Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 10 21:36:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/07_2023/8f8q_28933_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/07_2023/8f8q_28933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/07_2023/8f8q_28933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/07_2023/8f8q_28933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/07_2023/8f8q_28933_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f8q_28933/07_2023/8f8q_28933_updated.pdb" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.018 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 12 5.49 5 Mg 6 5.21 5 S 143 5.16 5 C 13862 2.51 5 N 3737 2.21 5 O 4246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 22006 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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 Chain: "B" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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 Chain: "D" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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 Chain: "E" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} 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 Chain: "F" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2893 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 Chain: "G" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2262 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 267} Chain: "H" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2138 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 259} 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: "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: "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: "F" 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} Time building chain proxies: 10.48, per 1000 atoms: 0.48 Number of scatterers: 22006 At special positions: 0 Unit cell: (81, 112.32, 258.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 143 16.00 P 12 15.00 Mg 6 11.99 O 4246 8.00 N 3737 7.00 C 13862 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: 8.57 Conformation dependent library (CDL) restraints added in 3.4 seconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 130 helices and 32 sheets defined 39.3% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.015A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.692A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.941A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 removed outlier: 4.233A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 370 through 373 No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 194 removed outlier: 4.119A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.987A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.981A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 338 through 348 removed outlier: 4.036A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 365 Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.241A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.846A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.027A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 338 through 348 removed outlier: 4.062A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 79 through 91 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 137 through 144 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.049A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 removed outlier: 3.985A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.927A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS D 257 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 264 through 267 Processing helix chain 'D' and resid 274 through 283 Processing helix chain 'D' and resid 287 through 294 removed outlier: 5.208A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 338 through 348 removed outlier: 4.003A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'E' and resid 79 through 91 Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 182 through 194 removed outlier: 4.196A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 removed outlier: 3.815A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 253 through 256 No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 290 through 294 Processing helix chain 'E' and resid 302 through 304 No H-bonds generated for 'chain 'E' and resid 302 through 304' Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 337 No H-bonds generated for 'chain 'E' and resid 335 through 337' Processing helix chain 'E' and resid 339 through 347 Processing helix chain 'E' and resid 359 through 365 Processing helix chain 'E' and resid 369 through 373 removed outlier: 4.262A pdb=" N LYS E 373 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 removed outlier: 3.717A pdb=" N SER F 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG F 62 " --> pdb=" O GLN F 59 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLY F 63 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE F 64 " --> pdb=" O LYS F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 91 Processing helix chain 'F' and resid 113 through 125 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 182 through 194 removed outlier: 4.069A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 216 removed outlier: 3.775A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 253 through 256 No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 274 through 283 Processing helix chain 'F' and resid 287 through 295 removed outlier: 4.317A pdb=" N LYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ASP F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 309 through 320 Processing helix chain 'F' and resid 339 through 347 Processing helix chain 'F' and resid 351 through 354 removed outlier: 3.671A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 351 through 354' Processing helix chain 'F' and resid 359 through 365 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'G' and resid 10 through 22 Processing helix chain 'G' and resid 30 through 39 Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 52 through 61 Processing helix chain 'G' and resid 119 through 135 removed outlier: 4.274A pdb=" N SER G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS G 124 " --> pdb=" O TRP G 120 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 248 removed outlier: 4.136A pdb=" N GLU G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 253 No H-bonds generated for 'chain 'G' and resid 250 through 253' Processing helix chain 'G' and resid 274 through 281 removed outlier: 4.330A pdb=" N GLY