Starting phenix.real_space_refine on Sat Mar 16 16:57:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/03_2024/8a2y_15108_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/03_2024/8a2y_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_15108/03_2024/8a2y_15108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/03_2024/8a2y_15108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/03_2024/8a2y_15108_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a2y_15108/03_2024/8a2y_15108_updated.pdb" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.85, per 1000 atoms: 0.45 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: 5.63 Conformation dependent library (CDL) restraints added in 2.5 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: 3.11 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: 4.45 Time building geometry restraints manager: 6.01 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 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: 2.830 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: 0.010 Extract box with map and model: 11.990 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.960 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 3.54 % Favored : 95.82 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 79 HIS 0.003 0.001 HIS D 371 PHE 0.010 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.004 0.001 ARG D 177 *********************** 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 : 1.703 Fit side-chains REVERT: C 167 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7753 (mm-30) REVERT: B 123 MET cc_start: 0.8908 (mmt) cc_final: 0.8560 (mmt) REVERT: B 305 MET cc_start: 0.8530 (mmm) cc_final: 0.8329 (mmm) outliers start: 10 outliers final: 2 residues processed: 263 average time/residue: 1.5683 time to fit residues: 446.7915 Evaluate side-chains 201 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 199 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 66 THR 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: C 246 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14860 Z= 0.183 Angle : 0.584 7.141 20170 Z= 0.282 Chirality : 0.046 0.146 2240 Planarity : 0.004 0.031 2570 Dihedral : 11.225 169.918 2062 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.16 % Allowed : 8.36 % Favored : 90.48 % 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: 0.20 (0.20), residues: 1800 helix: -0.64 (0.17), residues: 790 sheet: -0.27 (0.25), residues: 335 loop : 1.81 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.012 0.001 PHE D 255 TYR 0.012 0.001 TYR C 143 ARG 0.002 0.000 ARG B 372 *********************** 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 224 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 206 time to evaluate : 1.923 Fit side-chains REVERT: C 167 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7734 (mm-30) REVERT: B 100 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: B 123 MET cc_start: 0.8916 (mmt) cc_final: 0.8654 (mmt) outliers start: 18 outliers final: 7 residues processed: 213 average time/residue: 1.4958 time to fit residues: 346.8804 Evaluate side-chains 199 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 191 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL 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: 2.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 176 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 A 314 GLN B 41 GLN B 353 GLN D 121 GLN D 225 ASN D 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14860 Z= 0.238 Angle : 0.612 7.411 20170 Z= 0.294 Chirality : 0.047 0.154 2240 Planarity : 0.004 0.033 2570 Dihedral : 11.170 176.772 2060 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.41 % Allowed : 9.20 % Favored : 89.39 % 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: 0.49 (0.20), residues: 1800 helix: -0.35 (0.18), residues: 790 sheet: -0.22 (0.26), residues: 325 loop : 1.90 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 79 HIS 0.006 0.001 HIS D 161 PHE 0.013 0.002 PHE B 262 TYR 0.013 0.001 TYR B 143 ARG 0.007 0.001 ARG D 28 *********************** 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: 22 poor density : 197 time to evaluate : 1.707 Fit side-chains REVERT: C 128 ASN cc_start: 0.8260 (m110) cc_final: 0.8013 (m-40) REVERT: C 167 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7735 (mm-30) REVERT: B 100 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7122 (pt0) outliers start: 22 outliers final: 11 residues processed: 211 average time/residue: 1.4332 time to fit residues: 330.0520 Evaluate side-chains 201 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain E residue 45 VAL 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: 3.9990 chunk 84 optimal weight: 10.0000 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: 6.9990 chunk 85 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 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 40 HIS A 41 GLN B 41 GLN B 353 GLN D 40 HIS 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: 0.8488 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 14860 Z= 0.469 Angle : 0.751 9.214 20170 Z= 0.373 Chirality : 0.055 0.201 2240 Planarity : 0.005 0.054 2570 Dihedral : 12.151 169.918 2060 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.19 % Allowed : 8.75 % Favored : 89.07 % 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: 0.42 (0.20), residues: 1800 helix: -0.31 (0.18), residues: 785 sheet: -0.54 (0.27), residues: 305 loop : 1.82 