Starting phenix.real_space_refine on Sat Mar 16 17:11:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8irv_35687/03_2024/8irv_35687_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 S 54 5.16 5 C 4887 2.51 5 N 1266 2.21 5 O 1340 1.98 5 H 7182 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 228": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 231": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 255": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 307": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 323": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 326": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 332": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 364": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 370": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 379": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 137": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 197": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 214": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 219": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 251": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 283": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 304": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 314": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 67": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 147": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 155": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 223": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 250": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 257": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 264": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14729 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3924 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5107 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 885 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 4813 Unusual residues: {'CLR': 10, 'PLM': 1, 'R5F': 1} Classifications: {'peptide': 279, 'undetermined': 12} Link IDs: {'PTRANS': 9, 'TRANS': 269, None: 12} Not linked: pdbres="GLY R 374 " pdbres="R5F R 501 " Not linked: pdbres="R5F R 501 " pdbres="CLR R 502 " Not linked: pdbres="CLR R 502 " pdbres="CLR R 503 " Not linked: pdbres="CLR R 503 " pdbres="CLR R 504 " Not linked: pdbres="CLR R 504 " pdbres="CLR R 505 " ... (remaining 7 not shown) Chain breaks: 3 Time building chain proxies: 6.87, per 1000 atoms: 0.47 Number of scatterers: 14729 At special positions: 0 Unit cell: (91.035, 101.745, 115.668, 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 54 16.00 O 1340 8.00 N 1266 7.00 C 4887 6.00 H 7182 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 113 " - pdb=" SG CYS R 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 322 " - pdb=" SG CYS R 335 " 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: 12.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 8 sheets defined 46.2% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.958A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.646A pdb=" N ARG A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.456A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 322 through 341 removed outlier: 3.670A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 380 removed outlier: 4.088A pdb=" N ALA A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 367 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 370 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 378 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 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 24 removed outlier: 3.524A pdb=" N ALA G 12 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU G 22 " --> pdb=" O LEU G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 3.507A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 66 removed outlier: 3.622A pdb=" N VAL R 66 " --> pdb=" O CYS R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 73 Processing helix chain 'R' and resid 75 through 93 removed outlier: 3.638A pdb=" N VAL R 81 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU R 83 " --> pdb=" O ILE R 80 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU R 93 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 104 Processing helix chain 'R' and resid 110 through 143 removed outlier: 4.184A pdb=" N ASP R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL R 115 " --> pdb=" O ALA R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 151 Processing helix chain 'R' and resid 154 through 177 Proline residue: R 175 - end of helix Processing helix chain 'R' and resid 223 through 233 Processing helix chain 'R' and resid 235 through 270 Processing helix chain 'R' and resid 290 through 322 removed outlier: 3.568A pdb=" N LEU R 298 " --> pdb=" O LEU R 295 