Starting phenix.real_space_refine on Sat Apr 6 13:35:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/04_2024/8hmp_34902_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/04_2024/8hmp_34902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/04_2024/8hmp_34902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/04_2024/8hmp_34902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/04_2024/8hmp_34902_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hmp_34902/04_2024/8hmp_34902_updated.pdb" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 57 5.16 5 C 5294 2.51 5 N 1433 2.21 5 O 1532 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 291": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 36": "OD1" <-> "OD2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 87": "OD1" <-> "OD2" Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 138": "OD1" <-> "OD2" Residue "R ARG 157": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "R PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 191": "OE1" <-> "OE2" Residue "R PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 249": "OD1" <-> "OD2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8319 Number of models: 1 Model: "" Number of chains: 6 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: 2308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2308 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "A" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1980 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'EN6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.59 Number of scatterers: 8319 At special positions: 0 Unit cell: (94.8486, 94.2939, 125.355, 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 57 16.00 F 3 9.00 O 1532 8.00 N 1433 7.00 C 5294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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=2.04 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS R 40 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 193 " distance=2.02 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 10 sheets defined 36.6% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.447A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 32 through 43 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 42 through 67 removed outlier: 4.063A pdb=" N VAL R 46 " --> pdb=" O PHE R 42 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS R 66 " --> pdb=" O ILE R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 103 Proline residue: R 97 - end of helix removed outlier: 4.254A pdb=" N LEU R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N HIS R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 144 Processing helix chain 'R' and resid 149 through 152 No H-bonds generated for 'chain 'R' and resid 149 through 152' Processing helix chain 'R' and resid 155 through 178 removed outlier: 3.720A pdb=" N PHE R 173 " --> pdb=" O SER R 169 " (cutoff:3.500A) Proline residue: R 175 - end of helix removed outlier: 3.797A pdb=" N PHE R 178 " --> pdb=" O LEU R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 189 removed outlier: 4.006A pdb=" N ILE R 189 " --> pdb=" O HIS R 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 186 through 189' Processing helix chain 'R' and resid 191 through 195 Processing helix chain 'R' and resid 207 through 243 Proline residue: R 214 - end of helix Processing helix chain 'R' and resid 265 through 288 removed outlier: 4.232A pdb=" N ARG R 269 " --> pdb=" O MET R 265 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR R 271 " --> pdb=" O LEU R 267 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Proline residue: R 280 - end of helix Processing helix chain 'R' and resid 296 through 320 removed outlier: 5.083A pdb=" N SER R 310 " --> pdb=" O ALA R 306 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N PHE R 311 " --> pdb=" O ILE R 307 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS R 312 " --> pdb=" O SER R 308 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASN R 313 " --> pdb=" O ASN R 309 " (cutoff:3.500A) Proline residue: R 314 - end of helix removed outlier: 3.613A pdb=" N TYR R 317 " --> pdb=" O ASN R 313 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER R 320 " --> pdb=" O ILE R 