Starting phenix.real_space_refine on Mon Aug 5 17:51:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/08_2024/7p1h_13159_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/08_2024/7p1h_13159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/08_2024/7p1h_13159.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/08_2024/7p1h_13159.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/08_2024/7p1h_13159_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p1h_13159/08_2024/7p1h_13159_trim.cif" } resolution = 3.9 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 34 5.16 5 C 4454 2.51 5 N 1171 2.21 5 O 1377 1.98 5 H 6926 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 20": "OD1" <-> "OD2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 86": "OD1" <-> "OD2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A ASP 129": "OD1" <-> "OD2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A ASP 153": "OD1" <-> "OD2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A ASP 277": "OD1" <-> "OD2" Residue "A ASP 294": "OD1" <-> "OD2" Residue "A ASP 304": "OD1" <-> "OD2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 206": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13966 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 6173 Classifications: {'peptide': 395} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 376} Chain: "B" Number of atoms: 5679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 5679 Classifications: {'peptide': 365} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2082 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.06, per 1000 atoms: 0.58 Number of scatterers: 13966 At special positions: 0 Unit cell: (119, 108.8, 82.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 34 16.00 P 3 15.00 O 1377 8.00 N 1171 7.00 C 4454 6.00 H 6926 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 12.59 Conformation dependent library (CDL) restraints added in 1.5 seconds 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 48.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 19 through 36 Proline residue: A 25 - end of helix Proline residue: A 29 - end of helix removed outlier: 3.854A pdb=" N ILE A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'A' and resid 252 through 260 removed outlier: 4.196A pdb=" N GLU A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.687A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 290 removed outlier: 3.643A pdb=" N ASP A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.579A pdb=" N PHE A 316 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.674A pdb=" N PHE A 327 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU A 329 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 376 through 384 removed outlier: 4.305A pdb=" N ASN A 380 " --> pdb=" O ASN A 376 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 383 " --> pdb=" O TRP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.701A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 144 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 195 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 285 through 288 removed outlier: 5.712A pdb=" N ASP B 288 " --> pdb=" O CYS B 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 285 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 349 removed outlier: 4.420A pdb=" N VAL B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP B 340 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 341 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 356 removed outlier: 4.046A pdb=" N MET B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.555A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 12 Processing helix chain 'P' and resid 38 through 42 Processing helix chain 'P' and resid 43 through 51 removed outlier: 3.514A pdb=" N VAL P 47 " --> pdb=" O THR P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 62 removed outlier: 3.961A pdb=" N VAL P 60 " --> pdb=" O SER P 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 119 through 137 removed outlier: 3.810A pdb=" N ILE P 123 " --> pdb=" O HIS P 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 353 removed outlier: 5.027A pdb=" N THR A 218 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 221 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 