Starting phenix.real_space_refine on Fri Feb 16 16:30:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2024/7snh_25226_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2024/7snh_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_2024/7snh_25226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2024/7snh_25226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2024/7snh_25226_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7snh_25226/02_2024/7snh_25226_updated.pdb" } resolution = 2.2 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= 0.009 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 8.23, per 1000 atoms: 0.52 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: 5.92 Conformation dependent library (CDL) restraints added in 2.6 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: 2.83 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: 4.66 Time building geometry restraints manager: 6.40 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: 8315 17.92 - 35.84: 1111 35.84 - 53.76: 423 53.76 - 71.69: 121 71.69 - 89.61: 58 Dihedral angle restraints: 10028 sinusoidal: 4484 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 10025 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 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: 0.010 Normalize map: mean=0, sd=1: 0.330 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: 2.320 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 42.740 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 20.228 89.608 6460 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 % Allowed : 21.22 % Favored : 77.46 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 164 HIS 0.004 0.001 HIS B 155 PHE 0.022 0.001 PHE C 88 TYR 0.020 0.002 TYR D 202 ARG 0.002 0.000 ARG C 246 *********************** 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 : 1.855 Fit side-chains REVERT: B 66 PHE cc_start: 0.7894 (m-80) cc_final: 0.7677 (m-80) outliers start: 22 outliers final: 16 residues processed: 221 average time/residue: 1.3657 time to fit residues: 331.7784 Evaluate side-chains 216 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 200 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TYR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 202 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain C residue 202 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 340 VAL 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 186 HIS ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16228 Z= 0.269 Angle : 0.588 6.348 22028 Z= 0.313 Chirality : 0.045 0.134 2344 Planarity : 0.007 0.087 2816 Dihedral : 14.834 82.357 2656 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.76 % Allowed : 20.02 % Favored : 77.22 % 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: 0.57 (0.20), residues: 708 sheet: -0.48 (0.26), residues: 392 loop : 0.53 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 164 HIS 0.004 0.001 HIS D 186 PHE 0.014 0.002 PHE D 373 TYR 0.018 0.002 TYR D 118 ARG 0.003 0.001 ARG D 487 *********************** 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 248 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 1.817 Fit side-chains REVERT: A 404 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8204 (ppp) REVERT: A 476 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8096 (mmtm) REVERT: B 404 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (ppp) REVERT: C 66 PHE cc_start: 0.7986 (m-80) cc_final: 0.7785 (m-80) REVERT: C 404 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (ppp) REVERT: C 411 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4068 (tmt) REVERT: D 404 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (ppp) outliers start: 46 outliers final: 21 residues processed: 229 average time/residue: 1.4440 time to fit residues: 362.4988 Evaluate side-chains 222 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR 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: 5.9990 chunk 116 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 B 133 GLN B 186 HIS C 133 GLN C 186 HIS D 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16228 Z= 0.342 Angle : 0.627 6.521 22028 Z= 0.334 Chirality : 0.047 0.131 2344 Planarity : 0.007 0.110 2816 Dihedral : 14.672 82.882 2644 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.66 % Allowed : 17.93 % Favored : 78.42 % 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: 0.18 (0.19), residues: 1888 helix: 0.35 (0.20), residues: 700 sheet: -0.50 (0.26), residues: 392 loop : 0.51 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 164 HIS 0.004 0.001 HIS A 186 PHE 0.017 0.002 PHE A 88 TYR 0.021 0.002 TYR C 118 ARG 0.004 0.001 ARG D 487 *********************** 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 262 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 201 time to evaluate : 1.907 Fit side-chains REVERT: A 411 MET cc_start: 0.5049 (OUTLIER) cc_final: 0.4127 (tmt) REVERT: A 476 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8120 (mmtm) REVERT: B 411 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4168 (tmt) REVERT: C 57 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.7041 (ttp80) REVERT: C 411 MET cc_start: 0.5111 (OUTLIER) cc_final: 0.4241 (tmt) REVERT: D 57 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.7039 (ttp80) REVERT: D 411 MET cc_start: 