Starting phenix.real_space_refine on Sun Jul 21 19:10:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/07_2024/8oid_16889_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/07_2024/8oid_16889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/07_2024/8oid_16889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/07_2024/8oid_16889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/07_2024/8oid_16889_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/07_2024/8oid_16889_neut.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9210 2.51 5 N 2460 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15206 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2937 Chain: "A" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2937 Chain: "B" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2937 Chain: "D" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2937 Chain: "E" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2937 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Classifications: {'water': 159} Link IDs: {None: 158} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Time building chain proxies: 15.91, per 1000 atoms: 1.05 Number of scatterers: 15206 At special positions: 0 Unit cell: (93.13, 92.435, 193.21, 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 105 16.00 P 10 15.00 Mg 5 11.99 O 3416 8.00 N 2460 7.00 C 9210 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: 6.30 Conformation dependent library (CDL) restraints added in 5.2 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 48.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.105A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.614A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.104A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.104A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.735A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.105A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.614A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.106A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.562A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.356A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.354A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 725 hydrogen bonds defined for protein. 1885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 6.90 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: 4716 1.34 - 1.46: 2340 1.46 - 1.57: 7664 1.57 - 1.69: 15 1.69 - 1.81: 185 Bond restraints: 14920 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.76e+00 ... (remaining 14915 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.96: 606 106.96 - 114.33: 8692 114.33 - 121.70: 7613 121.70 - 129.07: 3239 129.07 - 136.43: 100 Bond angle restraints: 20250 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 115.96 -5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 115.94 -5.44 1.70e+00 3.46e-01 1.02e+01 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 115.93 -5.43 1.70e+00 3.46e-01 1.02e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.91 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 115.91 -5.41 1.70e+00 3.46e-01 1.01e+01 ... (remaining 20245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 8805 32.43 - 64.86: 140 64.86 - 97.28: 20 97.28 - 129.71: 5 129.71 - 162.14: 5 Dihedral angle restraints: 8975 sinusoidal: 3615 harmonic: 5360 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.14 -162.14 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.10 -162.10 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.08 -162.07 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1189 0.029 - 0.058: 693 0.058 - 0.087: 177 0.087 - 0.115: 159 0.115 - 0.144: 27 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 2242 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO C 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 164 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO E 164 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 138 2.45 - 3.06: 10189 3.06 - 3.68: 24368 3.68 - 4.29: 40105 4.29 - 4.90: 62710 Nonbonded interactions: 137510 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O HOH C 557 " model vdw 1.840 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 548 " model vdw 1.857 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 514 " model vdw 1.873 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 526 " model vdw 1.877 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 532 " model vdw 1.880 2.170 ... (remaining 137505 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 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'D' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'E' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 7.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 53.810 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 0.057 14920 Z= 0.273 Angle : 0.608 7.494 20250 Z= 0.303 Chirality : 0.044 0.144 2245 Planarity : 0.004 0.039 2585 Dihedral : 13.008 162.140 5545 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.96 % Allowed : 4.17 % Favored : 94.87 % 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: -0.64 (0.19), residues: 1830 helix: -1.33 (0.16), residues: 790 sheet: 0.07 (0.26), residues: 335 loop : 0.83 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.002 0.001 HIS E 173 PHE 0.006 0.001 PHE B 262 TYR 0.012 0.001 TYR C 143 ARG 0.003 0.001 ARG A 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 280 time to evaluate : 1.687 Fit side-chains REVERT: C 47 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5836 (tpt) REVERT: C 180 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8581 (tp) REVERT: C 269 MET cc_start: 0.8436 (mtp) cc_final: 0.8207 (mtt) REVERT: A 180 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8753 (tp) REVERT: D 47 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.5143 (tpt) REVERT: D 121 GLN cc_start: 0.7959 (tt0) cc_final: 0.7674 (tm130) REVERT: D 325 MET cc_start: 0.8917 (mmp) cc_final: 0.8625 (mmp) REVERT: D 351 THR cc_start: 0.8906 (m) cc_final: 0.8674 (m) REVERT: E 47 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.4766 (tpt) outliers start: 15 outliers final: 0 residues processed: 287 average time/residue: 1.4802 time to fit residues: 461.1953 Evaluate side-chains 206 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 201 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 88 optimal