G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS G 281 " --> pdb=" O TYR G 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 Processing helix chain 'H' and resid 21 through 26 Processing helix chain 'H' and resid 36 through 41 removed outlier: 3.578A pdb=" N LEU H 40 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 36 through 41' Processing helix chain 'H' and resid 91 through 111 removed outlier: 3.680A pdb=" N GLU H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 230 Processing helix chain 'H' and resid 232 through 243 Processing helix chain 'H' and resid 252 through 255 removed outlier: 4.046A pdb=" N PHE H 255 " --> pdb=" O ASN H 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 252 through 255' Processing helix chain 'H' and resid 258 through 270 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 12 Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 103 through 107 Processing sheet with id= D, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.507A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= F, first strand: chain 'B' and resid 8 through 12 Processing sheet with id= G, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= H, first strand: chain 'B' and resid 103 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.275A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= K, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.550A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.394A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= O, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.644A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= Q, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.390A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= S, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.610A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= U, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.256A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 238 through 241 Processing sheet with id= W, first strand: chain 'F' and resid 8 through 12 Processing sheet with id= X, first strand: chain 'F' and resid 35 through 38 Processing sheet with id= Y, first strand: chain 'F' and resid 103 through 107 Processing sheet with id= Z, first strand: chain 'F' and resid 297 through 300 removed outlier: 6.388A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 238 through 241 Processing sheet with id= AB, first strand: chain 'G' and resid 63 through 65 removed outlier: 3.890A pdb=" N THR G 63 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 86 through 89 removed outlier: 3.597A pdb=" N ILE G 94 " --> pdb=" O ASP G 89 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 139 through 147 removed outlier: 4.445A pdb=" N THR G 180 " --> pdb=" O GLN G 187 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLN G 187 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 48 through 52 removed outlier: 4.032A pdb=" N LYS H 48 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 116 through 123 removed outlier: 4.067A pdb=" N LYS H 145 " --> pdb=" O GLN H 178 " (cutoff:3.500A) 828 hydrogen bonds defined for protein. 2292 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: 7.56 Time building geometry restraints manager: 9.23 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: 7146 1.34 - 1.46: 4159 1.46 - 1.58: 10905 1.58 - 1.69: 18 1.69 - 1.81: 248 Bond restraints: 22476 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.23e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 22471 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.17: 881 107.17 - 114.49: 12980 114.49 - 121.81: 11572 121.81 - 129.12: 4897 129.12 - 136.44: 148 Bond angle restraints: 30478 Sorted by residual: angle pdb=" C ASP H 247 " pdb=" N ALA H 248 " pdb=" CA ALA H 248 " ideal model delta sigma weight residual 121.31 128.47 -7.16 1.49e+00 4.50e-01 2.31e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 121.54 129.48 -7.94 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 129.30 -7.76 1.91e+00 2.74e-01 1.65e+01 angle pdb=" N ALA H 248 " pdb=" CA ALA H 248 " pdb=" C ALA H 248 " ideal model delta sigma weight residual 110.35 115.46 -5.11 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 122.61 128.25 -5.64 1.56e+00 4.11e-01 1.31e+01 ... (remaining 30473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 12707 23.20 - 46.41: 705 46.41 - 69.61: 117 69.61 - 92.82: 14 92.82 - 116.02: 6 Dihedral angle restraints: 13549 sinusoidal: 5506 harmonic: 8043 Sorted by residual: dihedral pdb=" CA PHE E 127 " pdb=" C PHE E 127 " pdb=" N ASN E 128 " pdb=" CA ASN E 128 " ideal model delta harmonic sigma weight residual -180.00 -150.42 -29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.02 116.02 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 -175.12 115.12 1 2.00e+01 2.50e-03 3.42e+01 ... (remaining 13546 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1956 0.034 - 0.068: 902 0.068 - 0.102: 337 0.102 - 0.137: 144 0.137 - 0.171: 28 Chirality restraints: 3367 Sorted by residual: chirality pdb=" CA CYS B 257 " pdb=" N CYS B 257 " pdb=" C CYS B 257 " pdb=" CB CYS B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.30e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA CYS E 257 " pdb=" N CYS E 257 " pdb=" C CYS E 257 " pdb=" CB CYS E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 ... (remaining 3364 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " 0.051 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO E 243 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO E 164 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO A 243 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.030 5.00e-02 4.00e+02 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 228 2.64 - 3.20: 17835 3.20 - 3.77: 34120 3.77 - 4.33: 48939 4.33 - 4.90: 80286 Nonbonded interactions: 181408 Sorted by model distance: nonbonded pdb=" O3B ADP E 401 " pdb="MG MG E 402 " model vdw 2.072 2.170 nonbonded pdb=" O3B ADP A 401 " pdb="MG MG A 402 " model vdw 2.077 2.170 nonbonded pdb=" O3B ADP D 401 " pdb="MG MG D 402 " model vdw 2.196 2.170 nonbonded pdb=" OH TYR G 198 " pdb=" OE1 GLU G 200 " model vdw 2.287 2.440 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.292 2.440 ... (remaining 181403 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 375 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'D' and (resid 6 through 375 or resid 401 through 402)) selection = (chain 'E' and (resid 6 through 375 or resid 401 through 402)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 14.720 Check model and map are aligned: 0.350 Set scattering table: 0.180 Process input model: 55.450 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 