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 39 Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.506A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 277 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 332 through 351 removed outlier: 3.606A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.879A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.995A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.612A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.044A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.696A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.596A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.462A 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: 4.905A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.875A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.039A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.203A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.175A 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) 377 hydrogen bonds defined for protein. 1098 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: 2.21 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2510 1.34 - 1.46: 2252 1.46 - 1.59: 3671 1.59 - 1.71: 0 1.71 - 1.84: 76 Bond restraints: 8509 Sorted by residual: bond pdb=" C1 EN6 R 401 " pdb=" N1 EN6 R 401 " ideal model delta sigma weight residual 1.410 1.510 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C22 EN6 R 401 " pdb=" N3 EN6 R 401 " ideal model delta sigma weight residual 1.344 1.442 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" C17 EN6 R 401 " pdb=" C18 EN6 R 401 " ideal model delta sigma weight residual 1.381 1.435 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" C17 EN6 R 401 " pdb=" N1 EN6 R 401 " ideal model delta sigma weight residual 1.356 1.406 -0.050 2.00e-02 2.50e+03 6.27e+00 bond pdb=" C18 EN6 R 401 " pdb=" C22 EN6 R 401 " ideal model delta sigma weight residual 1.479 1.525 -0.046 2.00e-02 2.50e+03 5.38e+00 ... (remaining 8504 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.05: 89 104.05 - 111.58: 3629 111.58 - 119.11: 3200 119.11 - 126.64: 4482 126.64 - 134.17: 143 Bond angle restraints: 11543 Sorted by residual: angle pdb=" CB MET R 276 " pdb=" CG MET R 276 " pdb=" SD MET R 276 " ideal model delta sigma weight residual 112.70 128.42 -15.72 3.00e+00 1.11e-01 2.74e+01 angle pdb=" C VAL R 64 " pdb=" N PHE R 65 " pdb=" CA PHE R 65 " ideal model delta sigma weight residual 120.58 112.87 7.71 1.71e+00 3.42e-01 2.03e+01 angle pdb=" N GLN R 115 " pdb=" CA GLN R 115 " pdb=" CB GLN R 115 " ideal model delta sigma weight residual 110.12 116.30 -6.18 1.47e+00 4.63e-01 1.76e+01 angle pdb=" CA GLN R 115 " pdb=" CB GLN R 115 " pdb=" CG GLN R 115 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" C HIS R 72 " pdb=" N HIS R 73 " pdb=" CA HIS R 73 " ideal model delta sigma weight residual 121.54 128.81 -7.27 1.91e+00 2.74e-01 1.45e+01 ... (remaining 11538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.41: 4833 27.41 - 54.82: 164 54.82 - 82.23: 26 82.23 - 109.64: 1 109.64 - 137.04: 1 Dihedral angle restraints: 5025 sinusoidal: 1979 harmonic: 3046 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -12.36 -73.64 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CB CYS R 114 " pdb=" SG CYS R 114 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual -86.00 -142.01 56.01 1 1.00e+01 1.00e-02 4.23e+01 ... (remaining 5022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 884 0.051 - 0.102: 295 0.102 - 0.153: 87 0.153 - 0.204: 16 0.204 - 0.255: 5 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA MET R 276 " pdb=" N MET R 276 " pdb=" C MET R 276 " pdb=" CB MET R 276 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU R 279 " pdb=" N LEU R 279 " pdb=" C LEU R 279 " pdb=" CB LEU R 279 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1284 not shown) Planarity restraints: 1465 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.034 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR B 59 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 244 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO R 245 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO R 245 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 245 