Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 14:17:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/10_2023/8dtp_27707_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/10_2023/8dtp_27707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/10_2023/8dtp_27707.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/10_2023/8dtp_27707.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/10_2023/8dtp_27707_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtp_27707/10_2023/8dtp_27707_updated.pdb" } resolution = 2.7 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= 0.004 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: 6 Type Number sf(0) Gaussians P 27 5.49 5 Mg 5 5.21 5 S 119 5.16 5 C 13244 2.51 5 N 3469 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 82": "OD1" <-> "OD2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 20944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "M" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 240 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "B" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "D" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3424 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.57, per 1000 atoms: 0.50 Number of scatterers: 20944 At special positions: 0 Unit cell: (112.608, 134.136, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 119 16.00 P 27 15.00 Mg 5 11.99 O 4080 8.00 N 3469 7.00 C 13244 6.00 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: 9.13 Conformation dependent library (CDL) restraints added in 2.7 seconds 5160 Ramachandran restraints generated. 2580 Oldfield, 0 Emsley, 2580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 117 helices and 12 sheets defined 47.6% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 22 Proline residue: A 21 - end of helix Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 32 through 46 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 87 through 117 Processing helix chain 'A' and resid 131 through 142 Proline residue: A 135 - end of helix removed outlier: 3.787A pdb=" N MET A 138 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.708A pdb=" N LEU A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.728A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 289 through 300 Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 391 through 395 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 13 through 22 Proline residue: B 21 - end of helix Processing helix chain 'B' and resid 25 through 27 No H-bonds generated for 'chain 'B' and resid 25 through 27' Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 89 through 118 Processing helix chain 'B' and resid 131 through 142 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 167 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.512A pdb=" N ILE B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 230 through 242 Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 287 through 300 Processing helix chain 'B' and resid 328 through 346 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 392 through 395 No H-bonds generated for 'chain 'B' and resid 392 through 395' Processing helix chain 'C' and resid 2 through 10 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 25 through 27 No H-bonds generated for 'chain 'C' and resid 25 through 27' Processing helix chain 'C' and resid 32 through 46 Processing helix chain 'C' and resid 53 through 62 Processing helix chain 'C' and resid 67 through 76 removed outlier: 4.001A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 118 Processing helix chain 'C' and resid 131 through 142 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 203 through 216 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 287 through 300 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 328 through 346 Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 376 through 380 Processing helix chain 'C' and resid 391 through 396 removed outlier: 3.550A pdb=" N ALA C 396 " --> pdb=" O GLU C 392 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.609A pdb=" N LYS D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) Proline residue: D 21 - end of helix Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 87 through 117 Processing helix chain 'D' and resid 131 through 142 Proline residue: D 135 - end of helix removed outlier: 3.522A pdb=" N LEU D 142 " --> pdb=" O ARG D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.849A pdb=" N SER D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 183 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 230 through 242 Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 287 through 300 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 328 through 346 Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 376 through 379 No H-bonds generated for 'chain 'D' and resid 376 through 379' Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 13 through 19 removed outlier: 3.593A pdb=" N LYS E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 32 through 46 Processing helix chain 'E' and resid 53 through 62 Processing helix chain 'E' and resid 67 through 78 Processing helix chain 'E' and resid 87 through 118 Processing helix chain 'E' and resid 131 through 142 Proline residue: E 135 - end of helix removed outlier: 3.687A pdb=" N GLN E 140 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA E 141 " --> pdb=" O MET E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 166 Processing helix chain 'E' and resid 177 through 183 Processing helix chain 'E' and resid 203 through 216 Processing helix chain 'E' and resid 230 through 241 Processing helix chain 'E' and resid 247 through 250 No H-bonds generated for 'chain 'E' and resid 247 through 250' Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 328 through 346 removed outlier: 3.843A pdb=" N LYS E 333 " --> pdb=" O TYR E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 391 through 396 Processing helix chain 'F' and resid 2 through 11 Processing helix chain 'F' and resid 14 through 22 Proline residue: F 21 - end of helix Processing helix chain 'F' and resid 25 through 27 No H-bonds generated for 'chain 'F' and resid 25 through 27' Processing helix chain 'F' and resid 32 