0.062 22476 Z= 0.255 Angle : 0.686 9.700 30478 Z= 0.364 Chirality : 0.049 0.171 3367 Planarity : 0.006 0.077 3918 Dihedral : 14.383 116.021 8391 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.96 (0.15), residues: 2744 helix: -1.31 (0.14), residues: 1094 sheet: 0.91 (0.21), residues: 589 loop : -0.58 (0.19), residues: 1061 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 704 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 30 residues processed: 767 average time/residue: 1.4327 time to fit residues: 1235.4706 Evaluate side-chains 665 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 635 time to evaluate : 2.521 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 7 average time/residue: 0.6027 time to fit residues: 8.8499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 216 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 250 optimal weight: 0.2980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 162 ASN A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 263 GLN C 353 GLN C 371 HIS D 12 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 203 ASN G 205 GLN G 240 GLN G 261 GLN H 20 GLN H 222 ASN H 241 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 22476 Z= 0.297 Angle : 0.598 8.965 30478 Z= 0.293 Chirality : 0.046 0.166 3367 Planarity : 0.005 0.119 3918 Dihedral : 7.202 107.779 3100 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.37 (0.16), residues: 2744 helix: -0.41 (0.15), residues: 1135 sheet: 0.86 (0.21), residues: 566 loop : -0.49 (0.19), residues: 1043 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 666 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 67 residues processed: 715 average time/residue: 1.4865 time to fit residues: 1191.3107 Evaluate side-chains 701 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 634 time to evaluate : 2.528 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 33 residues processed: 34 average time/residue: 0.7763 time to fit residues: 36.0516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 139 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 170 optimal weight: 0.7980 chunk 69 optimal weight: 0.2980 chunk 251 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 223 optimal weight: 0.6980 chunk 248 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 138 ASN G 162 GLN G 164 GLN G 205 GLN G 240 GLN G 261 GLN H 241 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22476 Z= 0.223 Angle : 0.568 8.037 30478 Z= 0.276 Chirality : 0.044 0.149 3367 Planarity : 0.004 0.073 3918 Dihedral : 6.999 105.525 3100 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 4.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.03 (0.16), residues: 2744 helix: 0.14 (0.16), residues: 1122 sheet: 0.87 (0.22), residues: 567 loop : -0.43 (0.19), residues: 1055 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 667 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 67 residues processed: 719 average time/residue: 1.4962 time to fit residues: 1206.0933 Evaluate side-chains 707 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 640 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 41 residues processed: 26 average time/residue: 0.6473 time to fit residues: 24.8383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 0.4980 chunk 188 optimal weight: 0.0470 chunk 130 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 chunk 266 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 chunk 238 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 225 ASN C 246 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 12 ASN F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN H 241 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 22476 Z= 0.225 Angle : 0.570 9.480 30478 Z= 0.275 Chirality : 0.044 0.147 3367 Planarity : 0.004 0.057 3918 Dihedral : 6.883 101.895 3100 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 4.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.23 (0.16), residues: 2744 helix: 0.32 (0.16), residues: 1134 sheet: 0.90 (0.22), residues: 569 loop : -0.30 (0.20), residues: 1041 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 655 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 66 residues processed: 718 average time/residue: 1.5138 time to fit residues: 1217.9906 Evaluate side-chains 726 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 660 time to evaluate : 2.790 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 41 residues processed: 25 average time/residue: 0.7842 time to fit residues: 27.5864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 222 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 110 optimal weight: 0.0370 chunk 227 optimal weight: 0.7980 chunk 184 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 225 ASN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN H 241 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 22476 Z= 0.231 Angle : 0.575 9.029 30478 Z= 0.278 Chirality : 0.045 0.146 3367 Planarity : 0.004 0.058 3918 Dihedral : 6.846 101.278 3100 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 5.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.31 (0.16), residues: 2744 helix: 0.45 (0.16), residues: 1128 sheet: 0.92 (0.22), residues: 569 loop : -0.31 (0.20), residues: 1047 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 673 time to evaluate : 2.465 Fit side-chains revert: symmetry clash outliers start: 121 outliers final: 76 residues processed: 731 average time/residue: 1.5591 time to fit residues: 1275.3618 Evaluate side-chains 726 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 650 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 42 residues processed: 35 average time/residue: 1.0304 time to fit residues: 46.3862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 89 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 221 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 225 ASN A 280 ASN B 162 ASN B 371 HIS C 121 GLN C 137 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN H 241 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 22476 Z= 0.328 Angle : 0.617 9.465 30478 Z= 0.301 Chirality : 0.047 0.189 3367 Planarity : 0.005 0.055 3918 Dihedral : 7.050 107.187 3100 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 4.