Starting phenix.real_space_refine on Wed Feb 14 06:05:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vab_31836/02_2024/7vab_31836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vab_31836/02_2024/7vab_31836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vab_31836/02_2024/7vab_31836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vab_31836/02_2024/7vab_31836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vab_31836/02_2024/7vab_31836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vab_31836/02_2024/7vab_31836_updated.pdb" } resolution = 3.2 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= 0.001 sd= 0.096 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5616 2.51 5 N 1525 2.21 5 O 1583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 183": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ARG 192": "NH1" <-> "NH2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 300": "NH1" <-> "NH2" Residue "R ARG 316": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 341": "NH1" <-> "NH2" Residue "R ARG 366": "NH1" <-> "NH2" Residue "R ARG 411": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2399 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 7, 'TRANS': 280} Chain breaks: 4 Chain: "P" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 220 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'AIB:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1950 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.16, per 1000 atoms: 0.59 Number of scatterers: 8772 At special positions: 0 Unit cell: (81.396, 101.745, 160.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1583 8.00 N 1525 7.00 C 5616 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 38.9% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'R' and resid 32 through 47 Processing helix chain 'R' and resid 128 through 161 removed outlier: 3.806A pdb=" N ALA R 150 " --> pdb=" O SER R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 192 removed outlier: 3.549A pdb=" N ILE R 172 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG R 192 " --> pdb=" O LEU R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 245 removed outlier: 3.739A pdb=" N ILE R 221 " --> pdb=" O ARG R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 280 removed outlier: 3.544A pdb=" N LEU R 260 " --> pdb=" O PHE R 256 " (cutoff:3.500A) Proline residue: R 267 - end of helix Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 297 through 325 Proline residue: R 302 - end of helix removed outlier: 4.271A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 318 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU R 325 " --> pdb=" O LEU R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 350 removed outlier: 3.959A pdb=" N LEU R 339 " --> pdb=" O TYR R 335 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 368 through 382 removed outlier: 4.103A pdb=" N GLU R 377 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE R 378 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE R 379 " --> pdb=" O PHE R 376 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU R 380 " --> pdb=" O GLU R 377 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER R 382 " --> pdb=" O PHE R 379 " (cutoff:3.500A) Processing helix chain 'R' and resid 384 through 393 Processing helix chain 'R' and resid 397 through 410 removed outlier: 3.581A pdb=" N GLY R 406 " --> pdb=" O GLU R 402 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 26 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.956A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.933A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.771A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.679A pdb=" N ARG A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 357 removed outlier: 4.262A pdb=" N ILE A 342 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 343 " --> pdb=" O ARG A 340 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 347 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 351 " --> pdb=" O ASP A 348 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 352 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 355 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.753A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.813A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 