Starting phenix.real_space_refine (version: dev) on Tue Dec 13 11:08:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/12_2022/8a2y_15108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/12_2022/8a2y_15108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/12_2022/8a2y_15108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/12_2022/8a2y_15108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/12_2022/8a2y_15108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/12_2022/8a2y_15108_updated.pdb" } resolution = 2.15 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= 0.000 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 207": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ARG 372": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 15078 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: "A" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 347} Chain breaks: 1 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "A" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 92 Classifications: {'water': 92} Link IDs: {None: 91} Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "D" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Time building chain proxies: 9.06, per 1000 atoms: 0.60 Number of scatterers: 15078 At special positions: 0 Unit cell: (94.52, 88.265, 192.515, 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) Ca 5 19.99 S 100 16.00 P 15 15.00 O 3338 8.00 N 2450 7.00 C 9170 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: 6.34 Conformation dependent library (CDL) restraints added in 2.3 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3410 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 44.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... 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 144 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: 3.741A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.594A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS C 257 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 287 through 294 removed outlier: 3.559A pdb=" N ARG C 290 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS C 291 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 305 Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 348 removed outlier: 3.509A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 346 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 4.150A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 367 through 371 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 144 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: 3.741A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.594A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 287 through 294 removed outlier: 3.560A pdb=" N ARG A 290 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS A 291 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 305 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.509A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY A 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 346 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 4.150A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 367 through 371 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 144 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 196 removed outlier: 3.741A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.595A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N CYS B 257 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 287 through 294 removed outlier: 3.559A pdb=" N ARG B 290 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 305 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 348 removed outlier: 3.509A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 346 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 4.150A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 367 through 371 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 196 removed outlier: 3.741A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG D 196 " --> pdb=" O ILE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 216 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.595A pdb=" N ARG D 256 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 4.459A 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 284 Processing helix chain 'D' and resid 287 through 294 removed outlier: 3.559A pdb=" N ARG D 290 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS D 291 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 305 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 335 through 348 removed outlier: 3.509A pdb=" N SER D 338 " --> pdb=" O ARG D 335 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL D 339 " --> pdb=" O LYS D 336 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 342 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 346 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA D 347 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 354 removed outlier: 4.150A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 351 through 354' Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 367 through 371 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 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 113 through 125 Processing helix chain 'E' and resid 137 through 144 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 196 removed outlier: 3.741A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG E 196 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 223 through 232 Processing helix chain 'E' and resid 252 through 261 removed outlier: 3.595A pdb=" N ARG E 256 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS E 257 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 264 through 267 Processing helix chain 'E' and resid 274 through 284 Processing helix chain 'E' and resid 287 through 294 removed outlier: 3.560A pdb=" N ARG E 290 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS E 291 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 305 Processing helix chain 'E' and resid 309 through 320 Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.509A pdb=" N SER E 338 " --> pdb=" O ARG E 335 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL E 339 " --> pdb=" O LYS E 336 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY E 342 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 346 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA E 347 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 4.150A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'E' and resid 359 through 363 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id= A, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.636A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.288A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.636A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.287A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.636A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.288A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 132 through 136 removed outlier: 6.635A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'D' and resid 297 through 300 removed outlier: 6.288A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 238 through 241 Processing sheet with id= Q, first strand: chain 'E' and resid 132 through 136 removed outlier: 6.636A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'E' and resid 297 through 300 removed outlier: 6.288A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 238 through 241 520 hydrogen bonds defined for protein. 