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.32 (0.16), residues: 2744 helix: 0.54 (0.16), residues: 1095 sheet: 0.89 (0.22), residues: 569 loop : -0.38 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 671 time to evaluate : 2.516 Fit side-chains revert: symmetry clash outliers start: 111 outliers final: 73 residues processed: 724 average time/residue: 1.5583 time to fit residues: 1261.1181 Evaluate side-chains 725 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 652 time to evaluate : 2.585 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 42 residues processed: 31 average time/residue: 0.8189 time to fit residues: 34.8026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 257 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 152 optimal weight: 0.2980 chunk 195 optimal weight: 0.7980 chunk 151 optimal weight: 0.4980 chunk 224 optimal weight: 0.8980 chunk 149 optimal weight: 0.4980 chunk 266 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 92 ASN A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 353 GLN D 12 ASN D 92 ASN D 115 ASN D 162 ASN E 78 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 22476 Z= 0.244 Angle : 0.590 8.771 30478 Z= 0.286 Chirality : 0.045 0.222 3367 Planarity : 0.004 0.074 3918 Dihedral : 6.942 105.574 3100 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.40 (0.16), residues: 2744 helix: 0.65 (0.16), residues: 1101 sheet: 0.92 (0.22), residues: 567 loop : -0.37 (0.19), residues: 1076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 660 time to evaluate : 2.631 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 65 residues processed: 712 average time/residue: 1.5716 time to fit residues: 1254.6599 Evaluate side-chains 714 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 649 time to evaluate : 2.604 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 44 residues processed: 21 average time/residue: 0.6700 time to fit residues: 21.2969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 164 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 158 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 169 optimal weight: 0.2980 chunk 181 optimal weight: 0.0030 chunk 131 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 209 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 225 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 22476 Z= 0.205 Angle : 0.592 10.618 30478 Z= 0.284 Chirality : 0.044 0.196 3367 Planarity : 0.004 0.058 3918 Dihedral : 6.791 101.562 3100 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 3.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.44 (0.16), residues: 2744 helix: 0.66 (0.16), residues: 1112 sheet: 0.94 (0.22), residues: 567 loop : -0.33 (0.19), residues: 1065 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 663 time to evaluate : 2.656 Fit side-chains revert: symmetry clash outliers start: 86 outliers final: 59 residues processed: 716 average time/residue: 1.5427 time to fit residues: 1235.9483 Evaluate side-chains 712 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 653 time to evaluate : 2.402 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 46 residues processed: 13 average time/residue: 0.5536 time to fit residues: 12.6881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 241 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 247 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 234 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 280 ASN B 162 ASN C 12 ASN C 121 GLN C 137 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 22476 Z= 0.317 Angle : 0.632 8.284 30478 Z= 0.307 Chirality : 0.047 0.196 3367 Planarity : 0.005 0.063 3918 Dihedral : 6.989 106.486 3100 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 3.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.32 (0.16), residues: 2744 helix: 0.57 (0.16), residues: 1106 sheet: 0.91 (0.22), residues: 567 loop : -0.43 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 671 time to evaluate : 3.376 Fit side-chains revert: symmetry clash outliers start: 84 outliers final: 66 residues processed: 724 average time/residue: 1.5727 time to fit residues: 1277.8800 Evaluate side-chains 725 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 659 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 49 residues processed: 17 average time/residue: 0.7682 time to fit residues: 19.7686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 262 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 124 optimal weight: 0.7980 chunk 182 optimal weight: 0.9980 chunk 274 optimal weight: 0.7980 chunk 253 optimal weight: 0.0670 chunk 218 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 0.0980 chunk 134 optimal weight: 0.0980 chunk 173 optimal weight: 0.6980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 280 ASN B 162 ASN C 121 GLN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 115 ASN D 162 ASN E 297 ASN E 353 GLN F 162 ASN F 246 GLN G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN H 222 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 22476 Z= 0.166 Angle : 0.584 10.842 30478 Z= 0.281 Chirality : 0.044 0.153 3367 Planarity : 0.004 0.062 3918 Dihedral : 6.667 99.104 3100 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: 0.35 (0.16), residues: 2744 helix: 0.44 (0.16), residues: 1170 sheet: 0.96 (0.22), residues: 567 loop : -0.28 (0.20), residues: 1007 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 662 time to evaluate : 2.748 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 51 residues processed: 712 average time/residue: 1.5640 time to fit residues: 1245.0727 Evaluate side-chains 708 residues out of total 2369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 657 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 43 residues processed: 8 average time/residue: 1.0087 time to fit residues: 13.0476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 233 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 201 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 115 ASN A 225 ASN A 280 ASN B 162 ASN C 12 ASN C 121 GLN C 137 GLN C 353 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 ASN E 297 ASN E 353 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN G 58 ASN G 135 HIS G 162 GLN G 164 GLN G 195 GLN G 205 GLN G 240 GLN H 19 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.093930 restraints weight = 30924.600| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.67 r_work: 0.3018 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.068 22476 Z= 0.519 Angle : 0.727 12.803 30478 Z= 0.358 Chirality : 0.053 0.200 3367 Planarity : 0.005 0.088 3918 Dihedral : 7.359 115.456 3100 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.11 (0.16), residues: 2744 helix: 0.39 (0.16), residues: 1095 sheet: 0.85 (0.22), residues: 567 loop : -0.56 (0.19), residues: 1082 =============================================================================== Job complete usr+sys time: 15388.57 seconds wall clock time: 270 minutes 3.51 seconds (16203.51 seconds total)