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP B 79 HIS 0.007 0.002 HIS B 371 PHE 0.023 0.002 PHE B 262 TYR 0.013 0.002 TYR C 169 ARG 0.006 0.001 ARG D 177 *********************** 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 223 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 189 time to evaluate : 2.203 Fit side-chains REVERT: C 118 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (mppt) REVERT: C 128 ASN cc_start: 0.8274 (m110) cc_final: 0.8036 (m-40) REVERT: C 167 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7754 (mm-30) REVERT: B 100 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7172 (pt0) outliers start: 34 outliers final: 18 residues processed: 210 average time/residue: 1.4922 time to fit residues: 342.3831 Evaluate side-chains 204 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 45 VAL 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: 0.9980 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 0.1980 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 162 ASN D 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1959 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= 0.158 Angle : 0.565 6.913 20170 Z= 0.269 Chirality : 0.045 0.155 2240 Planarity : 0.003 0.033 2570 Dihedral : 11.037 174.349 2060 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.22 % Allowed : 10.23 % Favored : 88.55 % 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: 0.72 (0.20), residues: 1800 helix: -0.10 (0.19), residues: 790 sheet: -0.19 (0.26), residues: 325 loop : 1.99 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 79 HIS 0.004 0.001 HIS D 161 PHE 0.010 0.001 PHE B 262 TYR 0.010 0.001 TYR B 143 ARG 0.004 0.000 ARG D 28 *********************** 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: 19 poor density : 195 time to evaluate : 1.742 Fit side-chains REVERT: C 128 ASN cc_start: 0.8231 (m110) cc_final: 0.7979 (m-40) REVERT: C 167 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7708 (mm-30) REVERT: B 100 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7098 (pt0) REVERT: E 314 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7691 (tp40) outliers start: 19 outliers final: 7 residues processed: 205 average time/residue: 1.4980 time to fit residues: 334.0344 Evaluate side-chains 195 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 186 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR 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: 7.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 41 GLN A 314 GLN B 41 GLN D 12 ASN D 162 ASN D 225 ASN E 59 GLN E 353 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1950 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= 0.391 Angle : 0.705 8.495 20170 Z= 0.346 Chirality : 0.052 0.182 2240 Planarity : 0.005 0.048 2570 Dihedral : 11.823 170.913 2060 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.67 % Allowed : 10.03 % Favored : 88.30 % 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: 0.62 (0.20), residues: 1800 helix: -0.14 (0.18), residues: 785 sheet: -0.34 (0.25), residues: 335 loop : 1.96 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP D 340 HIS 0.006 0.002 HIS B 371 PHE 0.020 0.002 PHE B 262 TYR 0.012 0.002 TYR C 169 ARG 0.005 0.001 ARG E 210 *********************** 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 209 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 183 time to evaluate : 1.864 Fit side-chains REVERT: C 128 ASN cc_start: 0.8283 (m110) cc_final: 0.8037 (m-40) REVERT: C 167 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7729 (mm-30) REVERT: B 99 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: B 100 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7135 (pt0) REVERT: E 314 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7787 (tp40) outliers start: 26 outliers final: 15 residues processed: 199 average time/residue: 1.4912 time to fit residues: 323.0113 Evaluate side-chains 197 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 179 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 351 THR 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: 1.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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: 0.8451 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14860 Z= 0.218 Angle : 0.606 7.262 20170 Z= 0.291 Chirality : 0.047 0.156 2240 Planarity : 0.004 0.034 2570 Dihedral : 11.363 178.771 2060 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.54 % Allowed : 10.35 % Favored : 88.10 % 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: 0.72 (0.20), residues: 1800 helix: -0.07 (0.19), residues: 790 sheet: -0.19 (0.26), residues: 325 loop : 1.96 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.013 0.002 PHE B 262 TYR 0.010 0.001 TYR B 143 ARG 0.004 0.000 ARG D 28 *********************** 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 210 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.813 Fit side-chains REVERT: C 128 ASN cc_start: 0.8255 (m110) cc_final: 0.8014 (m-40) REVERT: C 167 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 64 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9061 (pp) REVERT: B 99 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: B 100 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7113 (pt0) REVERT: E 314 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7736 (tp40) outliers start: 24 outliers final: 12 residues processed: 200 average time/residue: 1.4887 time to fit residues: 324.2285 Evaluate side-chains 199 