Starting phenix.real_space_refine on Sun May 19 16:30:35 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+local_grid_search+nqh_flips 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 } 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: 0.01s 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: 2.82, per 1000 atoms: 0.16 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: 4.38 Conformation dependent library (CDL) restraints added in 541.6 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 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: 0.44 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: 3.19 Time building geometry restraints manager: 4.93 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 - 17.61: 7800 17.61 - 35.23: 475 35.23 - 52.84: 173 52.84 - 70.46: 40 70.46 - 88.07: 8 Dihedral angle restraints: 8496 sinusoidal: 4516 harmonic: 3980 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 8493 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: 0.030 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: 0.090 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 20.870 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:0.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:15.250 Internal consistency checks: 0.000 Total: 37.330 ------------------------------------------------------------------------------- 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 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 248 time to evaluate : 0.547 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: 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 24 LYS cc_start: 0.6995 (tmmt) cc_final: 0.6774 (tptt) REVERT: A 42 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7648 (mtm110) REVERT: A 59 GLN cc_start: 0.7091 (mt0) cc_final: 0.6677 (tp40) REVERT: A 253 TYR cc_start: 0.7752 (m-80) cc_final: 0.7477 (m-80) REVERT: A 255 ARG cc_start: 0.6839 (mtp-110) cc_final: 0.6563 (mtp180) REVERT: A 290 LYS cc_start: 0.7011 (ttmm) cc_final: 0.6789 (tttt) REVERT: A 337 ARG cc_start: 0.7038 (tmt-80) cc_final: 0.6647 (ttm-80) REVERT: B 13 GLN cc_start: 0.6295 (tm-30) cc_final: 0.6089 (tp40) REVERT: B 152 LEU cc_start: 0.8064 (mt) cc_final: 0.7775 (mp) REVERT: B 205 ASP cc_start: 0.7485 (p0) cc_final: 0.7207 (p0) REVERT: B 239 ASN cc_start: 0.8022 (m-40) cc_final: 0.7718 (m-40) REVERT: B 277 SER cc_start: 0.8603 (m) cc_final: 0.8379 (p) REVERT: B 322 ASP cc_start: 0.7104 (m-30) cc_final: 0.6746 (m-30) REVERT: N 46 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7954 (mt-10) REVERT: N 80 TYR cc_start: 0.7799 (m-80) cc_final: 0.7437 (m-80) REVERT: N 85 SER cc_start: 0.7342 (t) cc_final: 0.7091 (m) REVERT: N 105 ARG cc_start: 0.6252 (mmt-90) cc_final: 0.5519 (mtp180) REVERT: N 106 ASP cc_start: 0.6538 (p0) cc_final: 0.6336 (p0) REVERT: N 109 ASP cc_start: 0.6948 (m-30) cc_final: 0.6601 (m-30) REVERT: N 117 TYR cc_start: 0.7132 (m-80) cc_final: 0.6634 (m-80) REVERT: P 34 PHE cc_start: 0.5545 (m-80) cc_final: 0.5290 (m-80) REVERT: R 114 HIS cc_start: 0.6747 (m-70) cc_final: 0.6442 (t70) REVERT: R 224 MET cc_start: 0.6974 (mmm) cc_final: 0.6519 (ttm) REVERT: R 311 PHE cc_start: 0.6938 (m-80) cc_final: 0.6721 (m-80) REVERT: R 312 MET cc_start: 0.7204 (mmm) cc_final: 0.6624 (mtt) REVERT: R 335 PHE cc_start: 0.6223 (p90) cc_final: 0.5687 (p90) REVERT: R 362 ILE cc_start: 0.6992 (mm) cc_final: 0.6731 (mt) REVERT: R 474 TRP cc_start: 0.5968 (t60) cc_final: 0.5258 (t-100) outliers start: 10 outliers final: 3 residues processed: 254 average time/residue: 0.5233 time to fit residues: 171.9043 Evaluate side-chains 169 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain R residue 374 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 261 ASN B 32 GLN B 35 ASN B 44 GLN B 156 GLN N 5 GLN N 13 GLN R 37 GLN R 374 ASN R 440 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9205 Z= 0.351 Angle : 0.654 6.964 12457 Z= 0.361 Chirality : 0.045 0.161 1367 Planarity : 0.006 0.059 1591 Dihedral : 6.109 60.716 1245 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.16 % Allowed : 8.66 % Favored : 89.18 % 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: -1.37 (0.24), residues: 1095 helix: -0.66 (0.24), residues: 426 sheet: -1.02 (0.33), residues: 216 loop : -0.89 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 146 TYR 0.018 0.002 TYR R 297 PHE 0.020 0.002 PHE R 327 TRP 0.019 0.002 TRP R 298 HIS 0.008 0.002 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 0.761 