326 through 330 removed outlier: 6.958A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.136A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.858A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.586A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.807A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.766A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.922A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.697A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1092 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: 2.46 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2839 1.34 - 1.46: 2008 1.46 - 1.58: 4052 1.58 - 1.70: 0 1.70 - 1.81: 66 Bond restraints: 8965 Sorted by residual: bond pdb=" C5 CLR R 603 " pdb=" C6 CLR R 603 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 CLR R 605 " pdb=" C6 CLR R 605 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.38e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.302 0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.30e+00 ... (remaining 8960 not shown) Histogram of bond angle deviations from ideal: 100.01 - 107.18: 248 107.18 - 114.35: 5236 114.35 - 121.52: 4547 121.52 - 128.69: 2063 128.69 - 135.85: 76 Bond angle restraints: 12170 Sorted by residual: angle pdb=" C ASP A 229 " pdb=" N TYR A 230 " pdb=" CA TYR A 230 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 119.75 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.93 -4.53 1.45e+00 4.76e-01 9.77e+00 angle pdb=" C MET R 140 " pdb=" N TYR R 141 " pdb=" CA TYR R 141 " ideal model delta sigma weight residual 121.14 116.04 5.10 1.75e+00 3.27e-01 8.49e+00 angle pdb=" CA LYS B 127 " pdb=" CB LYS B 127 " pdb=" CG LYS B 127 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.05e+00 ... (remaining 12165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 5379 14.99 - 29.98: 158 29.98 - 44.98: 52 44.98 - 59.97: 16 59.97 - 74.96: 6 Dihedral angle restraints: 5611 sinusoidal: 2484 harmonic: 3127 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 142.34 -49.34 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -117.55 31.55 1 1.00e+01 1.00e-02 1.42e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.33 18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1223 0.085 - 0.169: 123 0.169 - 0.254: 11 0.254 - 0.338: 6 0.338 - 0.423: 6 Chirality restraints: 1369 Sorted by residual: chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 1366 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 298 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 299 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 299 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 299 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 309 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C ILE R 309 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE R 309 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN R 310 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO N 88 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.025 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2024 2.80 - 3.32: 7596 3.32 - 3.85: 13855 3.85 - 4.37: 16057 4.37 - 4.90: 28268 Nonbonded interactions: 67800 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.270 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.307 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.313 2.440 nonbonded pdb=" NH1 ARG A 209 " pdb=" OD2 ASP N 109 " model vdw 2.360 2.520 ... (remaining 67795 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 4.100 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.620 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8965 Z= 0.230 Angle : 0.800 15.553 12170 Z= 0.416 Chirality : 0.062 0.423 1369 Planarity : 0.006 0.049 1514 Dihedral : 9.193 74.961 3582 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1050 helix: -1.67 (0.18), residues: 409 sheet: -0.85 (0.33), residues: 224 loop : -1.80 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 248 HIS 0.004 0.001 HIS R 173 PHE 0.021 0.002 PHE B 199 TYR 0.022 0.002 TYR B 264 ARG 0.007 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 137 LEU cc_start: 0.8137 (mt) cc_final: 0.7863 (mt) REVERT: R 181 MET cc_start: 0.7377 (ttm) cc_final: 0.7058 (mtt) REVERT: R 192 ARG cc_start: 0.7505 (mmt-90) cc_final: 0.6621 (mmp-170) REVERT: R 193 LEU cc_start: 0.7916 (mt) cc_final: 0.7613 (tt) REVERT: R 194 LEU cc_start: 0.6093 (tp) cc_final: 0.5861 (tp) REVERT: R 217 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7108 (ttm110) REVERT: R 252 GLU cc_start: 0.4957 (mp0) cc_final: 0.4501 (pt0) REVERT: R 253 GLU cc_start: 0.4555 (pm20) cc_final: 0.3975 (mm-30) REVERT: R 327 THR cc_start: 0.6131 (m) cc_final: 0.5836 (p) REVERT: R 402 GLU cc_start: 0.7518 (tp30) cc_final: 0.7311 (tp30) REVERT: A 15 ARG cc_start: 0.6827 (ttt180) cc_final: 0.6540 (ttt-90) REVERT: A 274 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7597 (ptpp) REVERT: A 310 ASP cc_start: 0.7029 (t70) cc_final: 0.6614 (t0) REVERT: A 311 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7251 (mm-30) REVERT: B 44 GLN cc_start: 0.7858 (mt0) cc_final: 0.7558 (mm-40) REVERT: B 135 VAL cc_start: 0.8096 (t) cc_final: 0.7832 (t) REVERT: B 156 GLN cc_start: 0.7924 (mt0) cc_final: 0.7715 (mt0) REVERT: B 217 MET cc_start: 0.7128 (mtm) cc_final: 0.6456 (mmt) REVERT: B 262 MET cc_start: 0.6874 (ttm) cc_final: 0.6607 (tpt) REVERT: B 280 LYS cc_start: 0.9014 (tttp) cc_final: 0.8766 (ttmm) REVERT: G 21 MET cc_start: 0.8139 (mmt) cc_final: 0.7898 (ttt) REVERT: N 21 SER cc_start: 0.8550 (m) cc_final: 0.8325 (t) REVERT: N 28 THR cc_start: 0.8087 (m) cc_final: 0.7708 (p) REVERT: N 87 LYS cc_start: 0.8100 (mttt) cc_final: 0.7617 (ttmt) REVERT: N 90 ASP cc_start: 0.8245 (t0) cc_final: 0.7937 (m-30) REVERT: N 117 TYR cc_start: 0.8123 (m-10) cc_final: 0.7381 (m-80) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.2818 time to fit residues: 96.8572 Evaluate side-chains 170 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 173 HIS R 224 GLN R 230 ASN R 408 HIS A 204 GLN A 324 HIS A 329 HIS B 13 GLN B 88 ASN B 91 HIS ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS N 31 ASN N 35 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 8965 Z= 0.323 Angle : 0.575 14.355 12170 Z= 0.294 Chirality : 0.042 0.149 1369 Planarity : 0.004 0.036 1514 Dihedral : 6.762 58.884 1582 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.52 % Allowed : 8.44 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1050 helix: 0.35 (0.23), residues: 434 sheet: -0.59 (0.33), residues: 216 loop : -1.40 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.009 0.002 HIS A 324 PHE 0.020 0.002 PHE A 343 TYR 0.026 0.002 TYR R 141 ARG 0.006 0.001 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.7530 (ttm) cc_final: 0.6872 (mtp) REVERT: R 192 ARG cc_start: 0.7345 (mmt-90) cc_final: 0.6562 (mmp-170) REVERT: R 193 LEU cc_start: 0.7831 (mt) cc_final: 0.7578 (tt) REVERT: R 213 LEU cc_start: 0.4887 (OUTLIER) cc_final: 0.4168 (tp) REVERT: R 217 ARG cc_start: 0.7830 (mtt180) cc_final: 0.6909 (ptt-90) REVERT: R 252 GLU cc_start: 0.5173 (mp0) cc_final: 0.4459 (pt0) REVERT: R 253 GLU cc_start: 0.4556 (pm20) cc_final: 0.3767 (mm-30) REVERT: R 289 ARG cc_start: 0.7716 (mtp180) cc_final: 0.7119 (mtm180) REVERT: R 336 ARG cc_start: 0.5741 (mtt180) cc_final: 0.5421 (tpt170) REVERT: R 345 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6854 (t80) REVERT: A 15 ARG cc_start: 0.6871 (ttt180) cc_final: 0.6573 (ttt90) REVERT: A 31 ARG cc_start: 0.7675 (mtm110) cc_final: 0.7301 (mtt-85) REVERT: A 53 MET cc_start: 0.7840 (mmt) cc_final: 0.7612 (mmt) REVERT: A 193 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7752 (mtmm) REVERT: A 207 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 274 LYS cc_start: 0.8198 (ptmt) cc_final: 0.7813 (ptpp) REVERT: A 310 ASP cc_start: 0.7181 (t70) cc_final: 0.6790 (t0) REVERT: A 323 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.6782 (mtm110) REVERT: B 13 GLN cc_start: 0.8830 (pt0) cc_final: 0.8527 (pt0) REVERT: B 44 GLN cc_start: 0.8162 (mt0) cc_final: 0.7723 (mm-40) REVERT: B 175 GLN cc_start: 0.7762 (mp10) cc_final: 0.7549 (mp10) REVERT: B 217 MET cc_start: 0.7262 (mtm) cc_final: 0.6605 (mmt) REVERT: B 280 LYS cc_start: 0.8995 (tttp) cc_final: 0.8692 (ttmm) REVERT: N 21 SER cc_start: 0.8685 (m) cc_final: 0.8476 (t) REVERT: N 28 THR cc_start: 0.8232 (m) cc_final: 0.7929 (p) REVERT: N 82 