weight: 0.0870 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 128 ASN C 225 GLN C 246 GLN A 128 ASN A 353 GLN B 12 ASN B 41 GLN B 128 ASN B 225 GLN B 353 GLN E 78 ASN E 121 GLN E 246 GLN E 353 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 14920 Z= 0.438 Angle : 0.713 8.634 20250 Z= 0.352 Chirality : 0.051 0.172 2245 Planarity : 0.006 0.051 2585 Dihedral : 12.372 174.071 2098 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.18 % Allowed : 8.33 % Favored : 89.49 % 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: 0.69 (0.20), residues: 1830 helix: 0.01 (0.18), residues: 785 sheet: 0.56 (0.26), residues: 345 loop : 1.31 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP C 340 HIS 0.005 0.002 HIS B 88 PHE 0.016 0.002 PHE D 262 TYR 0.013 0.002 TYR A 143 ARG 0.009 0.001 ARG C 183 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 1.780 Fit side-chains REVERT: C 47 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5913 (tpt) REVERT: C 51 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7213 (p0) REVERT: C 180 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8665 (tp) REVERT: A 180 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8693 (tt) REVERT: A 276 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: A 314 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: B 47 MET cc_start: 0.4268 (mmt) cc_final: 0.3953 (tpt) REVERT: B 153 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7911 (ttp) REVERT: D 47 MET cc_start: 0.5580 (OUTLIER) cc_final: 0.5160 (tpt) REVERT: D 351 THR cc_start: 0.8955 (m) cc_final: 0.8655 (m) REVERT: E 47 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.4755 (tpt) REVERT: E 72 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6751 (mt-10) outliers start: 34 outliers final: 6 residues processed: 215 average time/residue: 1.3841 time to fit residues: 325.7593 Evaluate side-chains 199 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 166 optimal weight: 0.4980 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN E 12 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14920 Z= 0.218 Angle : 0.597 7.511 20250 Z= 0.287 Chirality : 0.045 0.156 2245 Planarity : 0.004 0.039 2585 Dihedral : 12.145 179.913 2098 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.67 % Allowed : 9.74 % Favored : 88.59 % 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: 1.37 (0.20), residues: 1830 helix: 0.61 (0.19), residues: 775 sheet: 0.81 (0.26), residues: 345 loop : 1.66 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 PHE 0.009 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.010 0.001 ARG D 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 193 time to evaluate : 1.730 Fit side-chains REVERT: C 47 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5937 (tpt) REVERT: C 51 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7137 (p0) REVERT: C 180 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 64 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9200 (pp) REVERT: A 180 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8685 (tt) REVERT: A 276 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7392 (mm-30) REVERT: B 47 MET cc_start: 0.4294 (mmt) cc_final: 0.3989 (tpt) REVERT: B 64 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8996 (pp) REVERT: B 72 GLU cc_start: 0.7510 (mp0) cc_final: 0.7297 (mp0) REVERT: B 314 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7540 (tp40) REVERT: D 47 MET cc_start: 0.5555 (OUTLIER) cc_final: 0.5161 (tpt) REVERT: D 314 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: D 351 THR cc_start: 0.8952 (m) cc_final: 0.8642 (m) REVERT: E 47 MET cc_start: 0.5356 (OUTLIER) cc_final: 0.4804 (tpt) outliers start: 26 outliers final: 3 residues processed: 211 average time/residue: 1.4148 time to fit residues: 326.1563 Evaluate side-chains 199 residues out of total 1550 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 65.6779 > 50: distance: 33 - 122: 25.273 distance: 36 - 119: 20.238 distance: 43 - 107: 10.809 distance: 46 - 104: 14.271 distance: 90 - 96: 6.211 distance: 96 - 97: 4.561 distance: 97 - 98: 9.054 distance: 97 - 100: 7.145 distance: 98 - 99: 17.266 distance: 98 - 104: 15.535 distance: 100 - 101: 3.142 distance: 101 - 102: 18.521 distance: 101 - 103: 17.269 distance: 104 - 105: 3.693 distance: 105 - 106: 12.738 distance: 105 - 108: 8.345 distance: 106 - 107: 13.222 distance: 106 - 111: 11.431 distance: 108 - 109: 8.527 distance: 108 - 110: 10.574 distance: 111 - 112: 8.946 distance: 112 - 113: 20.613 distance: 112 - 115: 22.815 distance: 113 - 114: 6.212 distance: 113 - 119: 8.950 distance: 115 - 116: 6.939 distance: 116 - 117: 13.901 distance: 116 - 118: 11.933 distance: 119 - 120: 6.463 distance: 120 - 121: 13.725 distance: 120 - 123: 13.099 distance: 121 - 122: 42.520 distance: 121 - 128: 14.935 distance: 123 - 124: 7.996 distance: 124 - 125: 26.201 distance: 125 - 126: 10.581 distance: 126 - 127: 22.759 distance: 128 - 129: 12.425 distance: 129 - 130: 13.845 distance: 129 - 132: 12.375 distance: 130 - 131: 41.555 distance: 130 - 140: 16.434 distance: 133 - 134: 34.864 distance: 133 - 135: 4.551 distance: 134 - 136: 20.747 distance: 135 - 137: 17.398 distance: 136 - 138: 5.262 distance: 137 - 138: 34.497 distance: 138 - 139: 10.188 distance: 140 - 141: 6.729 distance: 140 - 146: 17.963 distance: 141 - 142: 29.010 distance: 141 - 144: 19.271 distance: 142 - 143: 18.548 distance: 142 - 147: 25.137 distance: 144 - 145: 4.814 distance: 145 - 146: 3.452 distance: 147 - 148: 19.442 distance: 148 - 149: 22.586 distance: 148 - 151: 14.723 distance: 149 - 150: 6.450 distance: 149 - 155: 20.176 distance: 151 - 152: 18.589 distance: 151 - 153: 42.161 distance: 152 - 154: 10.370 distance: 155 - 156: 16.694 distance: 155 - 182: 17.647 distance: 156 - 157: 16.745 distance: 156 - 159: 16.440 distance: 157 - 158: 11.789 distance: 157 - 164: 34.089 distance: 158 - 179: 19.610 distance: 159 - 160: 13.914 distance: 160 - 161: 16.866 distance: 161 - 162: 17.962 distance: 164 - 165: 11.064 distance: 165 - 166: 13.487 distance: 165 - 168: 22.758 distance: 166 - 167: 9.975 distance: 166 - 175: 18.682 distance: 168 - 169: 8.993 distance: 169 - 170: 24.141 distance: 169 - 171: 4.527 distance: 170 - 172: 4.566 distance: 171 - 173: 24.959 distance: 173 - 174: 19.876 distance: 175 - 176: 23.449 distance: 176 - 177: 14.511 distance: 177 - 178: 17.640 distance: 177 - 179: 12.693