Starting phenix.real_space_refine (version: dev) on Tue Feb 21 23:16:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2023/7snh_25226_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2023/7snh_25226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2023/7snh_25226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2023/7snh_25226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2023/7snh_25226_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2023/7snh_25226_updated.pdb" } resolution = 2.2 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= 0.009 sd= 0.234 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 Process input model Symmetric amino acids flipped Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 252": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 416": "OE1" <-> "OE2" Residue "C GLU 438": "OE1" <-> "OE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D GLU 494": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15828 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "B" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "C" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "D" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3861 Classifications: {'peptide': 476} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 452} Chain breaks: 1 Chain: "A" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'NAP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.65, per 1000 atoms: 0.55 Number of scatterers: 15828 At special positions: 0 Unit cell: (90.47, 115.37, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 24 15.00 O 2972 8.00 N 2724 7.00 C 10028 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: 6.56 Conformation dependent library (CDL) restraints added in 2.3 seconds 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 37.6% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 42 through 57 removed outlier: 5.022A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 77 through 88 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.776A pdb=" N LEU A 96 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 144 through 157 removed outlier: 5.098A pdb=" N GLU A 148 " --> pdb=" O THR A 145 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 151 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 157 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 216 removed outlier: 4.551A pdb=" N MET A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.600A pdb=" N CYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 455 through 475 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'B' and resid 42 through 57 removed outlier: 5.023A pdb=" N TYR B 49 " --> pdb=" O LYS B 45 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 77 through 88 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 92 through 101 removed outlier: 4.798A pdb=" N LEU B 96 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 127 Processing helix chain 'B' and resid 144 through 157 removed outlier: 5.136A pdb=" N GLU B 148 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 157 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.659A pdb=" N LEU B 190 " --> pdb=" O HIS B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 206 through 216 removed outlier: 4.551A pdb=" N MET B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 213 " --> pdb=" O GLN B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.599A pdb=" N CYS B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 436 through 446 Processing helix chain 'B' and resid 455 through 475 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'C' and resid 42 through 57 removed outlier: 5.025A pdb=" N TYR C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Proline residue: C 50 - end of helix Processing helix chain 'C' and resid 77 through 88 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 92 through 101 removed outlier: 4.772A pdb=" N LEU C 96 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 144 through 157 removed outlier: 5.094A pdb=" N GLU C 148 " --> pdb=" O THR C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 removed outlier: 3.651A pdb=" N LEU C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 201 through 204 Processing helix chain 'C' and resid 206 through 216 removed outlier: 4.536A pdb=" N MET C 212 " --> pdb=" O VAL C 208 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL C 213 " --> pdb=" O GLN C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.600A pdb=" N CYS C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 302 No H-bonds generated for 'chain 'C' and resid 300 through 302' Processing helix chain 'C' and resid 316 through 319 Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 455 through 475 Proline residue: C 467 - end of helix Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'D' and resid 42 through 57 removed outlier: 5.019A pdb=" N TYR D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Proline residue: D 50 - end of helix Processing helix chain 'D' and resid 77 through 88 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 92 through 101 removed outlier: 4.780A pdb=" N LEU D 96 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 Processing helix chain 'D' and resid 144 through 157 removed outlier: 5.099A pdb=" N GLU D 148 " --> pdb=" O THR D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 201 through 204 Processing helix chain 'D' and resid 206 through 216 removed outlier: 4.541A pdb=" N MET D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL D 213 " --> pdb=" O GLN D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 251 Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 263 through 272 Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.602A pdb=" N CYS D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 302 No H-bonds generated for 'chain 'D' and resid 300 through 302' Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 436 through 446 Processing helix chain 'D' and resid 455 through 475 Proline residue: D 467 - end of helix Processing helix chain 'D' and resid 490 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 196 through 198 removed outlier: 7.984A pdb=" N TYR A 197 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE A 167 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 136 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE A 168 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 138 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 