129 Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132 removed outlier: 5.039A pdb=" N ILE A 190 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THR A 171 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.377A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.861A pdb=" N ILE B 75 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.638A pdb=" N LEU B 176 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.280A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'P' and resid 29 through 33 removed outlier: 5.404A pdb=" N VAL P 30 " --> pdb=" O GLY P 23 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N GLY P 23 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN P 99 " --> pdb=" O GLY P 114 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N SER P 84 " --> pdb=" O ASP P 75 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP P 75 " --> pdb=" O SER P 84 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP P 86 " --> pdb=" O ILE P 73 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU P 63 " --> pdb=" O CYS P 70 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.13 Time building geometry restraints manager: 13.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 6910 1.03 - 1.22: 19 1.22 - 1.42: 2972 1.42 - 1.61: 4151 1.61 - 1.81: 60 Bond restraints: 14112 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" HE1 HIC B 73 " ideal model delta sigma weight residual 0.930 1.095 -0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" CA HIC B 73 " pdb=" HA HIC B 73 " ideal model delta sigma weight residual 0.970 1.131 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" CD2 HIC B 73 " pdb=" HD2 HIC B 73 " ideal model delta sigma weight residual 0.930 1.087 -0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" CB HIC B 73 " pdb=" HB2 HIC B 73 " ideal model delta sigma weight residual 0.970 1.124 -0.154 2.00e-02 2.50e+03 5.90e+01 bond pdb=" CZ HIC B 73 " pdb=" HZ1 HIC B 73 " ideal model delta sigma weight residual 0.970 1.123 -0.153 2.00e-02 2.50e+03 5.84e+01 ... (remaining 14107 not shown) Histogram of bond angle deviations from ideal: 97.27 - 105.13: 161 105.13 - 112.99: 16728 112.99 - 120.84: 5280 120.84 - 128.70: 3316 128.70 - 136.56: 44 Bond angle restraints: 25529 Sorted by residual: angle pdb=" PB ATP B 402 " pdb=" O3B ATP B 402 " pdb=" PG ATP B 402 " ideal model delta sigma weight residual 139.87 120.02 19.85 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PA ATP B 402 " pdb=" O3A ATP B 402 " pdb=" PB ATP B 402 " ideal model delta sigma weight residual 136.83 122.53 14.30 1.00e+00 1.00e+00 2.05e+02 angle pdb=" C5 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N3 ATP B 402 " ideal model delta sigma weight residual 126.80 119.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" N3 ATP B 402 " pdb=" C4 ATP B 402 " pdb=" N9 ATP B 402 " ideal model delta sigma weight residual 127.04 134.55 -7.51 1.15e+00 7.59e-01 4.28e+01 angle pdb=" N LEU A 217 " pdb=" CA LEU A 217 " pdb=" C LEU A 217 " ideal model delta sigma weight residual 110.80 97.76 13.04 2.13e+00 2.20e-01 3.75e+01 ... (remaining 25524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5825 17.47 - 34.93: 528 34.93 - 52.40: 181 52.40 - 69.86: 123 69.86 - 87.33: 17 Dihedral angle restraints: 6674 sinusoidal: 3653 harmonic: 3021 Sorted by residual: dihedral pdb=" CA LEU A 217 " pdb=" C LEU A 217 " pdb=" N THR A 218 " pdb=" CA THR A 218 " ideal model delta harmonic sigma weight residual 180.00 -150.56 -29.44 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA SER A 127 " pdb=" C SER A 127 " pdb=" N ALA A 128 " pdb=" CA ALA A 128 " ideal model delta harmonic sigma weight residual 180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA ASP A 129 " pdb=" C ASP A 129 " pdb=" N LEU A 130 " pdb=" CA LEU A 130 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 6671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 642 0.037 - 0.075: 282 0.075 - 0.112: 115 0.112 - 0.149: 37 0.149 - 0.186: 6 Chirality restraints: 1082 Sorted by residual: chirality pdb=" CA LYS A 402 " pdb=" N LYS A 402 " pdb=" C LYS A 402 " pdb=" CB LYS A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CG LEU A 399 " pdb=" CB LEU A 399 " pdb=" CD1 LEU A 399 " pdb=" CD2 LEU A 399 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CA