Starting phenix.real_space_refine on Sun May 19 16:32:00 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.map Found model, /net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.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=3.3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.pdb" real_map_files = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.map" default_real_map = "/net/anaconda/raid1/afonine/work/ANI/result/cryoem/regularized/7vvk_32142.map" } resolution = 3.3 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= 0.010 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 58 5.16 5 C 5720 2.51 5 N 1576 2.21 5 O 1655 1.98 5 H 8871 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 "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 403": "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: 17880 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3835 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: 5140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5140 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 864 Classifications: {'peptide': 55} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 580 Classifications: {'peptide': 34} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 5549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 5549 Inner-chain residues flagged as termini: ['pdbres="GLU R 49 "', 'pdbres="GLU R 111 "', 'pdbres="TRP R 118 "', 'pdbres="VAL R 127 "', 'pdbres="VAL R 157 "', 'pdbres="THR R 163 "', 'pdbres="LEU R 174 "', 'pdbres="ARG R 179 "', 'pdbres="SER R 246 "', 'pdbres="TYR R 278 "', 'pdbres="THR R 392 "', 'pdbres="ASP R 398 "'] Classifications: {'peptide': 334} Modifications used: {'COO': 7, 'NH3': 7} Link IDs: {'PTRANS': 6, 'TRANS': 327} Chain breaks: 6 Time building chain proxies: 5.19, per 1000 atoms: 0.29 Number of scatterers: 17880 At special positions: 0 Unit cell: (129.48, 101.814, 129.48, 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 58 16.00 O 1655 8.00 N 1576 7.00 C 5720 6.00 H 8871 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 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=2.05 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: 8.42 Conformation dependent library (CDL) restraints added in 978.5 milliseconds Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 38.8% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.676A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.557A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 284 through 293 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 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.616A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 380 Processing helix chain 'B' and resid 2 through 24 removed outlier: 4.005A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (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 9 through 23 removed outlier: 3.630A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.857A pdb=" N ALA G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ALA G 35 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR G 40 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS G 41 " --> pdb=" O MET G 38 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS G 44 " --> pdb=" O CYS G 41 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS G 46 " --> pdb=" O ALA G 43 " (cutoff:3.500A) 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 33 Processing helix chain 'R' and resid 34 through 48 Processing helix chain 'R' and resid 170 through 173 removed outlier: 5.266A pdb=" N PHE R 173 " --> pdb=" O CYS R 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 170 through 173' Processing helix chain 'R' and resid 180 through 211 removed outlier: 3.880A pdb=" N PHE R 184 " --> pdb=" O ARG R 181 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP R 185 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY R 188 " --> pdb=" O ASP R 185 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET R 189 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N TYR R 191 " --> pdb=" O GLY R 188 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL R 193 " --> pdb=" O ILE R 190 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR R 195 " --> pdb=" O THR R 192 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL R 197 " --> pdb=" O GLY R 194 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER R 201 " --> pdb=" O SER R 198 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU R 202 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR R 203 " --> pdb=" O ALA R 200 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL R 206 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR R 211 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 215 No H-bonds generated for 'chain 'R' and resid 213 through 215' Processing helix chain 'R' and resid 218 through 245 removed outlier: 3.829A pdb=" N ILE R 237 " --> pdb=" O ARG R 233 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE R 238 " --> pdb=" O ALA R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 311 removed outlier: 4.019A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE R 310 " --> pdb=" O LEU R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 330 Processing helix chain 'R' and resid 332 through 345 Processing helix chain 'R' and resid 357 through 391 removed outlier: 3.608A pdb=" N ILE R 362 " --> pdb=" O LYS R 359 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE R 363 " --> pdb=" O LYS R 360 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN R 364 " --> pdb=" O TRP R 361 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL R 365 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 4.265A pdb=" N VAL R 372 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU R 373 " --> pdb=" O SER R 370 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASN R 374 " --> pdb=" O ILE R 371 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE R 381 " --> pdb=" O PHE R 378 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU R 385 " --> pdb=" O VAL R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 399 through 417 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 421 through 423 No H-bonds generated for 'chain 'R' and resid 421 through 423' Processing helix chain 'R' and resid 435 through 460 removed outlier: 4.219A pdb=" N PHE R 450 " --> pdb=" O LEU R 446 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 477 removed outlier: 3.538A pdb=" N GLU R 469 " --> pdb=" O GLU R 465 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 276 through 282 removed outlier: 3.807A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.985A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.168A 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: 6.967A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 158 through 160 removed outlier: 6.539A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.986A 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: 7.068A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.271A 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: 6.876A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.893A 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: 6.604A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.195A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 128 through 130 380 hydrogen bonds defined for protein. 966 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: 5.38 Time building geometry restraints manager: 8.30 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: 8848 1.16 - 1.34: 2954 1.34 - 1.52: 3213 1.52 - 1.70: 2978 1.70 - 1.88: 83 Bond restraints: 18076 Sorted by residual: bond pdb=" N TRP R 118 " pdb=" H TRP R 118 " ideal model delta sigma weight residual 0.860 1.030 -0.170 2.00e-02 2.50e+03 7.27e+01 bond pdb=" N GLU P 19 " pdb=" H GLU P 19 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.17e+01 bond pdb=" NE1 TRP R 112 " pdb=" HE1 TRP R 112 " ideal model delta sigma weight residual 0.860 1.029 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" N LYS P 13 " pdb=" H LYS P 13 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" N TRP R 474 " pdb=" H TRP R 474 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.77e+01 ... (remaining 18071 not shown) Histogram of bond angle deviations from ideal: 97.28 - 104.66: 89 104.66 - 112.04: 19948 112.04 - 119.42: 4652 119.42 - 126.80: 7644 126.80 - 134.18: 143 Bond angle restraints: 32476 Sorted by residual: angle pdb=" C GLN R 47 " pdb=" N CYS R 48 " pdb=" CA CYS R 48 " ideal model delta sigma weight residual 122.38 113.85 8.53 1.81e+00 3.05e-01 2.22e+01 angle pdb=" C GLU A 360 " pdb=" N ASN A 361 " pdb=" CA ASN A 361 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.98e+00 angle pdb=" CA GLU P 19 " pdb=" C GLU P 19 " pdb=" O GLU P 19 " ideal model delta sigma weight residual 120.90 118.12 2.78 1.03e+00 9.43e-01 7.29e+00 angle pdb=" CA LYS R 34 " pdb=" CB LYS R 34 " pdb=" CG LYS R 34 " ideal model delta sigma weight residual 114.10 119.48 -5.38 2.00e+00 2.50e-01 7.24e+00 angle pdb=" N LEU R 116 " pdb=" CA LEU R 116 " pdb=" C LEU R 116 " ideal model delta sigma weight residual 109.07 113.03 -3.96 1.52e+00 4.33e-01 6.79e+00 ... (remaining 32471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5688 17.62 - 35.23: 475 35.23 - 52.84: 173 52.84 - 70.46: 40 70.46 - 88.07: 8 Dihedral angle restraints: 6384 sinusoidal: 4516 harmonic: 1868 Sorted by residual: dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 130.88 -37.88 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" CB CYS R 48 " pdb=" SG CYS R 48 " pdb=" SG CYS R 117 " pdb=" CB CYS R 117 " ideal model delta sinusoidal sigma weight residual 93.00 60.68 32.32 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" CA CYS R 131 " pdb=" C CYS R 131 " pdb=" N PRO R 132 " pdb=" CA PRO R 132 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 6381 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1003 0.040 - 0.079: 270 0.079 - 0.119: 71 0.119 - 0.158: 21 0.158 - 0.197: 2 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CB VAL P 31 " pdb=" CA VAL P 31 " pdb=" CG1 VAL P 31 " pdb=" CG2 VAL P 31 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ILE A 245 " pdb=" N ILE A 245 " pdb=" C ILE A 245 " pdb=" CB ILE A 245 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ILE N 51 " pdb=" N ILE N 51 " pdb=" C ILE N 51 " pdb=" CB ILE N 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 1364 not shown) Planarity restraints: 2672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP P 23 " 0.016 2.00e-02 2.50e+03 7.07e-03 2.00e+00 pdb=" CG TRP P 23 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP P 23 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP P 23 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP P 23 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP P 23 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 23 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP P 23 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP P 23 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP P 23 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP P 23 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 23 " 0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 23 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP P 