0.5037 (OUTLIER) cc_final: 0.4124 (tmt) outliers start: 61 outliers final: 27 residues processed: 246 average time/residue: 1.4160 time to fit residues: 382.3714 Evaluate side-chains 224 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 57 ARG Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** B 133 GLN B 178 GLN B 186 HIS C 133 GLN C 178 GLN C 186 HIS D 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16228 Z= 0.261 Angle : 0.575 6.228 22028 Z= 0.307 Chirality : 0.045 0.132 2344 Planarity : 0.006 0.078 2816 Dihedral : 14.291 81.944 2644 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.90 % Allowed : 17.33 % Favored : 78.78 % 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: 0.26 (0.19), residues: 1888 helix: 0.39 (0.20), residues: 704 sheet: -0.50 (0.26), residues: 392 loop : 0.61 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 164 HIS 0.008 0.001 HIS A 186 PHE 0.018 0.002 PHE A 88 TYR 0.019 0.002 TYR C 118 ARG 0.003 0.000 ARG A 487 *********************** 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 265 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 200 time to evaluate : 1.814 Fit side-chains REVERT: A 57 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6986 (ttp80) REVERT: A 404 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8161 (ppp) REVERT: A 411 MET cc_start: 0.5078 (OUTLIER) cc_final: 0.4128 (tmt) REVERT: A 476 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8104 (mmtm) REVERT: B 404 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8165 (ppp) REVERT: B 411 MET cc_start: 0.5104 (OUTLIER) cc_final: 0.4169 (tmt) REVERT: C 404 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8162 (ppp) REVERT: C 411 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4294 (tmt) REVERT: D 404 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8162 (ppp) REVERT: D 411 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4109 (tmt) outliers start: 65 outliers final: 28 residues processed: 244 average time/residue: 1.3245 time to fit residues: 356.3338 Evaluate side-chains 226 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 188 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 9.9990 chunk 103 optimal weight: 30.0000 chunk 2 optimal weight: 6.9990 chunk 135 optimal weight: 20.0000 chunk 74 optimal weight: 0.0060 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 7.0004 ------------------------------------------------------------------------------- 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** B 133 GLN B 186 HIS C 133 GLN C 186 HIS D 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16228 Z= 0.359 Angle : 0.641 6.826 22028 Z= 0.342 Chirality : 0.048 0.129 2344 Planarity : 0.007 0.119 2816 Dihedral : 14.251 81.064 2644 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.02 % Allowed : 17.03 % Favored : 78.96 % 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: 0.17 (0.19), residues: 1888 helix: 0.29 (0.20), residues: 700 sheet: -0.46 (0.26), residues: 392 loop : 0.53 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 164 HIS 0.007 0.001 HIS A 186 PHE 0.022 0.002 PHE A 88 TYR 0.025 0.002 TYR C 118 ARG 0.004 0.001 ARG A 487 *********************** 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 275 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 208 time to evaluate : 1.790 Fit side-chains REVERT: A 57 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7093 (ttm110) REVERT: A 404 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8165 (ppp) REVERT: A 411 MET cc_start: 0.5240 (OUTLIER) cc_final: 0.4332 (tmt) REVERT: A 476 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8112 (mmtm) REVERT: B 57 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7142 (ttm110) REVERT: B 404 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8169 (ppp) REVERT: B 411 MET cc_start: 0.5239 (OUTLIER) cc_final: 0.4357 (tmt) REVERT: C 404 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8174 (ppp) REVERT: C 411 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.4337 (tmt) REVERT: C 476 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8378 (mttm) REVERT: D 156 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7073 (mm-30) REVERT: D 404 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.8165 (ppp) REVERT: D 411 MET cc_start: 0.5220 (OUTLIER) cc_final: 0.4317 (tmt) outliers start: 67 outliers final: 38 residues processed: 257 average time/residue: 1.4139 time to fit residues: 398.1500 Evaluate side-chains 249 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 502 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 57 ARG Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 502 GLN Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 502 GLN Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 502 GLN Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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** B 133 GLN B 186 HIS C 133 GLN C 186 HIS D 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.174 Angle : 0.521 5.728 22028 Z= 0.278 Chirality : 0.043 0.137 2344 Planarity : 0.004 0.034 2816 Dihedral : 13.079 77.441 2644 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.48 % Allowed : 17.51 % Favored : 79.02 % 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: 0.37 (0.19), residues: 1888 helix: 0.56 (0.20), residues: 692 sheet: -0.49 (0.26), residues: 