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7655 (tp-100) REVERT: N 87 LYS cc_start: 0.7993 (mttt) cc_final: 0.7536 (ttmt) REVERT: N 90 ASP cc_start: 0.8391 (t0) cc_final: 0.7665 (t0) outliers start: 14 outliers final: 6 residues processed: 183 average time/residue: 0.2724 time to fit residues: 64.0902 Evaluate side-chains 158 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS B 13 GLN B 239 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8965 Z= 0.198 Angle : 0.505 13.286 12170 Z= 0.256 Chirality : 0.040 0.143 1369 Planarity : 0.003 0.029 1514 Dihedral : 6.222 49.179 1582 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.60 % Allowed : 10.39 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1050 helix: 1.21 (0.25), residues: 426 sheet: -0.48 (0.33), residues: 221 loop : -1.03 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 233 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.001 PHE B 199 TYR 0.025 0.002 TYR R 141 ARG 0.005 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.7550 (ttm) cc_final: 0.6904 (mtp) REVERT: R 192 ARG cc_start: 0.7298 (mmt-90) cc_final: 0.6489 (mmp-170) REVERT: R 193 LEU cc_start: 0.7810 (mt) cc_final: 0.7525 (tt) REVERT: R 237 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: R 252 GLU cc_start: 0.5154 (mp0) cc_final: 0.4745 (mp0) REVERT: R 289 ARG cc_start: 0.7624 (mtp180) cc_final: 0.7066 (mtm180) REVERT: R 336 ARG cc_start: 0.5662 (mtt180) cc_final: 0.5198 (tpt170) REVERT: R 345 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7035 (t80) REVERT: A 193 LYS cc_start: 0.8073 (mtpt) cc_final: 0.7707 (mtmm) REVERT: A 310 ASP cc_start: 0.7224 (t70) cc_final: 0.6879 (t0) REVERT: A 323 ARG cc_start: 0.7421 (mtm-85) cc_final: 0.6738 (mtm110) REVERT: B 280 LYS cc_start: 0.8992 (tttp) cc_final: 0.8664 (ttmm) REVERT: N 21 SER cc_start: 0.8744 (m) cc_final: 0.8490 (t) REVERT: N 28 THR cc_start: 0.8141 (m) cc_final: 0.7801 (p) REVERT: N 90 ASP cc_start: 0.8293 (t0) cc_final: 0.7646 (t0) outliers start: 24 outliers final: 15 residues processed: 173 average time/residue: 0.2906 time to fit residues: 64.9343 Evaluate side-chains 163 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 237 GLU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8965 Z= 0.166 Angle : 0.477 12.265 12170 Z= 0.241 Chirality : 0.039 0.138 1369 Planarity : 0.003 0.029 1514 Dihedral : 5.844 44.267 1582 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.38 % Allowed : 10.82 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1050 helix: 1.52 (0.25), residues: 432 sheet: -0.44 (0.33), residues: 220 loop : -0.98 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 233 HIS 0.004 0.001 HIS B 142 PHE 0.014 0.001 PHE B 199 TYR 0.021 0.001 TYR R 141 ARG 0.004 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.7556 (ttm) cc_final: 0.6930 (mtp) REVERT: R 192 ARG cc_start: 0.7282 (mmt-90) cc_final: 0.6477 (mmp-170) REVERT: R 193 LEU cc_start: 0.7780 (mt) cc_final: 0.7501 (tt) REVERT: R 237 GLU cc_start: 0.7614 (tt0) cc_final: 0.7408 (tt0) REVERT: R 252 GLU cc_start: 0.5170 (mp0) cc_final: 0.4754 (mp0) REVERT: R 289 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7040 (mtm180) REVERT: R 336 ARG cc_start: 0.5672 (mtt180) cc_final: 0.5143 (tpt170) REVERT: R 345 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.6998 (t80) REVERT: A 31 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7595 (mtt-85) REVERT: A 47 SER cc_start: 0.8369 (m) cc_final: 0.8080 (p) REVERT: A 193 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7720 (mtmm) REVERT: A 310 ASP cc_start: 0.7228 (t70) cc_final: 0.6906 (t0) REVERT: A 323 ARG cc_start: 0.7463 (mtm-85) cc_final: 0.6902 (mtm110) REVERT: B 175 GLN cc_start: 0.7811 (mp10) cc_final: 0.7586 (mp10) REVERT: B 280 LYS cc_start: 0.8956 (tttp) cc_final: 0.8622 (ttmm) REVERT: N 21 SER cc_start: 0.8741 (m) cc_final: 0.8483 (t) REVERT: N 28 THR cc_start: 0.8112 (m) cc_final: 0.7729 (p) REVERT: N 82 GLN cc_start: 0.7904 (tp-100) cc_final: 0.7700 (tp-100) REVERT: N 90 ASP cc_start: 0.8243 (t0) cc_final: 0.7608 (t0) outliers start: 22 outliers final: 15 residues processed: 170 average time/residue: 0.2778 time to fit residues: 60.7486 Evaluate side-chains 164 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.2980 