Starting phenix.real_space_refine on Mon May 13 09:03:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/05_2024/8ep0_28494.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/05_2024/8ep0_28494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/05_2024/8ep0_28494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/05_2024/8ep0_28494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/05_2024/8ep0_28494.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ep0_28494/05_2024/8ep0_28494.pdb" } resolution = 4.9 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= 0.004 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 15696 2.51 5 N 4108 2.21 5 O 4488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "C PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "D PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 377": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 24408 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "B" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "C" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "D" Number of atoms: 5220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5220 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 457 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 371 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 246 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "F" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 13.16, per 1000 atoms: 0.54 Number of scatterers: 24408 At special positions: 0 Unit cell: (169.56, 169.56, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 4488 8.00 N 4108 7.00 C 15696 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: 11.41 Conformation dependent library (CDL) restraints added in 5.0 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 20 sheets defined 65.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 242 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 269 Processing helix chain 'A' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR A 347 " --> pdb=" O HIS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 418 through 435 Processing helix chain 'A' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE A 468 " --> pdb=" O TYR A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 570 Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 696 Processing helix chain 'A' and resid 704 through 706 No H-bonds generated for 'chain 'A' and resid 704 through 706' Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'B' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.059A pdb=" N ASP B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 242 Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 248 through 269 Processing helix chain 'B' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE B 298 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 4.114A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG B 339 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS B 340 " --> pdb=" O ARG B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR B 347 " --> pdb=" O HIS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 418 through 435 Processing helix chain 'B' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE B 468 " --> pdb=" O TYR B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 Processing helix chain 'B' and resid 524 through 532 Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 545 through 552 Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 559 through 570 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 647 through 657 Processing helix chain 'B' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 696 Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 707 through 722 Processing helix chain 'C' and resid 16 through 26 removed outlier: 3.995A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.845A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.057A pdb=" N ASP C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 242 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 269 Processing helix chain 'C' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N MET C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE C 298 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 329 removed outlier: 3.646A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 342 removed outlier: 4.094A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 4.565A pdb=" N TYR C 347 " --> pdb=" O HIS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 379 removed outlier: 3.650A pdb=" N LEU C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 390 through 400 Processing helix chain 'C' and resid 418 through 435 Processing helix chain 'C' and resid 446 through 473 removed outlier: 3.918A pdb=" N THR C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE C 467 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE C 468 " --> pdb=" O TYR C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 499 removed outlier: 4.876A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 570 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 696 Processing helix chain 'C' and resid 704 through 706 No H-bonds generated for 'chain 'C' and resid 704 through 706' Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.996A pdb=" N ASN D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.846A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.058A pdb=" N ASP D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 242 Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 248 through 269 Processing helix chain 'D' and resid 283 through 304 removed outlier: 3.602A pdb=" N ARG D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N MET D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 4.115A pdb=" N ASN D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 removed outlier: 3.645A pdb=" N LEU D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 342 removed outlier: 4.095A pdb=" N ARG D 339 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N LYS D 340 " --> pdb=" O ARG D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 removed outlier: 4.566A pdb=" N TYR D 347 " --> pdb=" O HIS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 379 removed outlier: 3.649A pdb=" N LEU D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N PHE D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 390 through 400 Processing helix chain 'D' and resid 418 through 435 Processing helix chain 'D' and resid 446 through 473 removed outlier: 3.917A pdb=" N THR D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE D 467 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE D 468 " --> pdb=" O TYR D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 499 removed outlier: 4.875A pdb=" N ASN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N THR D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 521 Processing helix chain 'D' and resid 524 through 532 Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 545 through 552 Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 559 through 570 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 647 through 657 Processing helix chain 'D' and resid 657 through 668 removed outlier: 3.874A pdb=" N SER D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 696 Processing helix chain 'D' and resid 704 through 706 No H-bonds generated for 'chain 'D' and resid 704 through 706' Processing helix chain 'D' and resid 707 through 722 Processing helix chain 'E' and resid 6 through 10 Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 146 Processing helix chain 'G' and resid 6 through 10 Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.600A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 64 through 77 removed outlier: 4.125A pdb=" N PHE G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'H' and resid 6 through 10 Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.599A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 77 removed outlier: 4.124A pdb=" N PHE H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE A 42 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN A 34 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 93 " --> pdb=" O ILE A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY A 275 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS A 592 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL A 634 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN A 603 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL A 607 " --> pdb=" O GLN A 603 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE B 42 " --> pdb=" O ASN B 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN B 34 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 125 " --> pdb=" O ILE B 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 93 " --> pdb=" O ILE B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY B 275 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS B 592 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR B 672 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL B 634 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA B 609 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 603 " --> pdb=" O VAL B 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL B 607 " --> pdb=" O GLN B 603 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 587 through 588 removed outlier: 4.356A pdb=" N ALA B 628 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.590A pdb=" N ILE C 42 " --> pdb=" O ASN C 34 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASN C 34 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 93 " --> pdb=" O ILE C 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 275 removed outlier: 4.898A pdb=" N GLY C 275 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 279 " --> pdb=" O GLY C 275 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS C 592 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 582 removed outlier: 6.870A pdb=" N VAL C 634 " --> pdb=" O ILE C 581 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN C 603 " --> pdb=" O VAL C 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL C 607 " --> pdb=" O GLN C 603 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 42 through 45 removed outlier: 6.591A pdb=" N ILE D 42 " --> pdb=" O ASN D 34 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ASN D 34 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 