1245 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: 4.62 Time building geometry restraints manager: 6.76 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: 4705 1.34 - 1.46: 2571 1.46 - 1.57: 7394 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14860 Sorted by residual: bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.499 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O4 PO4 D 403 " pdb=" P PO4 D 403 " ideal model delta sigma weight residual 1.568 1.499 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O4 PO4 B 403 " pdb=" P PO4 B 403 " ideal model delta sigma weight residual 1.568 1.499 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 14855 not shown) Histogram of bond angle deviations from ideal: 100.13 - 107.35: 693 107.35 - 114.58: 8667 114.58 - 121.81: 7665 121.81 - 129.04: 3050 129.04 - 136.27: 95 Bond angle restraints: 20170 Sorted by residual: angle pdb=" NE ARG A 372 " pdb=" CZ ARG A 372 " pdb=" NH2 ARG A 372 " ideal model delta sigma weight residual 119.20 121.54 -2.34 9.00e-01 1.23e+00 6.74e+00 angle pdb=" NE ARG B 372 " pdb=" CZ ARG B 372 " pdb=" NH2 ARG B 372 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.71e+00 angle pdb=" NE ARG E 372 " pdb=" CZ ARG E 372 " pdb=" NH2 ARG E 372 " ideal model delta sigma weight residual 119.20 121.53 -2.33 9.00e-01 1.23e+00 6.71e+00 angle pdb=" NE ARG C 372 " pdb=" CZ ARG C 372 " pdb=" NH2 ARG C 372 " ideal model delta sigma weight residual 119.20 121.52 -2.32 9.00e-01 1.23e+00 6.67e+00 angle pdb=" NE ARG B 37 " pdb=" CZ ARG B 37 " pdb=" NH2 ARG B 37 " ideal model delta sigma weight residual 119.20 121.49 -2.29 9.00e-01 1.23e+00 6.49e+00 ... (remaining 20165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 8820 34.89 - 69.77: 80 69.77 - 104.66: 20 104.66 - 139.54: 5 139.54 - 174.42: 5 Dihedral angle restraints: 8930 sinusoidal: 3615 harmonic: 5315 Sorted by residual: 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 300.00 125.58 174.42 1 2.00e+01 2.50e-03 4.79e+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 300.00 125.59 174.41 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual 300.00 125.60 174.40 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 8927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1096 0.029 - 0.058: 723 0.058 - 0.088: 262 0.088 - 0.117: 129 0.117 - 0.146: 30 Chirality restraints: 2240 Sorted by residual: 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 -2.66 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.26e-01 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 -2.66 0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2237 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 340 " 0.015 2.00e-02 2.50e+03 7.48e-03 1.40e+00 pdb=" CG TRP D 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP D 340 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 340 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 340 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 340 " 0.015 2.00e-02 2.50e+03 7.44e-03 1.38e+00 pdb=" CG TRP C 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP C 340 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 340 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 340 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 340 " 0.015 2.00e-02 2.50e+03 7.41e-03 1.37e+00 pdb=" CG TRP E 340 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP E 340 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP E 340 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 340 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 340 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 340 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 340 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 340 " 0.003 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 800 2.72 - 3.27: 15527 3.27 - 3.81: 27905 3.81 - 4.36: 36586 4.36 - 4.90: 57283 Nonbonded interactions: 138101 Sorted by model distance: nonbonded pdb="CA CA E 402 " pdb=" O4 PO4 E 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA A 402 " pdb=" O4 PO4 A 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA B 402 " pdb=" O4 PO4 B 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA C 402 " pdb=" O4 PO4 C 403 " model vdw 2.177 2.510 nonbonded pdb="CA CA D 402 " pdb=" O4 PO4 D 403 " model vdw 2.178 2.510 ... (remaining 138096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 100 5.16 5 C 9170 2.51 5 N 2450 2.21 5 O 3338 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 4.580 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: 12.760 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.130 Process input model: 43.140 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 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 : 0.005 0.069 14860 Z= 0.335 Angle : 0.605 7.247 20170 Z= 0.302 Chirality : 0.046 0.146 2240 Planarity : 0.004 0.026 2570 Dihedral : 13.416 174.425 5520 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.64 % 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: -1.01 (0.19), residues: 1800 helix: -1.84 (0.15), residues: 775 sheet: -0.50 (0.25), residues: 335 loop : 1.14 (0.25), residues: 690 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.805 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 263 average time/residue: 1.5354 time to fit residues: 437.9845 Evaluate side-chains 200 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.783 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.4208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 137 GLN B 41 GLN B 59 GLN B 161 HIS B 353 GLN D 12 ASN D 59 GLN D 92 ASN D 225 ASN D 246 GLN E 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 14860 Z= 0.184 Angle : 0.584 7.127 20170 Z= 0.281 Chirality : 0.046 0.147 2240 Planarity : 0.004 0.031 2570 Dihedral : 11.150 169.543 2060 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 1.16 % 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: 0.16 (0.20), residues: 1800 helix: -0.69 (0.17), residues: 790 sheet: -0.27 (0.25), residues: 335 loop : 1.80 (0.25), residues: 675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.944 Fit side-chains outliers start: 18 outliers final: 7 residues processed: 212 average time/residue: 1.4099 time to fit residues: 327.2719 Evaluate side-chains 197 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 190 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.1300 time to fit residues: 3.2000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 0.0040 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 overall best weight: 1.