet: -0.15 (0.22), residues: 528 loop : -0.16 (0.19), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 187 HIS 0.004 0.001 HIS E 274 PHE 0.020 0.002 PHE C 377 TYR 0.016 0.002 TYR E 583 ARG 0.003 0.000 ARG F 427 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5558 Ramachandran restraints generated. 2779 Oldfield, 0 Emsley, 2779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 115 time to evaluate : 2.405 Fit side-chains REVERT: A 110 ASP cc_start: 0.7905 (t70) cc_final: 0.7663 (t70) REVERT: A 430 ARG cc_start: 0.7495 (OUTLIER) cc_final: 0.6560 (mpp80) REVERT: A 491 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: B 172 HIS cc_start: 0.7036 (t70) cc_final: 0.6768 (t70) REVERT: B 352 ILE cc_start: 0.8694 (mt) cc_final: 0.8463 (mt) REVERT: B 463 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6757 (t0) REVERT: C 160 GLU cc_start: 0.7787 (pm20) cc_final: 0.7315 (pm20) REVERT: C 281 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: D 122 MET cc_start: 0.7055 (mmt) cc_final: 0.6716 (mmm) REVERT: D 167 ILE cc_start: 0.6613 (OUTLIER) cc_final: 0.6389 (tp) REVERT: D 486 MET cc_start: 0.6631 (tmm) cc_final: 0.6405 (tmm) REVERT: D 497 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.6112 (pm20) REVERT: E 508 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7684 (mtp) REVERT: F 244 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6167 (pp20) outliers start: 80 outliers final: 57 residues processed: 186 average time/residue: 0.2917 time to fit residues: 89.6701 Evaluate side-chains 170 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 105 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 430 ARG Chi-restraints excluded: chain A residue 491 ASP Chi-restraints excluded: chain A residue 492 ASP Chi-restraints excluded: chain A residue 518 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 248 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 348 HIS Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain B residue 432 ASP Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 564 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 500 TYR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 345 THR Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 497 GLU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 228 TYR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 406 LEU Chi-restraints excluded: chain E residue 408 ASN Chi-restraints excluded: chain E residue 508 MET Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain E residue 581 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 337 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 507 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: 58.6165 > 50: distance: 116 - 121: 14.120 distance: 121 - 122: 16.221 distance: 122 - 125: 6.004 distance: 123 - 124: 29.182 distance: 123 - 129: 18.084 distance: 125 - 126: 22.963 distance: 126 - 127: 16.246 distance: 126 - 128: 13.725 distance: 129 - 130: 13.776 distance: 130 - 131: 29.067 distance: 130 - 133: 15.942 distance: 131 - 132: 37.222 distance: 131 - 136: 5.846 distance: 133 - 134: 18.397 distance: 133 - 135: 30.636 distance: 136 - 137: 11.597 distance: 137 - 138: 19.338 distance: 137 - 140: 20.694 distance: 138 - 139: 35.547 distance: 138 - 145: 15.230 distance: 140 - 141: 17.211 distance: 141 - 142: 5.518 distance: 143 - 144: 15.499 distance: 145 - 146: 24.075 distance: 146 - 147: 20.898 distance: 146 - 149: 26.189 distance: 147 - 148: 46.585 distance: 147 - 150: 6.220 distance: 150 - 151: 30.800 distance: 151 - 152: 14.289 distance: 152 - 153: 29.895 distance: 152 - 154: 11.521 distance: 154 - 155: 14.626 distance: 155 - 156: 4.342 distance: 155 - 158: 15.008 distance: 156 - 157: 23.624 distance: 156 - 166: 21.489 distance: 158 - 159: 13.473 distance: 159 - 160: 26.153 distance: 159 - 161: 16.689 distance: 160 - 162: 8.280 distance: 161 - 163: 12.803 distance: 162 - 164: 5.961 distance: 163 - 164: 15.159 distance: 164 - 165: 11.585 distance: 166 - 167: 3.728 distance: 167 - 168: 46.392 distance: 167 - 170: 24.385 distance: 168 - 169: 25.735 distance: 168 - 171: 15.857 distance: 171 - 172: 12.809 distance: 172 - 173: 30.578 distance: 172 - 175: 29.674 distance: 173 - 174: 11.444 distance: 173 - 182: 23.960 distance: 175 - 176: 4.017 distance: 176 - 177: 19.670 distance: 176 - 178: 23.169 distance: 177 - 179: 12.647 distance: 178 - 180: 19.964 distance: 179 - 181: 24.542 distance: 180 - 181: 13.606 distance: 182 - 183: 14.357 distance: 183 - 184: 9.359 distance: 183 - 186: 20.581 distance: 184 - 185: 12.825 distance: 184 - 191: 6.101 distance: 186 - 187: 16.076 distance: 187 - 188: 13.551 distance: 188 - 189: 5.803 distance: 188 - 190: 5.487 distance: 191 - 192: 12.163 distance: 192 - 193: 17.601 distance: 192 - 195: 19.258 distance: 193 - 194: 18.972 distance: 193 - 202: 14.412 distance: 195 - 196: 25.571 distance: 196 - 197: 14.725 distance: 197 - 198: 18.068 distance: 198 - 199: 6.484 distance: 199 - 200: 4.623 distance: 199 - 201: 6.449