125 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN D 93 " --> pdb=" O ILE D 113 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 275 removed outlier: 4.899A pdb=" N GLY D 275 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU D 279 " --> pdb=" O GLY D 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 571 through 575 removed outlier: 3.510A pdb=" N CYS D 592 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR D 672 " --> pdb=" O VAL D 616 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 580 through 582 removed outlier: 6.871A pdb=" N VAL D 634 " --> pdb=" O ILE D 581 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 609 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN D 603 " --> pdb=" O VAL D 607 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N VAL D 607 " --> pdb=" O GLN D 603 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 587 through 588 removed outlier: 4.355A pdb=" N ALA D 628 " --> pdb=" O VAL D 588 " (cutoff:3.500A) 1572 hydrogen bonds defined for protein. 4536 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.31 Time building geometry restraints manager: 12.20 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: 7950 1.34 - 1.46: 4433 1.46 - 1.58: 12409 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 24964 Sorted by residual: bond pdb=" N PHE C 359 " pdb=" CA PHE C 359 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.17e-02 7.31e+03 4.25e+00 bond pdb=" N PHE B 359 " pdb=" CA PHE B 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.99e+00 bond pdb=" N PHE A 359 " pdb=" CA PHE A 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.97e+00 bond pdb=" N PHE D 359 " pdb=" CA PHE D 359 " ideal model delta sigma weight residual 1.459 1.436 0.023 1.17e-02 7.31e+03 3.70e+00 bond pdb=" CD1 TYR B 428 " pdb=" CE1 TYR B 428 " ideal model delta sigma weight residual 1.382 1.324 0.058 3.00e-02 1.11e+03 3.70e+00 ... (remaining 24959 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.27: 582 106.27 - 113.22: 13358 113.22 - 120.17: 8819 120.17 - 127.11: 11129 127.11 - 134.06: 276 Bond angle restraints: 34164 Sorted by residual: angle pdb=" N MET B 431 " pdb=" CA MET B 431 " pdb=" CB MET B 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.70e+01 angle pdb=" N MET D 431 " pdb=" CA MET D 431 " pdb=" CB MET D 431 " ideal model delta sigma weight residual 110.01 102.48 7.53 1.45e+00 4.76e-01 2.69e+01 angle pdb=" N MET C 431 " pdb=" CA MET C 431 " pdb=" CB MET C 431 " ideal model delta sigma weight residual 110.01 102.52 7.49 1.45e+00 4.76e-01 2.67e+01 angle pdb=" N MET A 431 " pdb=" CA MET A 431 " pdb=" CB MET A 431 " ideal model delta sigma weight residual 110.01 102.53 7.48 1.45e+00 4.76e-01 2.66e+01 angle pdb=" C LYS B 450 " pdb=" CA LYS B 450 " pdb=" CB LYS B 450 " ideal model delta sigma weight residual 109.67 118.57 -8.90 2.01e+00 2.48e-01 1.96e+01 ... (remaining 34159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 13283 15.64 - 31.29: 966 31.29 - 46.93: 171 46.93 - 62.57: 32 62.57 - 78.21: 28 Dihedral angle restraints: 14480 sinusoidal: 4608 harmonic: 9872 Sorted by residual: dihedral pdb=" CA TYR D 499 " pdb=" C TYR D 499 " pdb=" N GLN D 500 " pdb=" CA GLN D 500 " ideal model delta harmonic sigma weight residual 180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR A 499 " pdb=" C TYR A 499 " pdb=" N GLN A 500 " pdb=" CA GLN A 500 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR C 499 " pdb=" C TYR C 499 " pdb=" N GLN C 500 " pdb=" CA GLN C 500 " ideal model delta harmonic sigma weight residual 180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3612 0.078 - 0.156: 348 0.156 - 0.234: 28 0.234 - 0.312: 10 0.312 - 0.389: 10 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CB ILE C 378 " pdb=" CA ILE C 378 " pdb=" CG1 ILE C 378 " pdb=" CG2 ILE C 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB ILE D 378 " pdb=" CA ILE D 378 " pdb=" CG1 ILE D 378 " pdb=" CG2 ILE D 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE B 378 " pdb=" CA ILE B 378 " pdb=" CG1 ILE B 378 " pdb=" CG2 ILE B 378 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 4005 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 47 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" CG ASP C 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP C 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 47 " -0.018 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" CG ASP D 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP D 47 " -0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP D 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 47 " -0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" CG ASP A 47 " 0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP A 47 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP A 47 " -0.023 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4831 2.77 - 3.30: 27126 3.30 - 3.83: 41904 3.83 - 4.37: 46091 4.37 - 4.90: 75741 Nonbonded interactions: 195693 Sorted by model distance: nonbonded pdb=" OG SER B 418 " pdb=" OD1 ASN B 420 " model vdw 2.237 2.440 nonbonded pdb=" OG SER A 418 " pdb=" OD1 ASN A 420 " model vdw 2.237 2.440 nonbonded pdb=" OG SER C 418 " pdb=" OD1 