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 278 " -0.018 2.00e-02 2.50e+03 1.96e-02 9.60e+00 pdb=" CG TRP R 278 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 278 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP R 278 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 278 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP R 278 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 278 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 278 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 278 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP R 278 " -0.000 2.00e-02 2.50e+03 ... (remaining 1462 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1280 2.76 - 3.30: 8004 3.30 - 3.83: 14468 3.83 - 4.37: 17253 4.37 - 4.90: 29418 Nonbonded interactions: 70423 Sorted by model distance: nonbonded pdb=" O THR R 199 " pdb=" OG SER R 290 " model vdw 2.228 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.240 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.260 2.440 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.318 2.440 ... (remaining 70418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 21.720 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 25.340 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.005 0.100 8509 Z= 0.348 Angle : 0.919 15.717 11543 Z= 0.489 Chirality : 0.057 0.255 1287 Planarity : 0.006 0.088 1465 Dihedral : 14.082 137.044 3047 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.73 (0.24), residues: 1031 helix: 0.01 (0.25), residues: 390 sheet: 0.04 (0.31), residues: 232 loop : -1.16 (0.28), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP R 278 HIS 0.011 0.001 HIS A 357 PHE 0.024 0.002 PHE N 108 TYR 0.062 0.003 TYR B 59 ARG 0.008 0.001 ARG R 291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7591 (mmm-85) cc_final: 0.7257 (mmm-85) REVERT: N 73 ASP cc_start: 0.7515 (m-30) cc_final: 0.7017 (m-30) REVERT: N 80 TYR cc_start: 0.8167 (m-80) cc_final: 0.7628 (m-80) REVERT: R 190 PHE cc_start: 0.7995 (m-80) cc_final: 0.7732 (m-80) REVERT: R 198 LEU cc_start: 0.8008 (mt) cc_final: 0.7681 (mm) REVERT: R 200 SER cc_start: 0.7924 (p) cc_final: 0.7630 (p) REVERT: R 220 CYS cc_start: 0.7605 (m) cc_final: 0.7173 (m) REVERT: R 265 MET cc_start: 0.5522 (tmm) cc_final: 0.4651 (mtt) REVERT: A 307 LYS cc_start: 0.8154 (mppt) cc_final: 0.7895 (mmtm) REVERT: A 311 TYR cc_start: 0.8130 (m-80) cc_final: 0.7914 (m-80) REVERT: A 343 ASP cc_start: 0.7294 (m-30) cc_final: 0.6963 (m-30) REVERT: A 369 THR cc_start: 0.7789 (p) cc_final: 0.7573 (p) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 1.2545 time to fit residues: 323.2277 Evaluate side-chains 192 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN R 81 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8509 Z= 0.262 Angle : 0.648 15.456 11543 Z= 0.335 Chirality : 0.046 0.174 1287 Planarity : 0.005 0.063 1465 Dihedral : 7.510 150.329 1156 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.32 % Allowed : 11.82 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -0.12 (0.25), residues: 1031 helix: 0.85 (0.26), residues: 393 sheet: 0.05 (0.31), residues: 233 loop : -1.00 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.010 0.001 HIS B 266 PHE 0.021 0.002 PHE A 212 TYR 0.030 0.002 TYR B 59 ARG 0.005 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 0.939 Fit side-chains REVERT: B 59 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: B 219 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.7067 (mmm-85) REVERT: R 137 VAL cc_start: 0.8488 (p) cc_final: 0.7711 (m) REVERT: R 235 LYS cc_start: 0.7319 (tppp) cc_final: 0.7070 (tptp) REVERT: R 265 MET cc_start: 0.5629 (tmm) cc_final: 0.4498 (mtt) REVERT: A 25 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.8011 (ttmp) REVERT: A 35 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7850 (mp10) REVERT: A 253 TYR cc_start: 0.8359 (m-80) cc_final: 0.8146 (m-80) REVERT: A 254 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7528 (m-40) outliers start: 21 outliers final: 10 residues processed: 216 average time/residue: 1.2327 time to fit residues: 282.8615 Evaluate side-chains 199 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 185 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 164 