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N MET R 302 " --> pdb=" O SER R 299 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY R 303 " --> pdb=" O VAL R 300 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL R 304 " --> pdb=" O ILE R 301 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE R 305 " --> pdb=" O MET R 302 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL R 306 " --> pdb=" O GLY R 303 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS R 307 " --> pdb=" O VAL R 304 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N CYS R 308 " --> pdb=" O PHE R 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP R 309 " --> pdb=" O VAL R 306 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU R 310 " --> pdb=" O CYS R 307 " (cutoff:3.500A) Proline residue: R 311 - end of helix removed outlier: 3.526A pdb=" N ILE R 314 " --> pdb=" O PRO R 311 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN R 316 " --> pdb=" O PHE R 313 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL R 319 " --> pdb=" O ASN R 316 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 338 through 360 removed outlier: 3.753A pdb=" N SER R 352 " --> pdb=" O GLY R 348 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER R 353 " --> pdb=" O TRP R 349 " (cutoff:3.500A) Proline residue: R 356 - end of helix Processing helix chain 'R' and resid 363 through 373 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 6.979A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.945A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.147A 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: 6.904A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.412A 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: 6.563A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.732A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.443A 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: 6.704A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.605A 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: 6.638A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.641A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 855 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: 5.42 Time building geometry restraints manager: 12.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 7155 1.12 - 1.29: 1198 1.29 - 1.47: 2781 1.47 - 1.64: 3695 1.64 - 1.82: 77 Bond restraints: 14906 Sorted by residual: bond pdb=" C9 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.752 -0.197 2.00e-02 2.50e+03 9.71e+01 bond pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " ideal model delta sigma weight residual 1.555 1.743 -0.188 2.00e-02 2.50e+03 8.81e+01 bond pdb=" C7 R5F R 501 " pdb=" C8 R5F R 501 " ideal model delta sigma weight residual 1.596 1.420 0.176 2.00e-02 2.50e+03 7.78e+01 bond pdb=" N LYS R 296 " pdb=" H LYS R 296 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR R 125 " pdb=" H THR R 125 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 14901 not shown) Histogram of bond angle deviations from ideal: 90.46 - 99.32: 35 99.32 - 108.19: 4161 108.19 - 117.05: 14178 117.05 - 125.91: 8093 125.91 - 134.77: 256 Bond angle restraints: 26723 Sorted by residual: angle pdb=" CB HIS B 54 " pdb=" CG HIS B 54 " pdb=" CD2 HIS B 54 " ideal model delta sigma weight residual 131.20 123.59 7.61 1.30e+00 5.92e-01 3.43e+01 angle pdb=" C6 R5F R 501 " pdb=" S1 R5F R 501 " pdb=" C9 R5F R 501 " ideal model delta sigma weight residual 107.56 90.46 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" N ASP B 186 " pdb=" CA ASP B 186 " pdb=" CB ASP B 186 " ideal model delta sigma weight residual 109.71 101.18 8.53 1.54e+00 4.22e-01 3.07e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" CB ASP B 228 " ideal model delta sigma weight residual 109.69 101.40 8.29 1.53e+00 4.27e-01 2.94e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.82 128.28 -7.46 1.41e+00 5.03e-01 2.80e+01 ... (remaining 26718 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6947 17.39 - 34.79: 387 34.79 - 52.18: 95 52.18 - 69.57: 85 69.57 - 86.96: 4 Dihedral angle restraints: 7518 sinusoidal: 4345 harmonic: 3173 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA LEU B 4 " pdb=" C LEU B 4 " pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA LEU B 70 " pdb=" C LEU B 70 " pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta harmonic sigma weight residual 180.00 153.05 26.95 0 5.00e+00 4.00e-02 2.91e+01 ... (remaining 7515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 866 0.096 - 0.192: 288 0.192 - 0.289: 44 0.289 - 0.385: 14 0.385 - 0.481: 4 Chirality restraints: 1216 Sorted by residual: chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA THR B 87 " pdb=" N THR B 87 " pdb=" C THR B 87 " pdb=" CB THR B 87 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CA TYR R 359 " pdb=" N TYR R 359 " pdb=" C TYR R 359 " pdb=" CB TYR R 359 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 1213 not shown) Planarity restraints: 2150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.211 2.00e-02 2.50e+03 8.32e-02 2.08e+02 pdb=" CG TYR B 105 " -0.135 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " -0.085 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR B 105 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR B 105 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR B 105 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR B 105 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 271 " 0.162 2.00e-02 2.50e+03 7.19e-02 2.07e+02 pdb=" CG TRP A 271 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 271 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 271 " -0.071 2.00e-02 2.50e+03 pdb=" NE1 TRP A 271 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 TRP A 271 " -0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP A 271 " -0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 271 " 0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 271 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP A 271 " 0.044 2.00e-02 2.50e+03 pdb=" HD1 TRP A 271 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 TRP A 271 " -0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP A 271 " -0.086 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 271 " 0.048 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 271 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP A 271 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 54 " 0.141 2.00e-02 2.50e+03 8.21e-02 1.52e+02 pdb=" CG HIS B 54 " -0.075 2.00e-02 2.50e+03 pdb=" ND1 HIS B 54 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS B 54 " -0.101 2.00e-02 2.50e+03 pdb=" CE1 HIS B 54 " -0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS B 54 " -0.053 2.00e-02 2.50e+03 pdb=" HD2 HIS B 54 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 HIS B 54 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 HIS B 54 " 0.132 2.00e-02 2.50e+03 ... (remaining 2147 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 950 2.18 - 2.79: 25533 2.79 - 3.39: 41149 3.39 - 4.00: 55677 4.00 - 4.60: 80595 Nonbonded interactions: 203904 Sorted by model distance: nonbonded pdb=" HG SER B 147 " pdb=" O VAL B 187 " model vdw 1.576 1.850 nonbonded pdb=" HH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 1.581 1.850 nonbonded pdb=" HG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 1.585 1.850 nonbonded pdb=" OD1 ASP R 218 " pdb=" HG SER R 220 " model vdw 1.600 1.850 nonbonded pdb=" HG SER A 13 " pdb=" OD2 ASP A 16 " model vdw 1.602 1.850 ... (remaining 203899 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: 0.390 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: 0.240 Extract box with map and model: 2.560 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 50.010 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.013 0.197 7724 Z= 0.842 Angle : 1.781 17.097 10518 Z= 1.187 Chirality : 0.098 0.481 1216 Planarity : 0.016 0.127 1270 Dihedral : 11.580 86.963 3337 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.46 % 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: 0.29 (0.26), residues: 896 helix: 0.10 (0.22), residues: 412 sheet: 1.02 (0.43), residues: 142 loop : 0.17 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.118 0.023 TRP A 271 HIS 0.014 0.004 HIS B 62 PHE 0.110 0.014 PHE R 312 TYR 0.199 0.020 TYR B 105 ARG 0.012 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8657 (tp) cc_final: 0.8438 (mt) REVERT: A 329 TYR cc_start: 0.8706 (m-80) cc_final: 0.8437 (m-80) REVERT: B 16 ASN cc_start: 0.8251 (m-40) cc_final: 0.7856 (m110) REVERT: R 58 ASN cc_start: 0.8239 (m-40) cc_final: 0.7980 (m-40) REVERT: R 156 MET cc_start: 0.8286 (tpp) cc_final: 0.8064 (tpt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.5710 time to fit residues: 162.4691 Evaluate side-chains 144 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7724 Z= 0.208 Angle : 0.582 5.143 10518 Z= 0.320 Chirality : 0.040 0.147 1216 Planarity : 0.005 0.047 1270 Dihedral : 6.631 64.881 1667 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.03 % Allowed : 6.60 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.27), residues: 896 helix: 0.67 (0.24), residues: 409 sheet: 0.48 (0.38), residues: 175 loop : 0.63 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.002 PHE B 235 TYR 0.031 0.001 TYR B 105 ARG 0.004 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8905 (tp) cc_final: 0.8645 (mt) REVERT: A 329 TYR cc_start: 0.8444 (m-80) cc_final: 0.8121 (m-80) REVERT: B 16 ASN cc_start: 0.8179 (m-40) cc_final: 0.7891 (m110) REVERT: R 215 GLU cc_start: 0.7841 (tp30) cc_final: 0.7570 (tp30) outliers start: 16 outliers final: 8 residues processed: 160 average time/residue: 0.4737 time to fit residues: 98.6986 Evaluate side-chains 140 