480 through 483 removed outlier: 6.905A pdb=" N GLN A 372 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL A 233 " --> pdb=" O ARG A 370 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG A 370 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU A 235 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 368 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE A 237 " --> pdb=" O LYS A 366 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS A 366 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL A 369 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG A 393 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU A 371 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL A 391 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE A 373 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU A 389 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 196 through 198 removed outlier: 7.984A pdb=" N TYR B 197 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 167 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N ILE B 168 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 138 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 480 through 483 removed outlier: 6.905A pdb=" N GLN B 372 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 233 " --> pdb=" O ARG B 370 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG B 370 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 235 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU B 368 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE B 237 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS B 366 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG B 393 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 371 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL B 391 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE B 373 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU B 389 " --> pdb=" O PHE B 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 196 through 198 removed outlier: 7.982A pdb=" N TYR C 197 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 167 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG C 136 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 168 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N PHE C 138 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 480 through 483 removed outlier: 6.905A pdb=" N GLN C 372 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL C 233 " --> pdb=" O ARG C 370 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG C 370 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 235 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU C 368 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 237 " --> pdb=" O LYS C 366 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS C 366 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 369 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG C 393 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU C 371 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL C 391 " --> pdb=" O LEU C 371 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE C 373 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU C 389 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 196 through 198 removed outlier: 7.982A pdb=" N TYR D 197 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE D 167 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG D 136 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE D 168 " --> pdb=" O ARG D 136 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE D 138 " --> pdb=" O ILE D 168 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 480 through 483 removed outlier: 6.904A pdb=" N GLN D 372 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL D 233 " --> pdb=" O ARG D 370 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ARG D 370 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU D 235 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU D 368 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE D 237 " --> pdb=" O LYS D 366 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LYS D 366 " --> pdb=" O PHE D 237 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG D 393 " --> pdb=" O VAL D 369 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU D 371 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL D 391 " --> pdb=" O LEU D 371 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE D 373 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU D 389 " --> pdb=" O PHE D 373 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1494 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: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3566 1.33 - 1.45: 3622 1.45 - 1.57: 8868 1.57 - 1.69: 40 1.69 - 1.81: 132 Bond restraints: 16228 Sorted by residual: bond pdb=" O2B NAP B 602 " pdb=" P2B NAP B 602 " ideal model delta sigma weight residual 1.736 1.597 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" O2B NAP A 602 " pdb=" P2B NAP A 602 " ideal model delta sigma weight residual 1.736 1.597 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O2B NAP D 602 " pdb=" P2B NAP D 602 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O2B NAP C 602 " pdb=" P2B NAP C 602 " ideal model delta sigma weight residual 1.736 1.598 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O2B NAP B 601 " pdb=" P2B NAP B 601 " ideal model delta sigma weight residual 1.736 1.603 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 16223 not shown) Histogram of bond angle deviations from ideal: 99.86 - 107.19: 661 107.19 - 114.53: 9249 114.53 - 121.86: 8738 121.86 - 129.19: 3260 129.19 - 136.53: 120 Bond angle restraints: 22028 Sorted by residual: angle pdb=" N PHE C 138 " pdb=" CA PHE C 138 " pdb=" C PHE C 138 " ideal model delta sigma weight residual 108.20 113.47 -5.27 1.71e+00 3.42e-01 9.51e+00 angle pdb=" C2A NAP B 601 " pdb=" N3A NAP B 601 " pdb=" C4A NAP B 601 " ideal model delta sigma weight residual 111.82 121.04 -9.22 3.00e+00 1.11e-01 9.44e+00 angle pdb=" N PHE D 138 " pdb=" CA PHE D 138 " pdb=" C PHE D 138 " ideal model delta sigma weight residual 108.20 113.43 -5.23 1.71e+00 3.42e-01 9.35e+00 angle pdb=" C2A NAP D 601 " pdb=" N3A NAP D 601 " pdb=" C4A NAP D 601 " ideal model delta sigma weight residual 111.82 120.99 -9.17 3.00e+00 1.11e-01 9.35e+00 angle pdb=" C2A NAP A 601 " pdb=" N3A NAP A 601 " pdb=" C4A NAP A 601 " ideal