chunk 1 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 overall best weight: 1.4722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8965 Z= 0.326 Angle : 0.549 11.103 12170 Z= 0.281 Chirality : 0.041 0.141 1369 Planarity : 0.004 0.032 1514 Dihedral : 5.698 44.304 1582 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.49 % Allowed : 12.23 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1050 helix: 1.55 (0.25), residues: 436 sheet: -0.65 (0.34), residues: 207 loop : -0.96 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 47 HIS 0.009 0.001 HIS B 142 PHE 0.017 0.002 PHE R 379 TYR 0.018 0.002 TYR R 141 ARG 0.005 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.7582 (ttm) cc_final: 0.6893 (mtp) REVERT: R 192 ARG cc_start: 0.7470 (mmt-90) cc_final: 0.6746 (mmp-170) REVERT: R 336 ARG cc_start: 0.5801 (mtt180) cc_final: 0.5179 (tpt170) REVERT: R 345 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 31 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7634 (mtt-85) REVERT: A 193 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7759 (mtmm) REVERT: A 259 ASN cc_start: 0.8486 (t0) cc_final: 0.7907 (t0) REVERT: A 310 ASP cc_start: 0.7303 (t70) cc_final: 0.6977 (t0) REVERT: A 323 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7380 (mtm110) REVERT: B 10 GLU cc_start: 0.8471 (tp30) cc_final: 0.8163 (tp30) REVERT: B 175 GLN cc_start: 0.7823 (mp10) cc_final: 0.7598 (mp10) REVERT: B 259 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: B 264 TYR cc_start: 0.9004 (m-80) cc_final: 0.8574 (m-80) REVERT: B 268 ASN cc_start: 0.7913 (p0) cc_final: 0.7707 (p0) REVERT: N 28 THR cc_start: 0.8347 (m) cc_final: 0.7866 (p) REVERT: N 82 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7376 (tp-100) outliers start: 23 outliers final: 14 residues processed: 171 average time/residue: 0.2665 time to fit residues: 59.0526 Evaluate side-chains 155 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain P residue 7 THR Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.0370 chunk 100 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 97 optimal weight: 0.0670 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8965 Z= 0.139 Angle : 0.469 10.358 12170 Z= 0.236 Chirality : 0.039 0.130 1369 Planarity : 0.003 0.029 1514 Dihedral : 5.297 40.306 1582 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.84 % Allowed : 13.53 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1050 helix: 1.88 (0.26), residues: 432 sheet: -0.48 (0.34), residues: 205 loop : -0.87 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.002 0.001 HIS B 142 PHE 0.012 0.001 PHE A 189 TYR 0.021 0.001 TYR R 281 ARG 0.006 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.7544 (ttm) cc_final: 0.6915 (mtp) REVERT: R 192 ARG cc_start: 0.7548 (mmt-90) cc_final: 0.6771 (mmp-170) REVERT: R 336 ARG cc_start: 0.5871 (mtt180) cc_final: 0.5228 (tpt170) REVERT: R 345 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7114 (t80) REVERT: A 31 ARG cc_start: 0.7860 (mtm110) cc_final: 0.7624 (mtt-85) REVERT: A 193 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7739 (mtpp) REVERT: A 274 LYS cc_start: 0.8126 (ptpt) cc_final: 0.7623 (ptpp) REVERT: A 310 ASP cc_start: 0.7254 (t70) cc_final: 0.6917 (t0) REVERT: A 323 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.6917 (mtm110) REVERT: B 10 GLU cc_start: 0.8413 (tp30) cc_final: 0.8131 (tp30) REVERT: B 264 TYR cc_start: 0.8971 (m-80) cc_final: 0.8690 (m-80) REVERT: N 21 SER cc_start: 0.8812 (m) cc_final: 0.8506 (t) REVERT: N 28 THR cc_start: 0.8251 (m) cc_final: 0.7811 (p) REVERT: N 82 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7316 (tp-100) REVERT: N 90 ASP cc_start: 0.7943 (m-30) cc_final: 0.7739 (m-30) REVERT: N 109 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6957 (p0) outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.2733 time to fit residues: 60.2889 Evaluate side-chains 171 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.0770 chunk 61 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8965 Z= 0.162 Angle : 0.474 9.970 12170 Z= 0.238 Chirality : 0.039 0.130 1369 Planarity : 0.003 0.029 1514 Dihedral : 5.147 39.120 1582 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.16 % Allowed : 