Starting phenix.real_space_refine on Sun May 19 16:32:01 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- run=minimization_global c_beta_restraints=False ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True resolution=3.8 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvn_32145.map" } resolution = 3.8 refinement { run = *minimization_global rigid_body local_grid_search morphing \ simulated_annealing adp occupancy nqh_flips } pdb_interpretation { c_beta_restraints = False ramachandran_plot_restraints { enabled = False } } 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 C 5549 2.51 5 N 1528 2.21 5 O 1595 1.98 5 H 8610 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 443": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 17338 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3832 Inner-chain residues flagged as termini: ['pdbres="ILE A 62 "', 'pdbres="GLY A 206 "'] Classifications: {'peptide': 230} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5107 Classifications: {'peptide': 338} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 874 Classifications: {'peptide': 56} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1912 Classifications: {'peptide': 128} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 578 Classifications: {'peptide': 34} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 5035 Inner-chain residues flagged as termini: ['pdbres="GLU R 49 "', 'pdbres="GLU R 111 "', 'pdbres="CYS R 117 "', 'pdbres="VAL R 129 "', 'pdbres="ILE R 135 "', 'pdbres="PHE R 138 "', 'pdbres="ARG R 146 "', 'pdbres="ARG R 162 "', 'pdbres="LEU R 174 "', 'pdbres="ARG R 181 "', 'pdbres="LEU R 244 "', 'pdbres="TYR R 278 "', 'pdbres="TRP R 352 "', 'pdbres="TRP R 361 "', 'pdbres="THR R 392 "', 'pdbres="ARG R 400 "', 'pdbres="THR R 430 "', 'pdbres="LEU R 436 "'] Classifications: {'peptide': 300} Modifications used: {'COO': 10, 'NH3': 10} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 9 Time building chain proxies: 5.09, per 1000 atoms: 0.29 Number of scatterers: 17338 At special positions: 0 Unit cell: (123.947, 108.454, 117.307, 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 56 16.00 O 1595 8.00 N 1528 7.00 C 5549 6.00 H 8610 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 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 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.02 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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: 9.64 Conformation dependent library (CDL) restraints added in 995.7 milliseconds Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 37.2% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.601A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 253 through 268 removed outlier: 3.819A pdb=" N GLN A 257 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLU A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 removed outlier: 3.653A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) 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 307 Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.799A pdb=" N ALA A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 381 removed outlier: 3.579A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.675A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (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 8 through 24 removed outlier: 3.725A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 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 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 3 through 14 Processing helix chain 'P' and resid 19 through 33 removed outlier: 3.823A pdb=" N GLU P 22 " --> pdb=" O GLU P 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 48 Processing helix chain 'R' and resid 182 through 210 removed outlier: 3.559A pdb=" N LEU R 187 " --> pdb=" O PHE R 184 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET R 189 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR R 191 " --> pdb=" O GLY R 188 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR R 192 " --> pdb=" O MET R 189 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL R 193 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR R 195 " --> pdb=" O THR R 192 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER R 198 " --> pdb=" O TYR R 195 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU R 199 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA R 200 " --> pdb=" O VAL R 197 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL R 206 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU R 207 " --> pdb=" O VAL R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 243 removed outlier: 5.635A pdb=" N MET R 224 " --> pdb=" O ASN R 220 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS R 225 " --> pdb=" O TYR R 221 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 306 removed outlier: 3.791A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 311 No H-bonds generated for 'chain 'R' and resid 308 through 311' Processing helix chain 'R' and resid 322 through 325 No H-bonds generated for 'chain 'R' and resid 322 through 325' Processing helix chain 'R' and resid 330 through 345 removed outlier: 3.828A pdb=" N VAL R 338 " --> pdb=" O VAL R 334 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TRP R 339 " --> pdb=" O PHE R 335 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER R 341 " --> pdb=" O ALA R 337 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL R 342 " --> pdb=" O VAL R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 