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.3980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 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: 3.9990 chunk 85 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 162 ASN D 225 ASN E 59 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2036 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= 0.146 Angle : 0.559 6.798 20170 Z= 0.263 Chirality : 0.045 0.155 2240 Planarity : 0.003 0.034 2570 Dihedral : 10.591 169.863 2060 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.09 % Allowed : 10.87 % Favored : 88.04 % 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: 0.85 (0.20), residues: 1800 helix: 0.05 (0.19), residues: 790 sheet: -0.11 (0.26), residues: 325 loop : 2.01 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 79 HIS 0.004 0.001 HIS D 161 PHE 0.009 0.001 PHE C 255 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 *********************** 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 209 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 192 time to evaluate : 1.722 Fit side-chains REVERT: C 128 ASN cc_start: 0.8226 (m110) cc_final: 0.7989 (m-40) REVERT: C 167 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7707 (mm-30) REVERT: B 100 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7101 (pt0) outliers start: 17 outliers final: 8 residues processed: 202 average time/residue: 1.4398 time to fit residues: 316.5998 Evaluate side-chains 199 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 151 optimal weight: 0.5980 chunk 161 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN B 41 GLN D 12 ASN D 225 ASN E 59 GLN E 246 GLN E 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14860 Z= 0.281 Angle : 0.641 7.414 20170 Z= 0.310 Chirality : 0.048 0.158 2240 Planarity : 0.004 0.038 2570 Dihedral : 11.186 175.158 2060 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.90 % Allowed : 11.19 % Favored : 87.91 % 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: -0.03 (0.19), residues: 790 sheet: -0.15 (0.26), residues: 325 loop : 2.01 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 79 HIS 0.006 0.002 HIS D 161 PHE 0.015 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG D 28 *********************** 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 197 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 183 time to evaluate : 1.591 Fit side-chains REVERT: C 128 ASN cc_start: 0.8264 (m110) cc_final: 0.8027 (m-40) REVERT: C 167 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7731 (mm-30) REVERT: B 100 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: E 314 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7674 (tp40) outliers start: 14 outliers final: 10 residues processed: 194 average time/residue: 1.4994 time to fit residues: 316.4184 Evaluate side-chains 194 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 182 time to evaluate : 1.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 314 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 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: 0.8440 moved from start: 0.2027 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= 0.191 Angle : 0.590 7.147 20170 Z= 0.281 Chirality : 0.046 0.158 2240 Planarity : 0.003 0.033 2570 Dihedral : 10.823 168.199 2060 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.90 % Allowed : 11.38 % Favored : 87.72 % 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: 0.84 (0.20), residues: 1800 helix: 0.03 (0.19), residues: 790 sheet: -0.11 (0.26), residues: 325 loop : 2.02 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 79 HIS 0.005 0.001 HIS D 161 PHE 0.011 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.000 ARG D 28 ********************** 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 194 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.838 Fit side-chains REVERT: C 128 ASN cc_start: 0.8248 (m110) cc_final: 0.8006 (m-40) REVERT: C 167 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 99 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: B 100 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.7109 (pt0) outliers start: 14 outliers final: 10 residues processed: 190 average time/residue: 1.5227 time to fit residues: 314.8300 Evaluate side-chains 191 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 179 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 99 GLU 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: 0.8980 chunk 131 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN D 12 ASN D 225 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.120914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103179 restraints weight = 13718.990| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 0.96 r_work: 0.3015 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14860 Z= 0.289 Angle : 0.645 7.369 20170 Z= 0.312 Chirality : 0.049 0.158 2240 Planarity : 0.004 0.037 2570 Dihedral : 11.228 173.580 2060 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.96 % Allowed : 11.38 % Favored : 87.65 % 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: 0.77 (0.20), residues: 1800 helix: -0.04 (0.19), residues: 790 sheet: -0.16 (0.26), residues: 325 loop : 2.00 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 79 HIS 0.006 0.002 HIS D 161 PHE 0.015 0.002 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.005 0.001 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6312.98 seconds wall clock time: 111 minutes 56.75 seconds (6716.75 seconds total)