12.99 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.26), residues: 1050 helix: 1.89 (0.26), residues: 438 sheet: -0.43 (0.34), residues: 206 loop : -0.87 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE A 189 TYR 0.016 0.001 TYR R 141 ARG 0.008 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.7557 (ttm) cc_final: 0.6934 (mtp) REVERT: R 192 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.6734 (mmp-170) REVERT: R 336 ARG cc_start: 0.5860 (mtt180) cc_final: 0.5331 (tpt170) REVERT: R 345 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7108 (t80) REVERT: A 31 ARG cc_start: 0.7835 (mtm110) cc_final: 0.7547 (mtt-85) REVERT: A 193 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7736 (mtpp) REVERT: A 200 ASP cc_start: 0.6773 (t0) cc_final: 0.6516 (t0) REVERT: A 274 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7700 (ptpp) REVERT: A 310 ASP cc_start: 0.7257 (t70) cc_final: 0.6934 (t0) REVERT: B 10 GLU cc_start: 0.8426 (tp30) cc_final: 0.8141 (tp30) REVERT: B 264 TYR cc_start: 0.8985 (m-80) cc_final: 0.8726 (m-80) REVERT: N 28 THR cc_start: 0.8237 (m) cc_final: 0.7786 (p) REVERT: N 109 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6878 (p0) outliers start: 20 outliers final: 14 residues processed: 171 average time/residue: 0.2654 time to fit residues: 59.1762 Evaluate side-chains 164 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 78 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8965 Z= 0.155 Angle : 0.465 9.466 12170 Z= 0.234 Chirality : 0.038 0.129 1369 Planarity : 0.003 0.031 1514 Dihedral : 5.009 37.168 1582 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.71 % Allowed : 12.55 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1050 helix: 2.02 (0.26), residues: 437 sheet: -0.46 (0.34), residues: 209 loop : -0.83 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 386 TYR 0.015 0.001 TYR R 141 ARG 0.007 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8177 (mm-30) REVERT: R 181 MET cc_start: 0.7542 (ttm) cc_final: 0.6925 (mtp) REVERT: R 192 ARG cc_start: 0.7544 (mmt-90) cc_final: 0.6757 (mmp-170) REVERT: R 336 ARG cc_start: 0.5870 (mtt180) cc_final: 0.5280 (tpt170) REVERT: R 345 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7202 (t80) REVERT: A 31 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7614 (mtt-85) REVERT: A 193 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7755 (mtpp) REVERT: A 200 ASP cc_start: 0.6753 (t0) cc_final: 0.6500 (t0) REVERT: A 274 LYS cc_start: 0.8117 (ptpt) cc_final: 0.7713 (ptpp) REVERT: A 310 ASP cc_start: 0.7284 (t70) cc_final: 0.6965 (t0) REVERT: A 323 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6763 (mmm160) REVERT: B 10 GLU cc_start: 0.8427 (tp30) cc_final: 0.8142 (tp30) REVERT: B 264 TYR cc_start: 0.8983 (m-80) cc_final: 0.8730 (m-80) REVERT: G 17 GLU cc_start: 0.8180 (tp30) cc_final: 0.7819 (tt0) REVERT: N 28 THR cc_start: 0.8211 (m) cc_final: 0.7781 (p) REVERT: N 109 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6857 (p0) outliers start: 25 outliers final: 20 residues processed: 166 average time/residue: 0.2660 time to fit residues: 57.6705 Evaluate side-chains 166 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8965 Z= 0.189 Angle : 0.483 9.170 12170 Z= 0.244 Chirality : 0.039 0.131 1369 Planarity : 0.003 0.034 1514 Dihedral : 4.918 36.241 1582 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.60 % Allowed : 12.88 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.26), residues: 1050 helix: 2.04 (0.25), residues: 438 sheet: -0.45 (0.33), residues: 208 loop : -0.81 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.005 0.001 HIS B 142 PHE 0.015 0.001 PHE R 386 TYR 0.014 0.001 TYR R 141 ARG 0.008 0.000 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 149 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8235 (mm-30) REVERT: R 140 MET cc_start: 0.8496 (tmm) cc_final: 0.7104 (mmm) REVERT: R 181 MET cc_start: 0.7558 (ttm) cc_final: 0.6936 (mtp) REVERT: R 192 ARG cc_start: 0.7504 (mmt-90) cc_final: 0.6698 (mmp-170) REVERT: R 336 ARG cc_start: 0.5982 (mtt180) cc_final: 0.5318 (tpt170) REVERT: R 345 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 31 ARG cc_start: 0.7875 (mtm110) cc_final: 0.7556 (mtt-85) REVERT: A 