378 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 382 through 390 removed outlier: 3.683A pdb=" N ARG R 390 " --> pdb=" O ALA R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 412 removed outlier: 3.710A pdb=" N VAL R 412 " --> pdb=" O LYS R 408 " (cutoff:3.500A) Processing helix chain 'R' and resid 419 through 425 removed outlier: 4.005A pdb=" N VAL R 423 " --> pdb=" O HIS R 420 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N MET R 425 " --> pdb=" O ILE R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 437 through 453 removed outlier: 3.698A pdb=" N GLU R 444 " --> pdb=" O GLN R 440 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 460 Processing helix chain 'R' and resid 464 through 479 removed outlier: 3.564A pdb=" N LYS R 472 " --> pdb=" O ALA R 468 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER R 475 " --> pdb=" O LYS R 471 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 276 through 282 removed outlier: 3.787A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.842A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 122 through 125 Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.722A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.063A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= G, first strand: chain 'B' and resid 327 through 329 Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.571A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.925A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.975A pdb=" N TRP N 36 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 71 through 73 removed outlier: 3.674A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 822 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: 5.73 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 8590 1.16 - 1.34: 2860 1.34 - 1.52: 3548 1.52 - 1.70: 2447 1.70 - 1.89: 80 Bond restraints: 17525 Sorted by residual: bond pdb=" NE ARG R 282 " pdb=" HE ARG R 282 " ideal model delta sigma weight residual 0.860 1.042 -0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" NH2 ARG R 181 " pdb="HH21 ARG R 181 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.23e+01 bond pdb=" N ALA R 426 " pdb=" H ALA R 426 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" N PHE R 424 " pdb=" H PHE R 424 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" N PHE R 315 " pdb=" H PHE R 315 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.89e+01 ... (remaining 17520 not shown) Histogram of bond angle deviations from ideal: 96.44 - 104.04: 82 104.04 - 111.64: 19081 111.64 - 119.24: 4624 119.24 - 126.84: 7576 126.84 - 134.44: 135 Bond angle restraints: 31498 Sorted by residual: angle pdb=" N VAL R 455 " pdb=" CA VAL R 455 " pdb=" C VAL R 455 " ideal model delta sigma weight residual 112.12 106.28 5.84 8.40e-01 1.42e+00 4.83e+01 angle pdb=" N ILE R 222 " pdb=" CA ILE R 222 " pdb=" C ILE R 222 " ideal model delta sigma weight residual 112.12 107.41 4.71 8.40e-01 1.42e+00 3.14e+01 angle pdb=" C GLN R 47 " pdb=" N CYS R 48 " pdb=" CA CYS R 48 " ideal model delta sigma weight residual 122.38 114.15 8.23 1.81e+00 3.05e-01 2.07e+01 angle pdb=" C ALA R 347 " pdb=" N ASN R 348 " pdb=" CA ASN R 348 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" C GLU R 317 " pdb=" N LYS R 318 " pdb=" CA LYS R 318 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.38e+00 ... (remaining 31493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5404 17.93 - 35.86: 559 35.86 - 53.79: 168 53.79 - 71.72: 40 71.72 - 89.65: 8 Dihedral angle restraints: 6179 sinusoidal: 4377 harmonic: 1802 Sorted by residual: dihedral pdb=" CA ASN R 220 " pdb=" C ASN R 220 " pdb=" N TYR R 221 " pdb=" CA TYR R 221 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+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 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA TYR R 421 " pdb=" C TYR R 421 " pdb=" N ILE R 422 " pdb=" CA ILE R 422 " ideal model delta harmonic sigma weight residual -180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 847 0.032 - 0.065: 346 0.065 - 0.097: 86 0.097 - 0.129: 41 0.129 - 0.161: 8 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1325 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 343 " 0.200 9.50e-02 1.11e+02 8.21e-02 5.39e+00 pdb=" NE ARG R 343 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG R 343 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG R 343 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG R 343 " 0.004 2.00e-02 2.50e+03 pdb="HH21 ARG R 343 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 315 " 0.018 2.00e-02 2.50e+03 1.13e-02 3.82e+00 pdb=" CG PHE R 315 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE R 315 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE R 315 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE R 315 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE R 315 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 315 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE R 315 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE R 315 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE R 315 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE R 315 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE R 315 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 48 " 0.011 2.00e-02 2.50e+03 1.84e-02 3.38e+00 pdb=" N GLU R 49 " -0.032 2.00e-02 2.50e+03 pdb=" CA GLU R 49 " 0.008 2.00e-02 2.50e+03 pdb=" H GLU R 49 " 0.013 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 952 2.08 - 2.71: 26754 2.71 - 3.34: 