388 loop : 0.60 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 164 HIS 0.005 0.001 HIS A 186 PHE 0.019 0.001 PHE A 88 TYR 0.019 0.001 TYR B 118 ARG 0.002 0.000 ARG C 136 *********************** 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 264 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 206 time to evaluate : 1.592 Fit side-chains REVERT: A 148 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: A 404 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8025 (ppp) REVERT: A 411 MET cc_start: 0.5046 (OUTLIER) cc_final: 0.4165 (tmt) REVERT: A 476 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8063 (mmtm) REVERT: B 404 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8020 (ppp) REVERT: B 411 MET cc_start: 0.5130 (OUTLIER) cc_final: 0.4273 (tmt) REVERT: C 404 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8128 (ppp) REVERT: C 411 MET cc_start: 0.5143 (OUTLIER) cc_final: 0.4222 (tmt) REVERT: D 102 PHE cc_start: 0.7164 (m-80) cc_final: 0.6705 (m-80) REVERT: D 404 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.8027 (ppp) outliers start: 58 outliers final: 32 residues processed: 247 average time/residue: 1.3341 time to fit residues: 363.0140 Evaluate side-chains 242 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 320 LYS Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 LYS Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 1.9990 chunk 20 optimal weight: 0.0060 chunk 103 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 153 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.1402 ------------------------------------------------------------------------------- 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** B 133 GLN B 186 HIS C 133 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16228 Z= 0.162 Angle : 0.505 5.751 22028 Z= 0.267 Chirality : 0.042 0.140 2344 Planarity : 0.004 0.041 2816 Dihedral : 12.226 68.168 2640 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.36 % Allowed : 17.93 % Favored : 78.72 % 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: 0.46 (0.19), residues: 1888 helix: 0.67 (0.20), residues: 700 sheet: -0.49 (0.26), residues: 388 loop : 0.66 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 164 HIS 0.004 0.001 HIS A 186 PHE 0.017 0.001 PHE A 88 TYR 0.020 0.001 TYR B 118 ARG 0.002 0.000 ARG D 175 *********************** 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 260 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 204 time to evaluate : 1.823 Fit side-chains REVERT: A 404 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8001 (ppp) REVERT: A 476 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8110 (mmtm) REVERT: B 153 ASN cc_start: 0.8119 (m-40) cc_final: 0.7806 (m110) REVERT: B 404 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7999 (ppp) REVERT: C 136 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7012 (mpp80) REVERT: C 404 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8000 (ppp) REVERT: C 411 MET cc_start: 0.5042 (OUTLIER) cc_final: 0.4170 (tmt) REVERT: C 476 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8360 (mttm) REVERT: D 102 PHE cc_start: 0.7158 (m-80) cc_final: 0.6702 (m-80) REVERT: D 404 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7998 (ppp) outliers start: 56 outliers final: 25 residues processed: 245 average time/residue: 1.3413 time to fit residues: 361.7985 Evaluate side-chains 233 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 0.0040 chunk 54 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 123 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 overall best weight: 2.8000 ------------------------------------------------------------------------------- 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** B 133 GLN B 186 HIS C 133 GLN C 186 HIS D 133 GLN D 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.186 Angle : 0.522 5.965 22028 Z= 0.276 Chirality : 0.043 0.139 2344 Planarity : 0.005 0.050 2816 Dihedral : 11.962 59.601 2640 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.12 % Allowed : 18.29 % Favored : 78.60 % 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: 0.48 (0.19), residues: 1888 helix: 0.64 (0.20), residues: 700 sheet: -0.45 (0.27), residues: 388 loop : 0.69 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 164 HIS 0.004 0.001 HIS A 186 PHE 0.017 0.001 PHE A 88 TYR 0.021 0.002 TYR B 118 ARG 0.007 0.000 ARG D 175 *********************** 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 258 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 1.797 Fit side-chains REVERT: A 64 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.6942 (m-40) REVERT: A 404 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7992 (ppp) REVERT: A 476 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8113 (mmtm) REVERT: B 153 ASN cc_start: 0.8134 (m-40) cc_final: 0.7809 (m110) REVERT: B 404 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7995 (ppp) REVERT: C 404 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7999 (ppp) REVERT: C 411 MET cc_start: 0.5043 (OUTLIER) cc_final: 0.4170 (tmt) REVERT: C 476 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8372 (mttm) REVERT: D 64 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.6924 (m-40) REVERT: D 404 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7996 (ppp) outliers start: 52 outliers