VAL A 179 " pdb=" N VAL A 179 " pdb=" C VAL A 179 " pdb=" CB VAL A 179 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 1079 not shown) Planarity restraints: 2106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 265 " -0.024 2.00e-02 2.50e+03 4.85e-02 2.36e+01 pdb=" C ASN A 265 " 0.084 2.00e-02 2.50e+03 pdb=" O ASN A 265 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS A 266 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 106 " 0.090 9.50e-02 1.11e+02 3.90e-02 1.47e+01 pdb=" NE ARG A 106 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 106 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 106 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG A 106 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 106 " 0.014 2.00e-02 2.50e+03 pdb="HH12 ARG A 106 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 106 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 106 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " 0.069 9.50e-02 1.11e+02 3.37e-02 1.41e+01 pdb=" NE ARG A 278 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " 0.051 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " -0.026 2.00e-02 2.50e+03 pdb="HH11 ARG A 278 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG A 278 " 0.007 2.00e-02 2.50e+03 pdb="HH21 ARG A 278 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 278 " 0.013 2.00e-02 2.50e+03 ... (remaining 2103 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 456 2.09 - 2.71: 24523 2.71 - 3.34: 41366 3.34 - 3.97: 51840 3.97 - 4.60: 81313 Nonbonded interactions: 199498 Sorted by model distance: nonbonded pdb=" H THR B 201 " pdb=" OE1 GLU B 205 " model vdw 1.457 2.450 nonbonded pdb=" HZ1 LYS A 176 " pdb=" OD2 ASP A 183 " model vdw 1.524 2.450 nonbonded pdb=" O SER B 344 " pdb=" HG SER B 348 " model vdw 1.526 2.450 nonbonded pdb=" O ALA A 103 " pdb=" HG SER A 104 " model vdw 1.537 2.450 nonbonded pdb=" OD2 ASP B 288 " pdb=" HZ1 LYS P 69 " model vdw 1.537 2.450 ... (remaining 199493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 3.090 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: 0.350 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 52.910 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 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 0.076 7186 Z= 0.323 Angle : 1.010 19.849 9739 Z= 0.630 Chirality : 0.051 0.186 1082 Planarity : 0.007 0.051 1253 Dihedral : 14.378 87.170 2681 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -1.60 (0.25), residues: 887 helix: -1.09 (0.24), residues: 327 sheet: -0.25 (0.39), residues: 154 loop : -1.25 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.006 TRP B 86 HIS 0.008 0.002 HIS B 40 PHE 0.029 0.003 PHE A 321 TYR 0.037 0.005 TYR A 144 ARG 0.058 0.008 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1774 Ramachandran restraints generated. 887 Oldfield, 0 Emsley, 887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 76 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.250 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 PHE cc_start: 0.8119 (m-80) cc_final: 0.7415 (m-80) REVERT: B 153 MET cc_start: 0.8489 (tmm) cc_final: 0.8277 (tmm) REVERT: B 208 ILE cc_start: 0.9124 (mt) cc_final: 0.8733 (tp) REVERT: B 292 ASP cc_start: 0.8639 (m-30) cc_final: 0.8230 (t0) REVERT: P 99 ASN cc_start: 0.7840 (m110) cc_final: 0.7575 (m-40) REVERT: P 125 LYS cc_start: 0.8703 (tttt) cc_final: 0.8353 (tmtt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.4321 time to fit residues: 120.1624 Evaluate side-chains 135 residues out of total 766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 58.3638 > 50: distance: 19 - 31: 3.260 distance: 20 - 87: 10.493 distance: 31 - 32: 5.162 distance: 31 - 45: 21.677 distance: 32 - 33: 6.936 distance: 32 - 35: 8.650 distance: 32 - 46: 7.646 distance: 33 - 34: 16.395 distance: 33 - 55: 14.095 distance: 34 - 111: 13.006 distance: 35 - 36: 7.773 distance: 35 - 47: 11.109 distance: 35 - 48: 9.044 distance: 36 - 37: 4.737 distance: 36 - 38: 10.652 distance: 37 - 39: 11.168 distance: 37 - 49: 6.177 distance: 38 - 40: 12.410 distance: 38 - 41: 5.381 distance: 39 - 40: 11.745 distance: 40 - 42: 7.760 distance: 41 - 43: 3.228 distance: 41 - 51: 4.375 distance: 42 - 44: 4.282 distance: 42 - 52: 7.950 distance: 43 - 