49952 3.34 - 3.97: 66527 3.97 - 4.60: 98189 Nonbonded interactions: 242374 Sorted by model distance: nonbonded pdb=" O GLN B 75 " pdb=" HG SER B 98 " model vdw 1.452 1.850 nonbonded pdb=" HG1 THR B 29 " pdb=" OE1 GLN B 32 " model vdw 1.459 1.850 nonbonded pdb=" O SER N 30 " pdb="HE22 GLN N 53 " model vdw 1.459 1.850 nonbonded pdb=" O VAL R 326 " pdb=" H GLY R 330 " model vdw 1.497 1.850 nonbonded pdb=" O VAL R 384 " pdb=" HG1 THR R 387 " model vdw 1.533 1.850 ... (remaining 242369 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: 5 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.47 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will not be refined 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: 0.030 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: 0.180 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.080 Process input model: 32.900 Find NCS groups from input model: 0.200 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:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:25.270 Internal consistency checks: 0.000 Total: 58.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 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 0.078 8915 Z= 0.237 Angle : 0.641 8.231 12061 Z= 0.362 Chirality : 0.041 0.161 1328 Planarity : 0.005 0.088 1539 Dihedral : 13.845 86.012 3220 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.26 % Favored : 93.55 % Rotamer: Outliers : 1.28 % Allowed : 7.58 % Favored : 91.14 % 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: -2.89 (0.22), residues: 1054 helix: -1.78 (0.21), residues: 410 sheet: -1.87 (0.35), residues: 192 loop : -1.90 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 343 TYR 0.017 0.001 TYR R 421 PHE 0.028 0.002 PHE R 315 TRP 0.027 0.002 TRP R 352 HIS 0.005 0.001 HIS R 140 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8915 Z= 0.354 Angle : 0.673 6.699 12061 Z= 0.374 Chirality : 0.056 0.315 1328 Planarity : 0.005 0.053 1539 Dihedral : 13.257 86.690 3220 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.76 % Allowed : 10.06 % Favored : 89.18 % Rotamer: Outliers : 1.28 % Allowed : 8.54 % Favored : 90.18 % 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: -4.10 (0.21), residues: 1054 helix: -2.58 (0.20), residues: 404 sheet: -2.32 (0.34), residues: 203 loop : -2.89 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 68 TYR 0.022 0.002 TYR G 40 PHE 0.027 0.002 PHE R 454 TRP 0.024 0.002 TRP R 352 HIS 0.004 0.001 HIS A 347 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 overall best weight: 9.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 8915 Z= 0.461 Angle : 0.714 7.246 12061 Z= 0.394 Chirality : 0.062 0.410 1328 Planarity : 0.005 0.069 1539 Dihedral : 14.608 88.777 3220 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 2.94 % Allowed : 14.42 % Favored : 82.64 % Rotamer: Outliers : 3.20 % Allowed : 10.89 % Favored : 85.91 % Cbeta Deviations : 0.10 % 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: -5.13 (0.20), residues: 1054 helix: -3.19 (0.18), residues: 406 sheet: -3.26 (0.32), residues: 201 loop : -3.54 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.019 0.002 TYR N 95 PHE 0.026 0.002 PHE R 454 TRP 0.021 0.003 TRP R 352 HIS 0.006 0.001 HIS R 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8915 Z= 0.350 Angle : 0.638 6.601 12061 Z= 0.353 Chirality : 0.056 0.320 1328 Planarity : 0.005 0.056 1539 Dihedral : 14.543 97.098 3220 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 3.13 % Allowed : 13.47 % Favored : 83.40 % Rotamer: Outliers : 4.38 % Allowed : 10.89 % 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: -5.11 (0.20), residues: 1054 helix: -3.20 (0.18), residues: 405 sheet: -3.02 (0.33), residues: 213 loop : -3.61 (0.24), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.017 0.002 TYR N 95 PHE 0.019 0.002 PHE R 454 TRP 0.014 0.002 TRP A 271 HIS 0.004 0.001 HIS A 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 overall best weight: 9.5998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8915 Z= 0.446 Angle : 0.710 7.037 12061 Z= 0.393 Chirality : 0.060 0.364 1328 Planarity : 0.006 0.071 1539 Dihedral : 15.243 106.013 3220 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 4.08 % Allowed : 16.41 % Favored : 79.51 % Rotamer: Outliers : 5.44 % Allowed : 12.91 % Favored : 81.64 % 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: -5.54 (0.20), residues: 1054 helix: -3.35 (0.18), residues: 392 sheet: -3.41 (0.30), residues: 222 loop : -4.00 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 256 TYR 0.019 0.002 TYR N 95 PHE 0.021 0.002 PHE R 454 TRP 0.019 0.003 TRP R 352 HIS 0.005 0.001 HIS A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 overall best weight: 8.9994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8915 Z= 0.380 Angle : 0.652 6.314 12061 Z= 0.360 Chirality : 0.056 0.331 1328 Planarity : 0.005 0.051 1539 Dihedral : 15.389 97.981 3220 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 3.32 % Allowed : 16.51 % Favored : 80.17 % Rotamer: Outliers : 6.72 % Allowed : 12.38 % Favored : 80.90 % 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: -5.61 (0.20), residues: 1054 helix: -3.40 (0.18), residues: 400 sheet: -3.21 (0.32), residues: 206 loop : -4.19 (0.22), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 256 TYR 0.018 0.002 TYR N 95 PHE 0.020 0.002 PHE B 199 TRP 0.016 0.002 TRP R 352 HIS 0.004 0.001 HIS A 347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 391.68 seconds wall clock time: 7 minutes 37.70 seconds (457.70 seconds total)