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: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7985 (mtm-85) cc_final: 0.7715 (mtm110) REVERT: A 59 GLN cc_start: 0.7474 (mt0) cc_final: 0.6870 (tp40) REVERT: B 152 LEU cc_start: 0.8065 (mt) cc_final: 0.7712 (mp) REVERT: B 215 GLU cc_start: 0.6266 (tp30) cc_final: 0.5945 (mm-30) REVERT: B 336 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8022 (tt) REVERT: G 38 MET cc_start: 0.6262 (ttp) cc_final: 0.6031 (ttp) REVERT: N 7 SER cc_start: 0.6174 (t) cc_final: 0.5438 (p) REVERT: N 34 MET cc_start: 0.8026 (mmm) cc_final: 0.7618 (mmm) REVERT: N 38 ARG cc_start: 0.8082 (ptm-80) cc_final: 0.7806 (ptt180) REVERT: N 46 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7572 (mm-30) REVERT: N 85 SER cc_start: 0.7300 (t) cc_final: 0.6898 (m) REVERT: N 91 THR cc_start: 0.6687 (t) cc_final: 0.6196 (m) REVERT: N 105 ARG cc_start: 0.6415 (mmt-90) cc_final: 0.5556 (mtp180) REVERT: N 117 TYR cc_start: 0.7380 (m-80) cc_final: 0.6966 (m-80) REVERT: R 317 GLU cc_start: 0.6120 (pt0) cc_final: 0.5887 (pt0) REVERT: R 416 LEU cc_start: 0.8148 (tt) cc_final: 0.7888 (tp) REVERT: R 440 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7136 (pp30) REVERT: R 458 ILE cc_start: 0.6429 (mt) cc_final: 0.6130 (mm) REVERT: R 474 TRP cc_start: 0.5762 (t60) cc_final: 0.5097 (t-100) outliers start: 21 outliers final: 14 residues processed: 198 average time/residue: 0.3243 time to fit residues: 85.8875 Evaluate side-chains 170 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 154 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 414 MET Chi-restraints excluded: chain R residue 440 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 79 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 13 GLN P 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9205 Z= 0.254 Angle : 0.562 6.541 12457 Z= 0.311 Chirality : 0.042 0.155 1367 Planarity : 0.004 0.037 1591 Dihedral : 5.659 63.547 1240 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.55 % Allowed : 10.41 % Favored : 88.04 % 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: -1.18 (0.24), residues: 1095 helix: -0.29 (0.24), residues: 424 sheet: -1.04 (0.34), residues: 216 loop : -0.96 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 146 TYR 0.014 0.002 TYR R 297 PHE 0.017 0.002 PHE R 335 TRP 0.015 0.002 TRP R 298 HIS 0.007 0.002 HIS R 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.439 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: A 59 GLN cc_start: 0.7550 (mt0) cc_final: 0.6932 (tp40) REVERT: A 253 TYR cc_start: 0.7622 (m-80) cc_final: 0.7374 (m-80) REVERT: B 138 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7000 (pp20) REVERT: B 152 LEU cc_start: 0.8099 (mt) cc_final: 0.7744 (mp) REVERT: B 212 ASP cc_start: 0.7144 (t0) cc_final: 0.6914 (t0) REVERT: B 262 MET cc_start: 0.7607 (tpp) cc_final: 0.7329 (tpp) REVERT: G 38 MET cc_start: 0.6201 (ttp) cc_final: 0.5937 (ttp) REVERT: N 7 SER cc_start: 0.6093 (t) cc_final: 0.5463 (p) REVERT: N 34 MET cc_start: 0.8001 (mmm) cc_final: 0.7740 (mmm) REVERT: N 38 ARG cc_start: 0.7987 (ptm-80) cc_final: 0.7725 (ptt180) REVERT: N 46 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7656 (mm-30) REVERT: N 85 SER cc_start: 0.7335 (t) cc_final: 0.6947 (m) REVERT: N 91 THR cc_start: 0.6640 (t) cc_final: 0.6136 (m) REVERT: N 105 ARG cc_start: 0.6441 (mmt-90) cc_final: 0.5603 (mtp180) REVERT: N 117 TYR cc_start: 0.7277 (m-80) cc_final: 0.6859 (m-80) REVERT: R 414 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7158 (mtp) REVERT: R 416 LEU cc_start: 0.8168 (tt) cc_final: 0.7914 (tp) REVERT: R 474 TRP cc_start: 0.5926 (t60) cc_final: 0.5108 (t-100) outliers start: 15 outliers final: 13 residues processed: 167 average time/residue: 0.2445 time to fit residues: 55.2209 Evaluate side-chains 167 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 153 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 5 GLN R 440 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9205 Z= 0.275 Angle : 0.573 6.387 12457 Z= 0.315 Chirality : 0.042 0.151 1367 Planarity : 0.005 0.041 1591 Dihedral : 6.156 82.957 1239 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.47 % Allowed : 11.34 % Favored : 86.19 % 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: -1.16 (0.24), residues: 1095 helix: -0.06 (0.25), residues: 419 sheet: -1.08 (0.34), residues: 216 loop : -1.14 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 255 TYR 0.021 0.002 TYR R 297 PHE 0.017 0.002 PHE R 335 