final: 27 residues processed: 240 average time/residue: 1.3716 time to fit residues: 362.5146 Evaluate side-chains 239 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 152 optimal weight: 0.0070 chunk 159 optimal weight: 7.9990 chunk 110 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 overall best weight: 5.4006 ------------------------------------------------------------------------------- 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** B 133 GLN B 186 HIS C 105 ASN C 133 GLN C 186 HIS D 133 GLN D 186 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16228 Z= 0.291 Angle : 0.593 6.639 22028 Z= 0.314 Chirality : 0.046 0.134 2344 Planarity : 0.006 0.096 2816 Dihedral : 12.408 59.804 2640 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.76 % Allowed : 18.82 % Favored : 78.42 % 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: 0.37 (0.19), residues: 1888 helix: 0.49 (0.20), residues: 700 sheet: -0.47 (0.27), residues: 392 loop : 0.68 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 164 HIS 0.005 0.001 HIS A 186 PHE 0.020 0.002 PHE A 88 TYR 0.026 0.002 TYR A 118 ARG 0.006 0.001 ARG D 175 *********************** 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 250 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 204 time to evaluate : 1.608 Fit side-chains REVERT: A 404 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: A 476 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8077 (mmtm) REVERT: B 404 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8153 (ppp) REVERT: C 404 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8153 (ppp) REVERT: C 411 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4195 (tmt) REVERT: C 476 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8412 (mttm) REVERT: D 64 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.6964 (m-40) REVERT: D 404 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8151 (ppp) outliers start: 46 outliers final: 29 residues processed: 234 average time/residue: 1.3268 time to fit residues: 341.6262 Evaluate side-chains 238 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 201 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 147 TYR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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** B 133 GLN ** B 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 186 HIS D 133 GLN D 186 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1328 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= 0.192 Angle : 0.528 5.912 22028 Z= 0.281 Chirality : 0.043 0.137 2344 Planarity : 0.005 0.045 2816 Dihedral : 11.757 59.378 2640 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.52 % Allowed : 19.06 % Favored : 78.42 % 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: 0.59 (0.20), residues: 700 sheet: -0.44 (0.27), residues: 388 loop : 0.69 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 164 HIS 0.004 0.001 HIS A 186 PHE 0.018 0.001 PHE A 88 TYR 0.022 0.002 TYR B 118 ARG 0.006 0.000 ARG D 175 ********************** 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 249 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 1.966 Fit side-chains REVERT: A 64 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.6963 (m-40) REVERT: A 404 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8025 (ppp) REVERT: A 476 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8087 (mmtm) REVERT: B 404 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8128 (ppp) REVERT: C 404 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8121 (ppp) REVERT: C 476 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8372 (mttm) REVERT: D 64 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.6926 (m-40) REVERT: D 404 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8123 (ppp) outliers start: 42 outliers final: 26 residues processed: 232 average time/residue: 1.3411 time to fit residues: 342.8564 Evaluate side-chains 237 residues out of total 1668 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 476 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 262 ASN Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 147 TYR Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 476 LYS Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 147 TYR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 510 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** B 133 GLN B 186 HIS C 133 GLN C 186 HIS D 133 GLN D 186 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.130861 restraints weight = 13349.358| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.88 r_work: 0.3115 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16228 Z= 0.346 Angle : 0.632 6.876 22028 Z= 0.335 Chirality : 0.047 0.149 2344 Planarity : 0.007 0.113 2816 Dihedral : 12.397 58.502 2640 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.40 % Allowed : 19.18 % Favored : 78.42 % 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: 0.31 (0.19), residues: 1888 helix: 0.38 (0.20), residues: 684 sheet: -0.44 (0.27), residues: 392 loop : 0.66 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 164 HIS 0.005 0.001 HIS A 186 PHE 0.022 0.002 PHE A 88 TYR 0.029 0.002 TYR A 118 ARG 0.006 0.001 ARG D 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6166.38 seconds wall clock time: 110 minutes 15.30 seconds (6615.30 seconds total)