54 ARG cc_start: 0.6524 (mtt180) cc_final: 0.5871 (ttp80) REVERT: A 193 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7743 (mtpp) REVERT: A 200 ASP cc_start: 0.6732 (t0) cc_final: 0.6501 (t0) REVERT: A 274 LYS cc_start: 0.8078 (ptpt) cc_final: 0.7687 (ptpp) REVERT: A 310 ASP cc_start: 0.7268 (t70) cc_final: 0.6956 (t0) REVERT: A 323 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6754 (mmm160) REVERT: B 10 GLU cc_start: 0.8428 (tp30) cc_final: 0.8129 (tp30) REVERT: B 264 TYR cc_start: 0.8978 (m-80) cc_final: 0.8734 (m-80) REVERT: G 17 GLU cc_start: 0.8181 (tp30) cc_final: 0.7858 (tt0) REVERT: N 28 THR cc_start: 0.8236 (m) cc_final: 0.7772 (p) REVERT: N 82 GLN cc_start: 0.7446 (tp-100) cc_final: 0.6856 (tp-100) REVERT: N 109 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6849 (p0) outliers start: 24 outliers final: 18 residues processed: 165 average time/residue: 0.2685 time to fit residues: 57.5258 Evaluate side-chains 169 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 395 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.0670 chunk 68 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8965 Z= 0.168 Angle : 0.505 10.555 12170 Z= 0.251 Chirality : 0.039 0.238 1369 Planarity : 0.003 0.038 1514 Dihedral : 4.917 36.699 1582 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.16 % Allowed : 13.42 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.75 (0.26), residues: 1050 helix: 2.10 (0.25), residues: 438 sheet: -0.39 (0.34), residues: 208 loop : -0.76 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.023 0.001 PHE R 379 TYR 0.013 0.001 TYR R 141 ARG 0.009 0.000 ARG A 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2100 Ramachandran restraints generated. 1050 Oldfield, 0 Emsley, 1050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 152 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8202 (mm-30) REVERT: R 140 MET cc_start: 0.8495 (tmm) cc_final: 0.7105 (mmm) REVERT: R 181 MET cc_start: 0.7537 (ttm) cc_final: 0.6925 (mtp) REVERT: R 192 ARG cc_start: 0.7477 (mmt-90) cc_final: 0.6664 (mmp-170) REVERT: R 336 ARG cc_start: 0.5983 (mtt180) cc_final: 0.5312 (tpt170) REVERT: R 345 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7242 (t80) REVERT: A 31 ARG cc_start: 0.7912 (mtm110) cc_final: 0.7621 (mtt-85) REVERT: A 54 ARG cc_start: 0.6512 (mtt180) cc_final: 0.5863 (ttp80) REVERT: A 193 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7745 (mtpp) REVERT: A 200 ASP cc_start: 0.6747 (t0) cc_final: 0.6491 (t0) REVERT: A 274 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7666 (ptpp) REVERT: A 310 ASP cc_start: 0.7288 (t70) cc_final: 0.6972 (t0) REVERT: A 323 ARG cc_start: 0.7351 (mtm110) cc_final: 0.6750 (mmm160) REVERT: B 264 TYR cc_start: 0.8968 (m-80) cc_final: 0.8720 (m-80) REVERT: G 17 GLU cc_start: 0.8185 (tp30) cc_final: 0.7855 (tt0) REVERT: N 28 THR cc_start: 0.8217 (m) cc_final: 0.7771 (p) REVERT: N 82 GLN cc_start: 0.7429 (tp-100) cc_final: 0.6837 (tp-100) REVERT: N 109 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6936 (p0) outliers start: 20 outliers final: 18 residues processed: 164 average time/residue: 0.2585 time to fit residues: 55.4767 Evaluate side-chains 169 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 216 CYS Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 284 ARG Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.0030 chunk 4 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.207975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155134 restraints weight = 8829.798| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.88 r_work: 0.3528 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8965 Z= 0.174 Angle : 0.487 8.827 12170 Z= 0.245 Chirality : 0.039 0.154 1369 Planarity : 0.003 0.037 1514 Dihedral : 4.850 36.843 1582 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.27 % Allowed : 13.53 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1050 helix: 2.13 (0.25), residues: 438 sheet: -0.43 (0.34), residues: 208 loop : -0.75 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 386 TYR 0.013 0.001 TYR A 56 ARG 0.009 0.000 ARG A 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2401.60 seconds wall clock time: 43 minutes 52.05 seconds (2632.05 seconds total)