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 365 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO R 366 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 366 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 366 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU P 24 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C LEU P 24 " -0.022 2.00e-02 2.50e+03 pdb=" O LEU P 24 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG P 25 " 0.008 2.00e-02 2.50e+03 ... (remaining 2669 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1239 2.13 - 2.75: 31026 2.75 - 3.37: 50928 3.37 - 3.98: 69744 3.98 - 4.60: 102697 Nonbonded interactions: 255634 Sorted by model distance: nonbonded pdb=" OE1 GLN N 123 " pdb=" HG1 THR N 125 " model vdw 1.516 1.850 nonbonded pdb=" HH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 1.523 1.850 nonbonded pdb=" HE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 1.545 1.850 nonbonded pdb="HE22 GLN R 364 " pdb=" OH TYR R 429 " model vdw 1.560 1.850 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.564 1.850 ... (remaining 255629 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=0.48 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.080 Process input model: 34.000 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:24.980 Internal consistency checks: 0.000 Total: 59.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 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 : 0.003 0.072 9205 Z= 0.204 Angle : 0.576 8.528 12457 Z= 0.323 Chirality : 0.041 0.197 1367 Planarity : 0.004 0.032 1591 Dihedral : 12.814 88.074 3326 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.46 % Allowed : 4.66 % Favored : 94.89 % Rotamer: Outliers : 1.03 % Allowed : 4.12 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1095 helix: -1.21 (0.22), residues: 434 sheet: -0.66 (0.35), residues: 216 loop : -1.06 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 146 TYR 0.010 0.001 TYR A 329 PHE 0.018 0.001 PHE R 335 TRP 0.015 0.001 TRP P 23 HIS 0.007 0.001 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 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: 5.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9205 Z= 0.340 Angle : 0.649 5.678 12457 Z= 0.360 Chirality : 0.060 0.272 1367 Planarity : 0.006 0.058 1591 Dihedral : 12.680 84.497 3326 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.91 % Allowed : 9.22 % Favored : 89.86 % Rotamer: Outliers : 1.13 % Allowed : 5.26 % Favored : 93.61 % 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: -3.52 (0.21), residues: 1095 helix: -2.35 (0.19), residues: 432 sheet: -1.76 (0.32), residues: 221 loop : -2.43 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 146 TYR 0.013 0.002 TYR N 94 PHE 0.015 0.002 PHE A 212 TRP 0.022 0.002 TRP R 298 HIS 0.007 0.002 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9205 Z= 0.482 Angle : 0.776 7.326 12457 Z= 0.431 Chirality : 0.066 0.277 1367 Planarity : 0.007 0.079 1591 Dihedral : 14.542 88.300 3326 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 3.56 % Allowed : 15.62 % Favored : 80.82 % Rotamer: Outliers : 4.74 % Allowed : 10.21 % Favored : 85.05 % 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: -5.06 (0.19), residues: 1095 helix: -3.13 (0.17), residues: 416 sheet: -2.36 (0.33), residues: 205 loop : -3.98 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 404 TYR 0.014 0.003 TYR N 80 PHE 0.018 0.003 PHE R 327 TRP 0.023 0.003 TRP R 298 HIS 0.008 0.002 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9205 Z= 0.337 Angle : 0.618 5.764 12457 Z= 0.343 Chirality : 0.059 0.241 1367 Planarity : 0.006 0.052 1591 Dihedral : 14.153 86.044 3326 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 2.37 % Allowed : 12.69 % Favored : 84.93 % Rotamer: Outliers : 4.12 % Allowed : 10.41 % Favored : 85.46 % 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: -4.59 (0.20), residues: 1095 helix: -2.62 (0.20), residues: 412 sheet: -2.50 (0.30), residues: 224 loop : -3.65 (0.22), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 404 TYR 0.017 0.002 TYR R 191 PHE 0.017 0.002 PHE R 327 TRP 0.017 0.002 TRP R 298 HIS 0.006 0.001 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 9205 Z= 0.457 Angle : 0.766 6.732 12457 Z= 0.425 Chirality : 0.066 0.269 1367 Planarity : 0.007 0.070 1591 Dihedral : 15.231 85.919 3326 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 4.20 % Allowed : 16.35 % Favored : 79.45 % Rotamer: Outliers : 6.39 % Allowed : 12.37 % Favored : 81.24 % 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: -5.20 (0.19), residues: 1095 helix: -3.12 (0.18), residues: 409 sheet: -2.73 (0.31), residues: 209 loop : -4.05 (0.21), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 404 TYR 0.018 0.003 TYR R 191 PHE 0.019 0.002 PHE R 327 TRP 0.025 0.003 TRP R 298 HIS 0.006 0.002 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 9205 Z= 0.436 Angle : 0.694 6.857 12457 Z= 0.385 Chirality : 0.062 0.282 1367 Planarity : 0.006 0.061 1591 Dihedral : 15.287 88.740 3326 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 3.38 % Allowed : 15.25 % Favored : 81.37 % Rotamer: Outliers : 6.80 % Allowed : 12.78 % Favored : 80.41 % 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: -5.00 (0.20), residues: 1095 helix: -2.93 (0.20), residues: 408 sheet: -2.76 (0.30), residues: 222 loop : -3.89 (0.22), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 404 TYR 0.021 0.002 TYR R 191 PHE 0.019 0.002 PHE R 327 TRP 0.020 0.002 TRP R 298 HIS 0.006 0.002 HIS P 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 397.81 seconds wall clock time: 7 minutes 40.18 seconds (460.18 seconds total)