model delta sigma weight residual 111.82 120.99 -9.17 3.00e+00 1.11e-01 9.33e+00 ... (remaining 22023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8171 17.92 - 35.84: 967 35.84 - 53.76: 367 53.76 - 71.69: 97 71.69 - 89.61: 58 Dihedral angle restraints: 9660 sinusoidal: 4116 harmonic: 5544 Sorted by residual: dihedral pdb=" CA ARG A 348 " pdb=" C ARG A 348 " pdb=" N TRP A 349 " pdb=" CA TRP A 349 " ideal model delta harmonic sigma weight residual -180.00 -162.25 -17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG D 348 " pdb=" C ARG D 348 " pdb=" N TRP D 349 " pdb=" CA TRP D 349 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG C 348 " pdb=" C ARG C 348 " pdb=" N TRP C 349 " pdb=" CA TRP C 349 " ideal model delta harmonic sigma weight residual -180.00 -162.30 -17.70 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 9657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1686 0.044 - 0.088: 466 0.088 - 0.133: 168 0.133 - 0.177: 16 0.177 - 0.221: 8 Chirality restraints: 2344 Sorted by residual: chirality pdb=" C1B NAP D 601 " pdb=" C2B NAP D 601 " pdb=" N9A NAP D 601 " pdb=" O4B NAP D 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1B NAP B 601 " pdb=" C2B NAP B 601 " pdb=" N9A NAP B 601 " pdb=" O4B NAP B 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1B NAP C 601 " pdb=" C2B NAP C 601 " pdb=" N9A NAP C 601 " pdb=" O4B NAP C 601 " both_signs ideal model delta sigma weight residual False 2.31 2.53 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2341 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 143 " 0.048 5.00e-02 4.00e+02 7.35e-02 8.64e+00 pdb=" N PRO D 144 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 144 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 143 " 0.048 5.00e-02 4.00e+02 7.30e-02 8.54e+00 pdb=" N PRO A 144 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 143 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO B 144 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 144 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 144 " -0.040 5.00e-02 4.00e+02 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1696 2.75 - 3.29: 15498 3.29 - 3.83: 28991 3.83 - 4.36: 35515 4.36 - 4.90: 57244 Nonbonded interactions: 138944 Sorted by model distance: nonbonded pdb=" OH TYR B 139 " pdb=" OE2 GLU B 170 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR B 202 " pdb=" NE2 GLN B 395 " model vdw 2.231 2.520 nonbonded pdb=" OH TYR D 202 " pdb=" NE2 GLN D 395 " model vdw 2.232 2.520 nonbonded pdb=" OH TYR C 202 " pdb=" NE2 GLN C 395 " model vdw 2.232 2.520 nonbonded pdb=" OH TYR A 202 " pdb=" NE2 GLN A 395 " model vdw 2.233 2.520 ... (remaining 138939 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' } 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 80 5.16 5 C 10028 2.51 5 N 2724 2.21 5 O 2972 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: 0.220 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: 2.610 Check model and map are aligned: 0.200 Process input model: 39.790 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 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 : 0.006 0.139 16228 Z= 0.423 Angle : 0.747 9.219 22028 Z= 0.347 Chirality : 0.047 0.221 2344 Planarity : 0.006 0.073 2816 Dihedral : 19.524 89.608 6092 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.19), residues: 1888 helix: 0.81 (0.20), residues: 696 sheet: -0.37 (0.23), residues: 444 loop : 0.49 (0.23), residues: 748 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 204 time to evaluate : 1.856 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 221 average time/residue: 1.3938 time to fit residues: 338.7863 Evaluate side-chains 216 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.3428 time to fit residues: 4.4662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 170 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 185 ASN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16228 Z= 0.269 Angle : 0.590 6.345 22028 Z= 0.314 Chirality : 0.045 0.136 2344 Planarity : 0.007 0.087 2816 Dihedral : 11.683 80.485 2268 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.30 (0.19), residues: 1888 helix: 0.54 (0.20), residues: 700 sheet: -0.47 (0.26), residues: 392 loop : 0.51 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 2.103 Fit side-chains outliers start: 45 outliers final: 25 residues processed: 228 average time/residue: 1.4258 time to fit residues: 357.2547 Evaluate side-chains 221 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 196 time to evaluate : 1.897 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.2461 time to fit residues: 5.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 chunk 142 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 169 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 186 HIS ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 16228 Z= 0.325 Angle : 0.623 6.466 22028 Z= 0.331 Chirality : 0.046 0.130 2344 Planarity : 0.007 0.103 2816 Dihedral : 11.658 79.259 2268 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.19 (0.19), residues: 1888 helix: 0.38 (0.20), residues: 700 sheet: -0.51 (0.26), residues: 392 loop : 0.51 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 205 time to evaluate : 1.949 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 31 residues processed: 247 average time/residue: 1.3835 time to fit residues: 375.6414 Evaluate side-chains 223 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 1.907 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 10 average time/residue: 0.4998 time to fit residues: 8.7921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 16228 Z= 0.182 Angle : 0.531 6.307 22028 Z= 0.281 Chirality : 0.043 0.134 2344 Planarity : 0.005 0.040 2816 Dihedral : 11.140 74.782 2268 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.36 (0.19), residues: 1888 helix: 0.52 (0.20), residues: 704 sheet: -0.51 (0.26), residues: 392 loop : 0.65 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 198 time to evaluate : 1.838 Fit side-chains revert: symmetry clash outliers start: 61 outliers final: 26 residues processed: 241 average time/residue: 1.3457 time to fit residues: 357.3133 Evaluate side-chains 216 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.743 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 17 residues processed: 9 average time/residue: 0.3762 time to fit residues: 6.