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 HIS C 246 GLN A 41 GLN A 161 HIS B 41 GLN B 353 GLN D 121 GLN D 225 ASN D 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14860 Z= 0.200 Angle : 0.589 7.301 20170 Z= 0.281 Chirality : 0.046 0.153 2240 Planarity : 0.004 0.033 2570 Dihedral : 10.699 168.304 2060 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 1.54 % 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: 0.54 (0.20), residues: 1800 helix: -0.30 (0.18), residues: 790 sheet: -0.20 (0.26), residues: 325 loop : 1.93 (0.25), residues: 685 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 1.913 Fit side-chains outliers start: 24 outliers final: 9 residues processed: 209 average time/residue: 1.3686 time to fit residues: 313.4542 Evaluate side-chains 192 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 1.781 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.1357 time to fit residues: 3.3410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS A 41 GLN A 314 GLN B 41 GLN D 40 HIS D 121 GLN D 162 ASN D 225 ASN E 161 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 14860 Z= 0.468 Angle : 0.750 9.013 20170 Z= 0.372 Chirality : 0.055 0.196 2240 Planarity : 0.005 0.053 2570 Dihedral : 12.097 170.127 2060 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 2.12 % 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: 0.45 (0.20), residues: 1800 helix: -0.29 (0.18), residues: 785 sheet: -0.53 (0.27), residues: 305 loop : 1.84 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 1.856 Fit side-chains outliers start: 33 outliers final: 18 residues processed: 207 average time/residue: 1.4349 time to fit residues: 325.9002 Evaluate side-chains 198 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 5 average time/residue: 0.4727 time to fit residues: 5.5202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN A 41 GLN B 41 GLN D 12 ASN D 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14860 Z= 0.206 Angle : 0.595 7.202 20170 Z= 0.286 Chirality : 0.046 0.157 2240 Planarity : 0.004 0.035 2570 Dihedral : 11.348 178.921 2060 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 1.67 % 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: 0.67 (0.20), residues: 1800 helix: -0.13 (0.18), residues: 790 sheet: -0.22 (0.26), residues: 325 loop : 1.96 (0.25), residues: 685 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.800 Fit side-chains outliers start: 26 outliers final: 11 residues processed: 203 average time/residue: 1.4165 time to fit residues: 314.2892 Evaluate side-chains 193 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 182 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.1332 time to fit residues: 3.4870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 225 ASN E 59 GLN E 246 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 14860 Z= 0.389 Angle : 0.702 8.328 20170 Z= 0.345 Chirality : 0.052 0.184 2240 Planarity : 0.005 0.047 2570 Dihedral : 11.895 170.463 2060 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.20), residues: 1800 helix: -0.16 (0.18), residues: 785 sheet: -0.36 (0.25), residues: 335 loop : 1.95 (0.25), residues: 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.935 Fit side-chains outliers start: 30 outliers final: 18 residues processed: 200 average time/residue: 1.4243 time to fit residues: 312.0107 Evaluate side-chains 196 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.4138 time to fit residues: 5.6110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 97 optimal weight: 0.0670 chunk 173 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 12 ASN D 162 ASN D 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 14860 Z= 0.144 Angle : 0.557 6.713 20170 Z= 0.263 Chirality : 0.045 0.156 2240 Planarity : 0.003 0.033 2570 Dihedral : 10.828 173.401 2060 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 1.29 % 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: 0.79 (0.20), residues: 1800 helix: -0.01 (0.19), residues: 790 sheet: -0.15 (0.26), residues: 325 loop : 2.00 (0.25), residues: 685 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 2.002 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 200 average time/residue: 1.4132 time to fit residues: 309.4654 Evaluate side-chains 188 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 182 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 2.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.0470 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 225 ASN D 246 GLN E 59 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 14860 Z= 0.156 Angle : 0.563 6.953 20170 Z= 0.265 Chirality : 0.045 0.154 2240 Planarity : 0.003 0.033 2570 Dihedral : 10.538 173.252 2060 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.96 % 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: 0.90 (0.20), residues: 1800 helix: 0.06 (0.19), residues: 790 sheet: -0.06 (0.26), residues: 325 loop : 2.04 (0.25), residues: 685 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 1.793 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 196 average time/residue: 1.4189 time to fit residues: 305.0492 Evaluate side-chains 189 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 180 time to evaluate : 1.853 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 2.3772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 8.9990 chunk 97 optimal weight: 0.0370 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 12 ASN D 225 ASN E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 14860 Z= 0.249 Angle : 0.621 7.367 20170 Z= 0.299 Chirality : 0.048 0.160 2240 Planarity : 0.004 0.034 2570 Dihedral : 10.941 170.930 2060 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer Outliers : 0.77 % 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: 0.83 (0.20), residues: 1800 helix: -0.00 (0.19), residues: 790 sheet: -0.12 (0.26), residues: 325 loop : 2.03 (0.25), residues: 685 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.812 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 189 average time/residue: 1.4574 time to fit residues: 300.9482 Evaluate side-chains 189 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 0.1268 time to fit residues: 2.8436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.4980 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN A 41 GLN B 41 GLN D 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 14860 Z= 0.130 Angle : 0.548 6.611 20170 Z= 0.257 Chirality : 0.044 0.154 2240 Planarity : 0.003 0.034 2570 Dihedral : 9.941 174.293 2060 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 0.71 % 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: 0.96 (0.20), residues: 1800 helix: 0.13 (0.19), residues: 790 sheet: -0.01 (0.27), residues: 325 loop : 2.04 (0.25), residues: 685 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 1.887 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 196 average time/residue: 1.4919 time to fit residues: 319.5120 Evaluate side-chains 187 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 2.7019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 41 GLN D 12 ASN D 225 ASN E 59 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103158 restraints weight = 13652.566| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 0.96 r_work: 0.3011 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 14860 Z= 0.274 Angle : 0.636 7.437 20170 Z= 0.306 Chirality : 0.048 0.161 2240 Planarity : 0.004 0.037 2570 Dihedral : 10.785 175.013 2060 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.77 % 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: 0.86 (0.20), residues: 1800 helix: 0.02 (0.19), residues: 790 sheet: -0.09 (0.26), residues: 325 loop : 2.05 (0.26), residues: 685 =============================================================================== Job complete usr+sys time: 5916.66 seconds wall clock time: 105 minutes 54.16 seconds (6354.16 seconds total)