ASN C 420 " model vdw 2.237 2.440 nonbonded pdb=" OG SER D 418 " pdb=" OD1 ASN D 420 " model vdw 2.237 2.440 nonbonded pdb=" OG SER B 25 " pdb=" OG1 THR B 28 " model vdw 2.239 2.440 ... (remaining 195688 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 3.210 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: 5.100 Check model and map are aligned: 0.180 Set scattering table: 0.260 Process input model: 69.110 Find NCS groups from input model: 1.890 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 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 : 0.004 0.071 24964 Z= 0.268 Angle : 0.785 9.468 34164 Z= 0.454 Chirality : 0.051 0.389 4008 Planarity : 0.006 0.103 4416 Dihedral : 12.186 78.213 8080 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.15), residues: 3340 helix: 0.25 (0.12), residues: 1928 sheet: 0.88 (0.36), residues: 172 loop : -0.21 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 108 HIS 0.010 0.001 HIS D 364 PHE 0.058 0.004 PHE B 17 TYR 0.040 0.003 TYR D 428 ARG 0.023 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9375 (tpp) cc_final: 0.9172 (tpp) REVERT: A 224 ILE cc_start: 0.9522 (pt) cc_final: 0.9231 (mm) REVERT: A 423 TYR cc_start: 0.8796 (t80) cc_final: 0.8410 (t80) REVERT: A 427 LEU cc_start: 0.9212 (tp) cc_final: 0.8876 (mt) REVERT: A 568 MET cc_start: 0.9272 (mmp) cc_final: 0.8953 (mmp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1316 time to fit residues: 15.2975 Evaluate side-chains 64 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.829 Evaluate side-chains 11 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.094 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.1628 time to fit residues: 2.0358 Evaluate side-chains 9 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 9 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.0870 chunk 254 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 86 optimal weight: 0.4980 chunk 171 optimal weight: 6.9990 chunk 136 optimal weight: 0.0470 chunk 263 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 160 optimal weight: 0.0170 chunk 196 optimal weight: 20.0000 chunk 305 optimal weight: 10.0000 overall best weight: 1.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24964 Z= 0.169 Angle : 0.578 7.656 34164 Z= 0.315 Chirality : 0.041 0.167 4008 Planarity : 0.004 0.050 4416 Dihedral : 5.059 60.650 3584 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.15), residues: 3340 helix: 0.78 (0.12), residues: 1952 sheet: 0.97 (0.38), residues: 172 loop : -0.15 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 365 HIS 0.004 0.001 HIS C 270 PHE 0.019 0.002 PHE D 452 TYR 0.021 0.001 TYR D 428 ARG 0.010 0.000 ARG G 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5286 Ramachandran restraints generated. 2643 Oldfield, 0 Emsley, 2643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 359 PHE cc_start: 0.9620 (t80) cc_final: 0.9351 (t80) REVERT: B 365 TRP cc_start: 0.9437 (m100) cc_final: 0.9159 (m100) REVERT: B 366 MET cc_start: 0.9084 (mmp) cc_final: 0.8502 (ptp) REVERT: B 377 GLU cc_start: 0.9559 (tp30) cc_final: 0.9199 (tp30) REVERT: B 449 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9184 (mt-10) REVERT: B 536 MET cc_start: 0.9401 (mmp) cc_final: 0.9134 (mmm) REVERT: B 568 MET cc_start: 0.9507 (mmp) cc_final: 0.9156 (mmp) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1291 time to fit residues: 15.2649 Evaluate side-chains 61 residues out of total 628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.638 Evaluate side-chains 11 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.109 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0568 time to fit residues: 0.8906 Evaluate side-chains 10 residues out of total 121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 798, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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: 55.9699 > 50: distance: 0 - 1: 31.212 distance: 0 - 6: 51.819 distance: 1 - 29: 13.995 distance: 2 - 3: 12.306 distance: 3 - 5: 13.209 distance: 6 - 7: 7.720 distance: 7 - 8: 52.854 distance: 7 - 10: 51.027 distance: 8 - 9: 42.851 distance: 8 - 13: 54.116 distance: 9 - 38: 14.652 distance: 10 - 11: 55.777 distance: 10 - 12: 29.261 distance: 13 - 14: 20.844 distance: 14 - 15: 11.339 distance: 14 - 17: 22.707 distance: 15 - 16: 9.375 distance: 15 - 20: 8.806 distance: 16 - 45: 8.403 distance: 17 - 18: 24.870 distance: 17 - 19: 22.008 distance: 20 - 21: 9.734 distance: 21 - 22: 7.676 distance: 21 - 24: 4.581 distance: 22 - 23: 7.245 distance: 22 - 29: 8.376 distance: 23 - 56: 26.656 distance: 29 - 30: 6.470 distance: 30 - 33: 5.577 distance: 33 - 34: 4.328 distance: 34 - 35: 12.630 distance: 35 - 36: 6.206 distance: 38 - 39: 12.725 distance: 39 - 40: 17.111 distance: 39 - 42: 18.472 distance: 40 - 45: 5.139 distance: 42 - 43: 42.879 distance: 42 - 44: 24.730 distance: 45 - 46: 35.775 distance: 46 - 47: 55.970 distance: 46 - 49: 40.066 distance: 47 - 48: 49.593 distance: 47 - 56: 52.834 distance: 49 - 50: 27.409 distance: 50 - 51: 3.354 distance: 51 - 52: 21.013 distance: 52 - 53: 40.518 distance: 53 - 54: 32.010 distance: 53 - 55: 22.110 distance: 56 - 57: 30.364 distance: 57 - 60: 5.138