Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 02:51:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/07_2023/6x19_21993_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 843 atoms to isotropic. 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 62 5.16 5 C 6462 2.51 5 N 1748 2.21 5 O 2003 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10277 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2876 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3268 Unusual residues: {'UK1': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 372, None: 1} Not linked: pdbres="GLU R 423 " pdbres="UK1 R 501 " Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 4.45, per 1000 atoms: 0.43 Number of scatterers: 10277 At special positions: 0 Unit cell: (115.37, 96.28, 170.15, 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 62 16.00 F 2 9.00 O 2003 8.00 N 1748 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.01 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: 7.36 Conformation dependent library (CDL) restraints added in 3.4 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 11 sheets defined 41.3% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.990A pdb=" N GLN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 109 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.848A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (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: 3.548A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'R' and resid 32 through 52 removed outlier: 4.029A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 116 No H-bonds generated for 'chain 'R' and resid 114 through 116' Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 137 through 140 No H-bonds generated for 'chain 'R' and resid 137 through 140' Processing helix chain 'R' and resid 142 through 166 Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 175 through 207 Processing helix chain 'R' and resid 211 through 222 removed outlier: 5.074A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 262 through 274 removed outlier: 3.698A pdb=" N PHE R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 291 removed outlier: 3.686A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.504A pdb=" N VAL R 287 " --> pdb=" O TRP R 284 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 337 removed outlier: 5.282A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.602A pdb=" N PHE R 315 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL R 319 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 322 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 327 " --> pdb=" O PHE R 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS R 336 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 369 Processing helix chain 'R' and resid 379 through 392 removed outlier: 3.691A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 402 Processing helix chain 'R' and resid 407 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.099A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.892A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.884A 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: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.555A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.738A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.342A 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: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.854A 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: 6.439A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.562A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 93 through 98 removed outlier: 5.970A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 80 through 83 451 hydrogen bonds defined for protein. 1149 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: 3.15 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1661 1.32 - 1.44: 2925 1.44 - 1.57: 5697 1.57 - 1.69: 11 1.69 - 1.82: 85 Bond restraints: 10379 Sorted by residual: bond pdb=" C03 UK1 R 501 " pdb=" N07 UK1 R 501 " ideal model delta sigma weight residual 1.478 1.722 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C46 UK1 R 501 " pdb=" C51 UK1 R 501 " ideal model delta sigma weight residual 1.390 1.546 -0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C28 UK1 R 501 " pdb=" C60 UK1 R 501 " ideal model delta sigma weight residual 1.524 1.674 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C46 UK1 R 501 " pdb=" N43 UK1 R 501 " ideal model delta sigma weight residual 1.481 1.628 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C25 UK1 R 501 " pdb=" N24 UK1 R 501 " ideal model delta sigma weight residual 1.384 1.516 -0.132 2.00e-02 2.50e+03 4.39e+01 ... (remaining 10374 not shown) Histogram of bond angle deviations from ideal: 70.00 - 83.47: 1 83.47 - 96.94: 0 96.94 - 110.41: 2475 110.41 - 123.87: 11019 123.87 - 137.34: 591 Bond angle restraints: 14086 Sorted by residual: angle pdb=" C21 UK1 R 501 " pdb=" C23 UK1 R 501 " pdb=" C27 UK1 R 501 " ideal model delta sigma weight residual 62.25 125.89 -63.64 3.00e+00 1.11e-01 4.50e+02 angle pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C58 UK1 R 501 " ideal model delta sigma weight residual 109.49 70.00 39.49 3.00e+00 1.11e-01 1.73e+02 angle pdb=" N PRO A 115 " pdb=" CA PRO A 115 " pdb=" C PRO A 115 " ideal model delta sigma weight residual 110.70 99.23 11.47 1.22e+00 6.72e-01 8.83e+01 angle pdb=" C PHE A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta sigma weight residual 119.66 125.30 -5.64 7.30e-01 1.88e+00 5.96e+01 angle pdb=" N ASN A 14 " pdb=" CA ASN A 14 " pdb=" C ASN A 14 " ideal model delta sigma weight residual 113.41 105.34 8.07 1.22e+00 6.72e-01 4.37e+01 ... (remaining 14081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 5685 20.04 - 40.07: 389 40.07 - 60.11: 46 60.11 - 80.15: 21 80.15 - 100.18: 6 Dihedral angle restraints: 6147 sinusoidal: 2462 harmonic: 3685 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C ASN A 371 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ARG A 317 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " pdb=" CB ARG A 317 " ideal model delta harmonic sigma weight residual -122.60 -110.51 -12.09 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1275 0.090 - 0.179: 200 0.179 - 0.269: 45 0.269 - 0.358: 17 0.358 - 0.448: 5 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ASP R 293 " pdb=" N ASP R 293 " pdb=" C ASP R 293 " pdb=" CB ASP R 293 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C60 UK1 R 501 " pdb=" N24 UK1 R 501 " both_signs ideal model delta sigma weight residual False -2.64 -2.20 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA ASN A 371 " pdb=" N ASN A 371 " pdb=" C ASN A 371 " pdb=" CB ASN A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 1539 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 290 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C LEU R 290 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU R 290 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 291 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C TYR R 101 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR R 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG R 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 155 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU A 155 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU A 155 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 303 2.69 - 3.24: 10570 3.24 - 3.79: 16952 3.79 - 4.35: 24311 4.35 - 4.90: 37159 Nonbonded interactions: 89295 Sorted by model distance: nonbonded pdb=" OH TYR B 105 " pdb=" O HOH B 401 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASP A 141 " pdb=" CD PRO A 143 " model vdw 2.158 3.440 nonbonded pdb=" OE1 GLU A 392 " pdb=" O HOH A 401 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU A 209 " pdb=" O HOH A 402 " model vdw 2.244 2.440 nonbonded pdb=" N GLU A 145 " pdb=" OE1 GLU A 145 " model vdw 2.269 2.520 ... (remaining 89290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 5.970 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 26.710 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: