Starting phenix.real_space_refine on Mon Aug 5 06:19:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2024/6ndy_0443.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2024/6ndy_0443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2024/6ndy_0443.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2024/6ndy_0443.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2024/6ndy_0443.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ndy_0443/08_2024/6ndy_0443.cif" } resolution = 3.6 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= 0.001 sd= 0.006 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 45 5.16 5 Be 3 3.05 5 C 7846 2.51 5 N 2143 2.21 5 O 2471 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 126": "OE1" <-> "OE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 233": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E GLU 247": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12531 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2427 Classifications: {'peptide': 314} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "C" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2491 Classifications: {'peptide': 322} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 305} Chain breaks: 1 Chain: "E" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2360 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 287} Chain breaks: 1 Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 80 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.45, per 1000 atoms: 0.59 Number of scatterers: 12531 At special positions: 0 Unit cell: (79.57, 141.7, 156.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 45 16.00 P 10 15.00 Mg 4 11.99 F 9 9.00 O 2471 8.00 N 2143 7.00 C 7846 6.00 Be 3 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.77 Conformation dependent library (CDL) restraints added in 2.2 seconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 11 sheets defined 50.2% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.783A pdb=" N LEU A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER A 120 " --> pdb=" O GLY A 117 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 122 " --> pdb=" O LEU A 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 122' Processing helix chain 'A' and resid 138 through 155 Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 208 through 224 removed outlier: 4.004A pdb=" N VAL A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 245 through 260 removed outlier: 4.709A pdb=" N ARG A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 290 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 356 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.891A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 208 through 224 removed outlier: 4.313A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 261 Processing helix chain 'B' and resid 283 through 290 Processing helix chain 'B' and resid 300 through 313 removed outlier: 3.584A pdb=" N GLY B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 335 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 402 through 413 removed outlier: 3.998A pdb=" N PHE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 433 Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 138 through 155 Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'C' and resid 209 through 224 removed outlier: 3.608A pdb=" N LEU C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 4.056A pdb=" N ASN C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 335 through 356 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 402 through 413 removed outlier: 3.967A pdb=" N PHE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 433 Processing helix chain 'D' and resid 113 through 120 Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.569A pdb=" N VAL D 135 " --> pdb=" O TRP D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 155 Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.736A pdb=" N LEU D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.659A pdb=" N ASN D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 245 through 261 removed outlier: 4.202A pdb=" N ASN D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 320 through 331 Processing helix chain 'D' and resid 335 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.944A pdb=" N PHE D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 433 Processing helix chain 'E' and resid 138 through 155 Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 178 through 190 Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.755A pdb=" N VAL E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 224 removed outlier: 3.592A pdb=" N ASN E 224 " --> pdb=" O MET E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 removed outlier: 3.718A pdb=" N THR E 238 " --> pdb=" O VAL E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 261 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 313 removed outlier: 4.147A pdb=" N GLY E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 Processing helix chain 'E' and resid 335 through 356 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N GLN E 355 " --> pdb=" O ILE E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.966A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 432 removed outlier: 3.643A pdb=" N LEU E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 276 removed outlier: 8.619A pdb=" N THR A 276 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU A 171 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 170 " --> pdb=" O ILE A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 363 removed outlier: 4.037A pdb=" N LYS A 372 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 197 removed outlier: 6.363A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AA6, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.503A pdb=" N ILE C 228 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP C 232 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 275 " --> pdb=" O ILE C 231 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLY C 168 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 294 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU C 170 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG C 293 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'D' and resid 193 through 197 removed outlier: 6.447A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASP D 232 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 197 " --> pdb=" O ASP D 232 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 372 through 375 removed outlier: 4.222A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 363 " --> pdb=" O LYS D 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.672A pdb=" N THR E 193 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE E 230 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE E 195 " --> pdb=" O PHE E 230 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP E 232 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 372 through 375 removed outlier: 4.255A pdb=" N LYS E 372 " --> pdb=" O VAL E 363 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1614 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: 3.43 Time building geometry restraints manager: 5.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4106 1.34 - 1.46: 2151 1.46 - 1.58: 6385 1.58 - 1.69: 15 1.69 - 1.81: 80 Bond restraints: 12737 Sorted by residual: bond pdb=" C4 ADP C 501 " pdb=" C5 ADP C 501 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C5 ADP C 501 " pdb=" C6 ADP C 501 " ideal model delta sigma weight residual 1.490 1.403 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C5 ADP A 501 " pdb=" C6 ADP A 501 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 12732 not shown) Histogram of bond angle deviations from ideal: 99.95 - 107.16: 446 107.16 - 114.36: 7570 114.36 - 121.57: 6182 121.57 - 128.78: 2946 128.78 - 135.99: 79 Bond angle restraints: 17223 Sorted by residual: angle pdb=" C ASN E 265 " pdb=" N ASP E 266 " pdb=" CA ASP E 266 " ideal model delta sigma weight residual 122.46 130.35 -7.89 1.41e+00 5.03e-01 3.13e+01 angle pdb=" C GLY B 239 " pdb=" N THR B 240 " pdb=" CA THR B 240 " ideal model delta sigma weight residual 121.54 131.26 -9.72 1.91e+00 2.74e-01 2.59e+01 angle pdb=" O1B ADP A 501 " pdb=" PB ADP A 501 " pdb=" O3B ADP A 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP B 501 " pdb=" PB ADP B 501 " pdb=" O3B ADP B 501 " ideal model delta sigma weight residual 119.90 104.96 14.94 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O2B ADP C 501 " pdb=" PB ADP C 501 " pdb=" O3B ADP C 501 " ideal model delta sigma weight residual 119.90 105.52 14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 17218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.41: 7581 32.41 - 64.82: 196 64.82 - 97.23: 14 97.23 - 129.63: 3 129.63 - 162.04: 2 Dihedral angle restraints: 7796 sinusoidal: 3213 harmonic: 4583 Sorted by residual: dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.04 -162.04 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 73.34 -133.34 1 2.00e+01 2.50e-03 4.05e+01 dihedral pdb=" C5' ADP A 501 " pdb=" O5' ADP A 501 " pdb=" PA ADP A 501 " pdb=" O2A ADP A 501 " ideal model delta sinusoidal sigma weight residual 300.00 178.17 121.83 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 7793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1612 0.056 - 0.113: 272 0.113 - 0.169: 62 0.169 - 0.225: 9 0.225 - 0.282: 2 Chirality restraints: 1957 Sorted by residual: chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CB ILE C 278 " pdb=" CA ILE C 278 " pdb=" CG1 ILE C 278 " pdb=" CG2 ILE C 278 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE A 228 " pdb=" CA ILE A 228 " pdb=" CG1 ILE A 228 " pdb=" CG2 ILE A 228 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 1954 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 147 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.52e+00 pdb=" C GLU C 147 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU C 147 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA C 148 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN C 349 " -0.038 5.00e-02 4.00e+02 5.60e-02 5.03e+00 pdb=" N PRO C 350 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 374 " 0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO D 375 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO D 375 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 375 " 0.030 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 166 2.61 - 3.18: 9937 3.18 - 3.75: 19375 3.75 - 4.33: 25287 4.33 - 4.90: 43033 Nonbonded interactions: 97798 Sorted by model distance: nonbonded pdb=" OG SER A 180 " pdb="MG MG A 503 " model vdw 2.037 2.170 nonbonded pdb=" OG SER C 180 " pdb="MG MG C 503 " model vdw 2.038 2.170 nonbonded pdb=" F1 BEF C 502 " pdb="MG MG C 503 " model vdw 2.038 2.120 nonbonded pdb=" OG SER B 180 " pdb="MG MG B 503 " model vdw 2.038 2.170 nonbonded pdb=" O2B ADP A 501 " pdb="MG MG A 503 " model vdw 2.038 2.170 ... (remaining 97793 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 126 through 433) selection = (chain 'B' and resid 126 through 433) selection = (chain 'C' and resid 126 through 433) selection = (chain 'D' and resid 126 through 433) selection = (chain 'E' and resid 126 through 433) } 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: 0.810 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: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 35.070 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 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 0.104 12737 Z= 0.298 Angle : 0.892 14.941 17223 Z= 0.451 Chirality : 0.048 0.282 1957 Planarity : 0.006 0.056 2206 Dihedral : 14.707 162.042 4830 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.16), residues: 1574 helix: -2.38 (0.12), residues: 751 sheet: -2.34 (0.39), residues: 160 loop : -2.54 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 280 HIS 0.001 0.000 HIS A 359 PHE 0.011 0.001 PHE A 308 TYR 0.008 0.001 TYR C 181 ARG 0.002 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 GLN cc_start: 0.6605 (mt0) cc_final: 0.6379 (tt0) REVERT: A 343 VAL cc_start: 0.7244 (t) cc_final: 0.6741 (t) REVERT: A 351 ILE cc_start: 0.6725 (mp) cc_final: 0.6227 (mm) REVERT: B 162 ASN cc_start: 0.6193 (m110) cc_final: 0.5772 (t0) REVERT: C 289 ARG cc_start: 0.4564 (mmt90) cc_final: 0.3295 (mmt90) REVERT: C 373 LEU cc_start: 0.7974 (mp) cc_final: 0.7663 (tp) REVERT: D 355 GLN cc_start: 0.6696 (mt0) cc_final: 0.6204 (tt0) REVERT: D 425 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5472 (mt0) REVERT: E 157 HIS cc_start: 0.5602 (p90) cc_final: 0.5375 (p-80) REVERT: E 233 GLU cc_start: 0.7046 (mp0) cc_final: 0.6580 (mp0) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2911 time to fit residues: 167.5808 Evaluate side-chains 207 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 63 optimal weight: 0.0270 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 355 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN B 427 GLN ** C 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN C 437 ASN D 216 GLN D 265 ASN ** D 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12737 Z= 0.206 Angle : 0.704 10.617 17223 Z= 0.340 Chirality : 0.043 0.227 1957 Planarity : 0.005 0.047 2206 Dihedral : 9.231 159.663 1756 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.29 % Allowed : 13.98 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.22 (0.19), residues: 1574 helix: -0.76 (0.17), residues: 796 sheet: -1.68 (0.41), residues: 160 loop : -2.27 (0.23), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 280 HIS 0.004 0.001 HIS C 359 PHE 0.014 0.002 PHE D 290 TYR 0.020 0.002 TYR C 181 ARG 0.007 0.001 ARG E 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 162 ASN cc_start: 0.6116 (m110) cc_final: 0.5907 (t0) REVERT: B 289 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6965 (mpt180) REVERT: B 307 MET cc_start: 0.5947 (mtp) cc_final: 0.5608 (mtp) REVERT: B 330 MET cc_start: 0.8850 (mmt) cc_final: 0.8578 (mmm) REVERT: B 431 ASP cc_start: 0.7204 (m-30) cc_final: 0.6921 (m-30) REVERT: C 259 GLN cc_start: 0.6220 (mm-40) cc_final: 0.3895 (mt0) REVERT: C 373 LEU cc_start: 0.7936 (mp) cc_final: 0.7719 (tp) REVERT: D 360 PHE cc_start: 0.4392 (m-10) cc_final: 0.4100 (m-80) REVERT: D 425 GLN cc_start: 0.6334 (mm-40) cc_final: 0.6039 (mt0) REVERT: E 233 GLU cc_start: 0.7159 (mp0) cc_final: 0.6607 (mp0) REVERT: E 386 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5587 (mtm) REVERT: E 425 GLN cc_start: 0.6313 (mm110) cc_final: 0.6023 (mm-40) outliers start: 31 outliers final: 17 residues processed: 254 average time/residue: 0.2108 time to fit residues: 79.8164 Evaluate side-chains 204 residues out of total 1352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 281 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain G residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 67.7839 > 50: distance: 38 - 54: 14.991 distance: 42 - 59: 11.923 distance: 46 - 67: 23.262 distance: 49 - 54: 13.224 distance: 50 - 76: 31.692 distance: 54 - 55: 6.000 distance: 55 - 56: 18.965 distance: 55 - 58: 9.895 distance: 56 - 57: 12.987 distance: 56 - 59: 12.119 distance: 57 - 82: 10.441 distance: 59 - 60: 18.893 distance: 60 - 61: 22.108 distance: 60 - 63: 23.363 distance: 61 - 62: 31.485 distance: 61 - 67: 26.271 distance: 63 - 64: 20.253 distance: 63 - 65: 39.376 distance: 64 - 66: 23.384 distance: 67 - 68: 12.238 distance: 68 - 69: 18.695 distance: 68 - 71: 14.269 distance: 69 - 70: 37.040 distance: 71 - 72: 35.982 distance: 73 - 74: 33.011 distance: 74 - 75: 25.455 distance: 76 - 77: 27.110 distance: 77 - 78: 34.504 distance: 77 - 80: 26.604 distance: 78 - 79: 30.728 distance: 78 - 82: 37.064 distance: 80 - 81: 27.090 distance: 82 - 83: 11.409 distance: 83 - 84: 32.875 distance: 83 - 86: 24.872 distance: 84 - 85: 19.018 distance: 84 - 89: 37.430 distance: 86 - 87: 34.030 distance: 86 - 88: 26.396 distance: 89 - 90: 29.193 distance: 90 - 91: 50.972 distance: 90 - 93: 34.779 distance: 91 - 92: 28.664 distance: 91 - 100: 46.836 distance: 93 - 94: 3.806 distance: 94 - 95: 47.210 distance: 95 - 96: 12.640 distance: 97 - 98: 3.639 distance: 97 - 99: 3.363 distance: 100 - 101: 36.153 distance: 100 - 106: 11.866 distance: 101 - 102: 27.764 distance: 101 - 104: 28.703 distance: 102 - 103: 32.505 distance: 102 - 107: 20.379 distance: 104 - 105: 19.147 distance: 105 - 106: 25.449 distance: 107 - 108: 21.738 distance: 108 - 109: 26.913 distance: 108 - 111: 11.116 distance: 109 - 110: 6.651 distance: 109 - 114: 36.691 distance: 111 - 112: 20.386 distance: 111 - 113: 30.653 distance: 114 - 115: 16.752 distance: 115 - 116: 29.829 distance: 115 - 118: 38.014 distance: 116 - 117: 28.283 distance: 116 - 121: 45.753 distance: 118 - 119: 6.511 distance: 118 - 120: 14.871 distance: 121 - 122: 15.439 distance: 122 - 123: 11.492 distance: 122 - 125: 14.548 distance: 123 - 124: 12.614 distance: 123 - 129: 9.262 distance: 125 - 126: 7.764 distance: 126 - 127: 7.115 distance: 126 - 128: 3.441