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 0.5980 chunk 163 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 overall best weight: 5.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 16228 Z= 0.308 Angle : 0.608 6.362 22028 Z= 0.323 Chirality : 0.046 0.131 2344 Planarity : 0.007 0.105 2816 Dihedral : 11.228 72.145 2268 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.29 (0.19), residues: 1888 helix: 0.44 (0.20), residues: 708 sheet: -0.50 (0.26), residues: 392 loop : 0.61 (0.22), residues: 788 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 203 time to evaluate : 1.988 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 31 residues processed: 250 average time/residue: 1.4189 time to fit residues: 390.0270 Evaluate side-chains 221 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 190 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 22 residues processed: 9 average time/residue: 0.4257 time to fit residues: 7.7188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 150 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.205 Angle : 0.538 5.899 22028 Z= 0.287 Chirality : 0.043 0.133 2344 Planarity : 0.005 0.053 2816 Dihedral : 10.675 66.336 2268 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.39 (0.19), residues: 1888 helix: 0.53 (0.20), residues: 708 sheet: -0.45 (0.26), residues: 388 loop : 0.65 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 198 time to evaluate : 1.875 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 29 residues processed: 237 average time/residue: 1.3561 time to fit residues: 353.8798 Evaluate side-chains 224 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.991 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.3485 time to fit residues: 4.5219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 16228 Z= 0.268 Angle : 0.579 6.312 22028 Z= 0.307 Chirality : 0.045 0.133 2344 Planarity : 0.006 0.086 2816 Dihedral : 10.500 59.575 2268 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.33 (0.19), residues: 1888 helix: 0.45 (0.20), residues: 708 sheet: -0.52 (0.27), residues: 392 loop : 0.68 (0.22), residues: 788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 201 time to evaluate : 1.871 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 34 residues processed: 236 average time/residue: 1.3902 time to fit residues: 360.6956 Evaluate side-chains 230 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 196 time to evaluate : 1.902 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 26 residues processed: 8 average time/residue: 0.2493 time to fit residues: 5.3987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 HIS ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 16228 Z= 0.157 Angle : 0.502 5.811 22028 Z= 0.267 Chirality : 0.042 0.135 2344 Planarity : 0.004 0.032 2816 Dihedral : 9.616 59.914 2268 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.47 (0.19), residues: 1888 helix: 0.68 (0.20), residues: 700 sheet: -0.49 (0.26), residues: 388 loop : 0.67 (0.22), residues: 800 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.978 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 235 average time/residue: 1.4201 time to fit residues: 368.1050 Evaluate side-chains 226 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 2.037 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 4 average time/residue: 0.4033 time to fit residues: 4.9657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 8.9990 chunk 158 optimal weight: 7.9990 chunk 168 optimal weight: 0.0270 chunk 101 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 132 optimal weight: 0.0980 chunk 51 optimal weight: 10.0000 chunk 152 optimal weight: 0.0770 chunk 159 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 16228 Z= 0.151 Angle : 0.493 5.653 22028 Z= 0.261 Chirality : 0.042 0.138 2344 Planarity : 0.004 0.036 2816 Dihedral : 8.856 59.867 2268 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1888 helix: 0.73 (0.20), residues: 700 sheet: -0.48 (0.27), residues: 388 loop : 0.73 (0.22), residues: 800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 209 time to evaluate : 1.863 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 241 average time/residue: 1.3887 time to fit residues: 368.3867 Evaluate side-chains 231 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 1.827 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 25 residues processed: 7 average time/residue: 0.3461 time to fit residues: 5.8707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 0.0970 chunk 187 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN C 133 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 16228 Z= 0.195 Angle : 0.526 6.021 22028 Z= 0.279 Chirality : 0.043 0.138 2344 Planarity : 0.005 0.053 2816 Dihedral : 8.986 58.561 2268 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.50 (0.20), residues: 1888 helix: 0.67 (0.20), residues: 700 sheet: -0.51 (0.27), residues: 392 loop : 0.75 (0.22), residues: 796 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3776 Ramachandran restraints generated. 1888 Oldfield, 0 Emsley, 1888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 202 time to evaluate : 2.015 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 26 residues processed: 230 average time/residue: 1.4181 time to fit residues: 358.5248 Evaluate side-chains 226 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.945 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 4 average time/residue: 0.3503 time to fit residues: 4.5731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 8 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 153 ASN B 186 HIS ** B 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS ** C 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.173782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131178 restraints weight = 13349.612| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.93 r_work: 0.3084 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 16228 Z= 0.252 Angle : 0.572 6.565 22028 Z= 0.303 Chirality : 0.045 0.134 2344 Planarity : 0.006 0.081 2816 Dihedral : 9.307 56.293 2268 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.43 (0.19), residues: 1888 helix: 0.56 (0.20), residues: 700 sheet: -0.51 (0.27), residues: 392 loop : 0.74 (0.22), residues: 796 =============================================================================== Job complete usr+sys time: 6059.26 seconds wall clock time: 107 minutes 49.51 seconds (6469.51 seconds total)