44: 5.589 distance: 43 - 53: 9.394 distance: 44 - 54: 7.986 distance: 55 - 56: 13.114 distance: 55 - 64: 16.807 distance: 56 - 57: 15.754 distance: 56 - 59: 13.148 distance: 56 - 65: 7.232 distance: 57 - 58: 9.928 distance: 57 - 70: 3.133 distance: 58 - 133: 17.717 distance: 59 - 60: 10.541 distance: 59 - 66: 10.891 distance: 59 - 67: 21.723 distance: 60 - 61: 12.340 distance: 60 - 68: 18.043 distance: 60 - 69: 22.574 distance: 61 - 62: 14.650 distance: 61 - 63: 10.876 distance: 70 - 71: 14.144 distance: 70 - 79: 5.802 distance: 71 - 72: 14.157 distance: 71 - 74: 20.101 distance: 71 - 80: 17.359 distance: 72 - 73: 8.652 distance: 72 - 87: 7.318 distance: 73 - 148: 21.983 distance: 74 - 75: 10.609 distance: 74 - 81: 11.997 distance: 74 - 82: 18.013 distance: 75 - 76: 6.667 distance: 75 - 83: 11.442 distance: 75 - 84: 15.231 distance: 76 - 77: 7.003 distance: 76 - 78: 3.053 distance: 78 - 85: 3.716 distance: 78 - 86: 3.106 distance: 87 - 88: 6.284 distance: 87 - 101: 14.243 distance: 88 - 91: 19.883 distance: 88 - 102: 19.285 distance: 89 - 90: 5.759 distance: 89 - 111: 9.533 distance: 90 - 159: 7.075 distance: 91 - 92: 11.422 distance: 91 - 103: 11.413 distance: 91 - 104: 5.817 distance: 92 - 93: 14.036 distance: 92 - 94: 8.355 distance: 93 - 95: 3.237 distance: 93 - 105: 5.549 distance: 94 - 96: 8.806 distance: 94 - 97: 3.266 distance: 95 - 106: 4.642 distance: 96 - 98: 5.626 distance: 97 - 99: 4.750 distance: 97 - 107: 9.380 distance: 98 - 100: 4.556 distance: 98 - 108: 3.726 distance: 99 - 100: 6.322 distance: 99 - 109: 7.339 distance: 100 - 110: 7.882 distance: 111 - 112: 8.054 distance: 111 - 120: 10.757 distance: 112 - 113: 4.700 distance: 112 - 115: 10.762 distance: 112 - 121: 9.921 distance: 113 - 114: 7.248 distance: 113 - 133: 9.133 distance: 115 - 116: 6.723 distance: 115 - 122: 15.489 distance: 115 - 123: 17.947 distance: 116 - 117: 3.716 distance: 116 - 124: 5.852 distance: 117 - 118: 7.334 distance: 117 - 126: 10.531 distance: 117 - 127: 6.118 distance: 118 - 119: 3.174 distance: 118 - 128: 5.174 distance: 118 - 129: 8.335 distance: 119 - 130: 3.123 distance: 119 - 132: 3.868 distance: 133 - 134: 6.360 distance: 133 - 142: 9.543 distance: 134 - 135: 7.974 distance: 134 - 137: 8.662 distance: 134 - 143: 7.524 distance: 135 - 136: 18.337 distance: 135 - 148: 11.887 distance: 137 - 138: 6.276 distance: 137 - 144: 8.055 distance: 137 - 145: 21.170 distance: 138 - 139: 11.418 distance: 138 - 146: 11.527 distance: 138 - 147: 12.560 distance: 139 - 140: 14.326 distance: 139 - 141: 19.073 distance: 148 - 149: 13.399 distance: 148 - 154: 11.042 distance: 149 - 150: 24.199 distance: 149 - 155: 14.782 distance: 150 - 151: 18.595 distance: 150 - 159: 23.303 distance: 152 - 153: 13.085 distance: 152 - 156: 7.430 distance: 152 - 157: 15.548 distance: 153 - 158: 8.755 distance: 159 - 160: 18.098 distance: 159 - 166: 14.007 distance: 160 - 161: 10.433 distance: 160 - 163: 18.858 distance: 160 - 167: 18.073 distance: 161 - 162: 25.521 distance: 161 - 175: 19.555 distance: 163 - 164: 15.255 distance: 163 - 165: 15.269 distance: 163 - 168: 19.676 distance: 164 - 169: 18.627 distance: 164 - 170: 34.943 distance: 164 - 171: 16.815 distance: 165 - 172: 26.035 distance: 165 - 173: 6.514 distance: 165 - 174: 17.415 distance: 175 - 176: 20.334 distance: 175 - 182: 13.634 distance: 176 - 177: 37.036 distance: 176 - 179: 39.857 distance: 176 - 183: 37.772 distance: 177 - 178: 26.246 distance: 177 - 189: 37.053 distance: 179 - 180: 23.218 distance: 179 - 181: 34.584 distance: 179 - 184: 41.358 distance: 180 - 185: 49.635 distance: 181 - 186: 19.181 distance: 181 - 187: 24.024 distance: 181 - 188: 11.651 distance: 189 - 190: 11.044 distance: 189 - 201: 8.144 distance: 190 - 191: 21.357 distance: 190 - 193: 15.599 distance: 190 - 202: 16.442 distance: 191 - 192: 21.976 distance: 191 - 210: 8.833 distance: 193 - 194: 16.880 distance: 193 - 203: 3.804 distance: 193 - 204: 24.024 distance: 194 - 195: 4.232 distance: 194 - 196: 5.181 distance: 195 - 197: 10.535 distance: 195 - 205: 3.754 distance: 196 - 198: 9.393 distance: 196 - 206: 5.780 distance: 197 - 199: 5.606 distance: 197 - 207: 8.001 distance: 198 - 199: 6.905 distance: 198 - 208: 6.720 distance: 199 - 200: 10.792 distance: 200 - 209: 14.828 distance: 260 - 300: 3.003