TRP 0.014 0.002 TRP R 298 HIS 0.005 0.002 HIS A 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.425 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: A 24 LYS cc_start: 0.7361 (tmmt) cc_final: 0.6941 (mptt) REVERT: A 59 GLN cc_start: 0.7551 (mt0) cc_final: 0.7010 (tp40) REVERT: A 336 LEU cc_start: 0.7897 (mt) cc_final: 0.7645 (mt) REVERT: B 212 ASP cc_start: 0.6955 (t0) cc_final: 0.6629 (t0) REVERT: B 219 ARG cc_start: 0.7623 (ptp-110) cc_final: 0.7039 (mtp180) REVERT: G 38 MET cc_start: 0.6294 (ttp) cc_final: 0.5980 (ttp) REVERT: N 7 SER cc_start: 0.5994 (t) cc_final: 0.5425 (p) REVERT: N 34 MET cc_start: 0.7921 (mmm) cc_final: 0.7484 (mmm) REVERT: N 38 ARG cc_start: 0.7980 (ptm-80) cc_final: 0.7734 (ptt180) REVERT: N 85 SER cc_start: 0.7431 (t) cc_final: 0.7033 (m) REVERT: N 105 ARG cc_start: 0.6526 (mmt-90) cc_final: 0.5833 (mtp180) REVERT: N 117 TYR cc_start: 0.7319 (m-80) cc_final: 0.6905 (m-80) REVERT: R 414 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7150 (mtp) REVERT: R 441 MET cc_start: 0.6747 (tpp) cc_final: 0.5428 (tpp) REVERT: R 474 TRP cc_start: 0.6132 (t60) cc_final: 0.5121 (t-100) outliers start: 24 outliers final: 19 residues processed: 173 average time/residue: 0.2361 time to fit residues: 55.1471 Evaluate side-chains 167 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 224 MET Chi-restraints excluded: chain R residue 246 SER Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 399 THR Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 60 optimal weight: 0.2980 chunk 71 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 81 optimal weight: 30.0000 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 257 GLN A 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9205 Z= 0.195 Angle : 0.513 6.022 12457 Z= 0.281 Chirality : 0.040 0.138 1367 Planarity : 0.004 0.036 1591 Dihedral : 5.930 82.513 1239 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.55 % Allowed : 12.27 % Favored : 86.19 % 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: -0.92 (0.24), residues: 1095 helix: 0.23 (0.25), residues: 419 sheet: -1.00 (0.34), residues: 216 loop : -1.09 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.014 0.001 TYR R 297 PHE 0.015 0.001 PHE R 335 TRP 0.012 0.001 TRP R 298 HIS 0.006 0.001 HIS P 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.381 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: A 24 LYS cc_start: 0.7313 (tmmt) cc_final: 0.6938 (mptt) REVERT: A 38 ARG cc_start: 0.7616 (mmt90) cc_final: 0.7358 (mtt-85) REVERT: A 59 GLN cc_start: 0.7559 (mt0) cc_final: 0.6944 (tp40) REVERT: A 358 ASP cc_start: 0.5663 (OUTLIER) cc_final: 0.5406 (t0) REVERT: B 152 LEU cc_start: 0.8059 (mt) cc_final: 0.7695 (mp) REVERT: B 212 ASP cc_start: 0.6822 (t0) cc_final: 0.6545 (t0) REVERT: B 219 ARG cc_start: 0.7663 (ptp-110) cc_final: 0.7069 (mtp180) REVERT: G 38 MET cc_start: 0.6187 (ttp) cc_final: 0.5938 (ttp) REVERT: N 7 SER cc_start: 0.6047 (t) cc_final: 0.5482 (p) REVERT: N 34 MET cc_start: 0.7943 (mmm) cc_final: 0.7699 (mmm) REVERT: N 38 ARG cc_start: 0.7932 (ptm-80) cc_final: 0.7712 (ptt180) REVERT: N 85 SER cc_start: 0.7397 (t) cc_final: 0.7040 (m) REVERT: N 105 ARG cc_start: 0.6417 (mmt-90) cc_final: 0.5777 (mtp180) REVERT: R 414 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7133 (mtp) REVERT: R 441 MET cc_start: 0.6789 (tpp) cc_final: 0.5537 (tpp) REVERT: R 474 TRP cc_start: 0.6178 (t60) cc_final: 0.5136 (t-100) outliers start: 15 outliers final: 13 residues processed: 162 average time/residue: 0.2253 time to fit residues: 48.3601 Evaluate side-chains 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 139 ASN Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 246 SER Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 414 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9205 Z= 0.180 Angle : 0.498 5.788 12457 Z= 0.272 Chirality : 0.040 0.136 1367 Planarity : 0.004 0.039 1591 Dihedral : 5.771 84.391 1239 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.44 % Allowed : 12.58 % Favored : 85.98 % 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: -0.75 (0.25), residues: 1095 helix: 0.46 (0.26), residues: 419 sheet: -1.02 (0.34), residues: 214 loop : -1.01 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.014 0.001 TYR R 297 PHE 0.015 0.001 PHE R 335 TRP 0.012 0.001 TRP R 298 HIS 0.006 0.001 HIS A 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1096.13 seconds wall clock time: 19 minutes 29.75 seconds (1169.75 seconds total)