LEU Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 254 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 0.0050 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8509 Z= 0.203 Angle : 0.595 15.499 11543 Z= 0.304 Chirality : 0.044 0.170 1287 Planarity : 0.004 0.052 1465 Dihedral : 7.351 154.847 1156 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.09 % Allowed : 14.14 % Favored : 82.76 % 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: 0.16 (0.25), residues: 1031 helix: 1.26 (0.26), residues: 389 sheet: -0.01 (0.31), residues: 232 loop : -0.88 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.019 0.002 PHE A 212 TYR 0.024 0.002 TYR B 59 ARG 0.004 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 0.906 Fit side-chains REVERT: B 59 TYR cc_start: 0.7673 (OUTLIER) cc_final: 0.7171 (m-10) REVERT: B 219 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.7149 (mmm-85) REVERT: N 73 ASP cc_start: 0.7500 (m-30) cc_final: 0.7237 (m-30) REVERT: N 80 TYR cc_start: 0.8243 (m-80) cc_final: 0.7992 (m-80) REVERT: R 137 VAL cc_start: 0.8479 (p) cc_final: 0.7702 (m) REVERT: R 143 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7966 (tp) REVERT: R 190 PHE cc_start: 0.8042 (m-80) cc_final: 0.7807 (m-80) REVERT: R 212 TYR cc_start: 0.6910 (m-80) cc_final: 0.6605 (m-10) REVERT: R 265 MET cc_start: 0.5639 (tmm) cc_final: 0.4389 (mtt) REVERT: A 25 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7976 (ttmp) REVERT: A 35 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7825 (mp10) REVERT: A 254 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7592 (m-40) REVERT: A 343 ASP cc_start: 0.7312 (m-30) cc_final: 0.7018 (m-30) outliers start: 28 outliers final: 11 residues processed: 207 average time/residue: 1.2212 time to fit residues: 269.3207 Evaluate side-chains 199 residues out of total 905 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 65 PHE Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 200 SER Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain A residue 9 THR Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 254 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2752 > 50: distance: 65 - 69: 13.128 distance: 68 - 130: 4.492 distance: 69 - 70: 38.198 distance: 69 - 75: 22.505 distance: 70 - 71: 62.275 distance: 70 - 73: 25.531 distance: 71 - 72: 47.116 distance: 71 - 76: 14.088 distance: 73 - 74: 11.112 distance: 74 - 75: 10.505 distance: 76 - 77: 52.609 distance: 77 - 78: 26.202 distance: 77 - 80: 19.479 distance: 78 - 79: 17.071 distance: 78 - 81: 18.546 distance: 81 - 82: 14.904 distance: 81 - 87: 12.956 distance: 82 - 83: 9.697 distance: 82 - 85: 10.762 distance: 83 - 84: 8.437 distance: 83 - 88: 10.951 distance: 85 - 86: 3.686 distance: 86 - 87: 6.461 distance: 89 - 90: 4.619 distance: 89 - 92: 5.053 distance: 90 - 91: 20.531 distance: 90 - 99: 10.249 distance: 93 - 94: 3.721 distance: 93 - 95: 8.525 distance: 94 - 96: 5.039 distance: 96 - 98: 4.574 distance: 99 - 100: 11.599 distance: 100 - 101: 3.568 distance: 100 - 103: 9.816 distance: 101 - 102: 12.933 distance: 101 - 106: 12.863 distance: 103 - 104: 13.418 distance: 103 - 105: 11.451 distance: 106 - 107: 15.430 distance: 107 - 108: 18.841 distance: 107 - 110: 20.733 distance: 108 - 109: 20.105 distance: 108 - 117: 29.522 distance: 110 - 111: 15.759 distance: 111 - 112: 4.402 distance: 112 - 113: 13.339 distance: 113 - 114: 9.029 distance: 114 - 115: 16.546 distance: 114 - 116: 10.464 distance: 117 - 118: 8.738 distance: 118 - 119: 19.085 distance: 118 - 121: 13.213 distance: 119 - 120: 19.519 distance: 119 - 125: 19.797 distance: 121 - 122: 15.681 distance: 122 - 123: 18.499 distance: 122 - 124: 6.084 distance: 125 - 126: 21.295 distance: 126 - 127: 42.272 distance: 126 - 129: 17.567 distance: 127 - 128: 19.811 distance: 127 - 131: 39.533 distance: 129 - 130: 8.425 distance: 131 - 132: 8.174 distance: 132 - 133: 10.438 distance: 132 - 135: 21.274 distance: 133 - 134: 5.466 distance: 133 - 142: 8.948 distance: 135 - 136: 10.370 distance: 136 - 138: 5.680 distance: 138 - 140: 10.479 distance: 139 - 141: 5.316 distance: 142 - 143: 12.017 distance: 143 - 144: 5.547 distance: 143 - 146: 16.346 distance: 144 - 145: 5.011 distance: 146 - 147: 10.648 distance: 147 - 148: 13.194 distance: 147 - 149: 26.500