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 113 CYS Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 336 VAL Chi-restraints excluded: chain R residue 364 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7724 Z= 0.291 Angle : 0.544 4.838 10518 Z= 0.296 Chirality : 0.039 0.161 1216 Planarity : 0.004 0.039 1270 Dihedral : 6.204 59.087 1667 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.28 % Allowed : 9.64 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 896 helix: 0.96 (0.26), residues: 402 sheet: 0.19 (0.36), residues: 179 loop : 0.50 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 82 HIS 0.006 0.001 HIS A 347 PHE 0.013 0.002 PHE B 199 TYR 0.024 0.001 TYR B 105 ARG 0.002 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8923 (tp) cc_final: 0.8685 (mt) REVERT: A 329 TYR cc_start: 0.8549 (m-80) cc_final: 0.8170 (m-80) REVERT: B 16 ASN cc_start: 0.8159 (m-40) cc_final: 0.7816 (m110) REVERT: R 218 ASP cc_start: 0.7492 (t70) cc_final: 0.7223 (t0) outliers start: 18 outliers final: 11 residues processed: 150 average time/residue: 0.5007 time to fit residues: 96.7586 Evaluate side-chains 142 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 336 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 380 GLN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7724 Z= 0.258 Angle : 0.503 4.500 10518 Z= 0.272 Chirality : 0.038 0.157 1216 Planarity : 0.004 0.045 1270 Dihedral : 5.949 58.010 1667 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.66 % Allowed : 10.53 % 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: 0.89 (0.28), residues: 896 helix: 1.18 (0.26), residues: 402 sheet: -0.09 (0.35), residues: 183 loop : 0.47 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.011 0.001 PHE B 199 TYR 0.016 0.001 TYR B 105 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8933 (tp) cc_final: 0.8707 (mt) REVERT: A 329 TYR cc_start: 0.8528 (m-80) cc_final: 0.8144 (m-80) REVERT: B 234 PHE cc_start: 0.9374 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: R 156 MET cc_start: 0.7842 (tpt) cc_final: 0.7374 (tpt) REVERT: R 218 ASP cc_start: 0.7497 (t70) cc_final: 0.7248 (t0) outliers start: 21 outliers final: 17 residues processed: 149 average time/residue: 0.4912 time to fit residues: 94.8305 Evaluate side-chains 149 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 135 SER Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 16 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7724 Z= 0.211 Angle : 0.486 5.259 10518 Z= 0.262 Chirality : 0.038 0.171 1216 Planarity : 0.003 0.040 1270 Dihedral : 5.840 55.432 1667 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.54 % Allowed : 11.42 % Favored : 86.04 % 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: 1.01 (0.28), residues: 896 helix: 1.23 (0.27), residues: 402 sheet: -0.11 (0.36), residues: 183 loop : 0.68 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 180 HIS 0.003 0.001 HIS A 220 PHE 0.010 0.001 PHE B 199 TYR 0.011 0.001 TYR B 105 ARG 0.002 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8924 (tp) cc_final: 0.8683 (mt) REVERT: A 329 TYR cc_start: 0.8423 (m-80) cc_final: 0.8011 (m-80) REVERT: B 197 ARG cc_start: 0.7294 (mtp85) cc_final: 0.7091 (mmm-85) REVERT: B 234 PHE cc_start: 0.9365 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: R 156 MET cc_start: 0.7777 (tpt) cc_final: 0.7300 (tpt) outliers start: 20 outliers final: 13 residues processed: 140 average time/residue: 0.5093 time to fit residues: 92.8000 Evaluate side-chains 143 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7724 Z= 0.236 Angle : 0.484 4.524 10518 Z= 0.261 Chirality : 0.038 0.197 1216 Planarity : 0.004 0.057 1270 Dihedral : 5.731 52.126 1667 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.28 % Allowed : 12.18 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 896 helix: 1.25 (0.27), residues: 403 sheet: -0.16 (0.36), residues: 183 loop : 0.66 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.010 0.001 PHE B 199 TYR 0.013 0.001 TYR B 105 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8892 (tp) cc_final: 0.8667 (mt) REVERT: B 234 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: B 266 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7442 (t-90) REVERT: G 46 LYS cc_start: 0.8312 (ttpp) cc_final: 0.7306 (ptmm) REVERT: R 156 MET cc_start: 0.7684 (tpt) cc_final: 0.7244 (tpt) REVERT: R 250 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6965 (mtp180) outliers start: 18 outliers final: 15 residues processed: 141 average time/residue: 0.5600 time to fit residues: 99.5886 Evaluate side-chains 139 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 122 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7724 Z= 0.163 Angle : 0.464 4.491 10518 Z= 0.250 Chirality : 0.037 0.135 1216 Planarity : 0.004 0.052 1270 Dihedral : 5.474 54.036 1667 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.78 % Allowed : 13.07 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 896 helix: 1.29 (0.27), residues: 405 sheet: -0.14 (0.36), residues: 183 loop : 0.63 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.010 0.001 PHE A 212 TYR 0.008 0.001 TYR A 329 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8900 (tp) cc_final: 0.8668 (mt) REVERT: B 234 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: R 156 MET cc_start: 0.7620 (tpt) cc_final: 0.7185 (tpt) REVERT: R 250 ARG cc_start: 0.7243 (mtm110) cc_final: 0.6938 (mtp180) outliers start: 14 outliers final: 11 residues processed: 133 average time/residue: 0.5388 time to fit residues: 91.4617 Evaluate side-chains 135 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.0010 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7724 Z= 0.133 Angle : 0.444 4.439 10518 Z= 0.237 Chirality : 0.037 0.152 1216 Planarity : 0.004 0.061 1270 Dihedral : 5.186 56.023 1667 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.52 % Allowed : 13.58 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.28), residues: 896 helix: 1.30 (0.27), residues: 411 sheet: 0.16 (0.38), residues: 169 loop : 0.51 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.008 0.001 TYR A 329 ARG 0.011 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8942 (tp) cc_final: 0.8645 (mt) REVERT: A 329 TYR cc_start: 0.8296 (m-80) cc_final: 0.8095 (m-80) REVERT: B 234 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: R 156 MET cc_start: 0.7515 (tpt) cc_final: 0.7147 (tpt) REVERT: R 250 ARG cc_start: 0.7245 (mtm110) cc_final: 0.6943 (mtp180) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 0.5233 time to fit residues: 90.9975 Evaluate side-chains 133 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 11 GLN Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7724 Z= 0.171 Angle : 0.461 4.786 10518 Z= 0.247 Chirality : 0.037 0.142 1216 Planarity : 0.004 0.063 1270 Dihedral : 5.212 54.850 1667 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.52 % Allowed : 14.59 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 896 helix: 1.33 (0.27), residues: 410 sheet: 0.22 (0.39), residues: 169 loop : 0.53 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.009 0.001 TYR A 329 ARG 0.012 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8956 (tp) cc_final: 0.8658 (mt) REVERT: B 234 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.7691 (m-80) REVERT: R 156 MET cc_start: 0.7556 (tpt) cc_final: 0.7162 (tpt) REVERT: R 250 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6950 (mtp180) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.5444 time to fit residues: 90.5099 Evaluate side-chains 133 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7724 Z= 0.266 Angle : 0.502 6.758 10518 Z= 0.267 Chirality : 0.038 0.154 1216 Planarity : 0.004 0.071 1270 Dihedral : 5.593 53.239 1667 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.78 % Allowed : 13.83 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.28), residues: 896 helix: 1.19 (0.27), residues: 411 sheet: -0.01 (0.38), residues: 175 loop : 0.55 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR B 105 ARG 0.013 0.001 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.8980 (tp) cc_final: 0.8685 (mt) REVERT: B 234 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: R 67 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6288 (ptp90) REVERT: R 156 MET cc_start: 0.7704 (tpt) cc_final: 0.7316 (tpt) REVERT: R 250 ARG cc_start: 0.7269 (mtm110) cc_final: 0.6958 (mtp180) outliers start: 14 outliers final: 12 residues processed: 131 average time/residue: 0.5353 time to fit residues: 89.0083 Evaluate side-chains 134 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain R residue 65 ILE Chi-restraints excluded: chain R residue 67 ARG Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 228 SER Chi-restraints excluded: chain R residue 260 SER Chi-restraints excluded: chain R residue 318 MET Chi-restraints excluded: chain R residue 361 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.136363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097962 restraints weight = 27860.487| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.57 r_work: 0.2988 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7724 Z= 0.145 Angle : 0.457 4.418 10518 Z= 0.243 Chirality : 0.037 0.143 1216 Planarity : 0.004 0.067 1270 Dihedral : 5.184 55.791 1667 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.78 % Allowed : 13.96 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.29), residues: 896 helix: 1.38 (0.27), residues: 413 sheet: 0.19 (0.39), residues: 169 loop : 0.54 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.007 0.001 TYR A 329 ARG 0.012 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4026.37 seconds wall clock time: 71 minutes 25.76 seconds (4285.76 seconds total)