through 47 Processing helix chain 'F' and resid 53 through 61 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 89 through 117 Processing helix chain 'F' and resid 131 through 143 Proline residue: F 135 - end of helix removed outlier: 3.870A pdb=" N ALA F 141 " --> pdb=" O MET F 138 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU F 142 " --> pdb=" O ARG F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 Processing helix chain 'F' and resid 177 through 183 Processing helix chain 'F' and resid 203 through 217 Processing helix chain 'F' and resid 230 through 242 Processing helix chain 'F' and resid 246 through 251 Processing helix chain 'F' and resid 256 through 268 Processing helix chain 'F' and resid 287 through 301 Processing helix chain 'F' and resid 328 through 346 Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing sheet with id= A, first strand: chain 'A' and resid 416 through 419 removed outlier: 6.512A pdb=" N MET A 384 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 383 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA A 353 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 420 through 422 Processing sheet with id= C, first strand: chain 'B' and resid 383 through 386 removed outlier: 3.626A pdb=" N PHE B 383 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 353 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 420 through 422 Processing sheet with id= E, first strand: chain 'C' and resid 402 through 406 removed outlier: 6.431A pdb=" N MET C 384 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C 383 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA C 353 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ARG C 274 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N TYR C 223 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 276 " --> pdb=" O TYR C 223 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER C 225 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS C 278 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 419 through 422 Processing sheet with id= G, first strand: chain 'D' and resid 349 through 354 removed outlier: 6.038A pdb=" N THR D 191 " --> pdb=" O LEU D 350 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR D 352 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASN D 193 " --> pdb=" O THR D 352 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA D 354 " --> pdb=" O ASN D 193 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU D 195 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N PHE D 383 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N MET D 196 " --> pdb=" O PHE D 383 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU D 385 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS D 405 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA D 386 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N GLN D 403 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE D 388 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ILE D 401 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 220 through 225 removed outlier: 6.316A pdb=" N ARG D 274 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N TYR D 223 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE D 276 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N SER D 225 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYS D 278 " --> pdb=" O SER D 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'E' and resid 416 through 418 removed outlier: 6.502A pdb=" N MET E 384 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE E 383 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL E 194 " --> pdb=" O PHE E 383 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 354 " --> pdb=" O LEU E 195 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E 353 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG E 274 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N TYR E 223 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE E 276 " --> pdb=" O TYR E 223 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER E 225 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS E 278 " --> pdb=" O SER E 225 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 349 through 352 removed outlier: 6.196A pdb=" N THR F 191 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N THR F 352 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN F 193 " --> pdb=" O THR F 352 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE F 383 " --> pdb=" O VAL F 194 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'F' and resid 221 through 225 Processing sheet with id= L, first strand: chain 'F' and resid 419 through 422 861 hydrogen bonds defined for protein. 2454 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: 5.61 Time building geometry restraints manager: 9.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 6695 1.35 - 1.50: 5600 1.50 - 1.65: 8864 1.65 - 1.80: 98 1.80 - 1.95: 111 Bond restraints: 21368 Sorted by residual: bond pdb=" CE1 HIS C 253 " pdb=" NE2 HIS C 253 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.66e+01 bond pdb=" CE1 HIS D 87 " pdb=" NE2 HIS D 87 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.52e+01 bond pdb=" CE1 HIS B 152 " pdb=" NE2 HIS B 152 " ideal model delta sigma weight residual 1.321 1.357 -0.036 1.00e-02 1.00e+04 1.27e+01 bond pdb=" N VAL E 19 " pdb=" CA VAL E 19 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.18e-02 7.18e+03 1.13e+01 bond pdb=" N VAL A 323 " pdb=" CA VAL A 323 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.19e-02 7.06e+03 9.93e+00 ... (remaining 21363 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.54: 579 106.54 - 113.48: 11884 113.48 - 120.41: 8188 120.41 - 127.35: 8094 127.35 - 134.28: 221 Bond angle restraints: 28966 Sorted by residual: angle pdb=" N ASP A 82 " pdb=" CA ASP A 82 " pdb=" C ASP A 82 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+01 angle pdb=" CA PHE D 383 " pdb=" CB PHE D 383 " pdb=" CG PHE D 383 " ideal model delta sigma weight residual 113.80 117.73 -3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" C GLY F 151 " pdb=" N HIS F 152 " pdb=" CA HIS F 152 " ideal model delta sigma weight residual 122.30 117.08 5.22 1.35e+00 5.49e-01 1.50e+01 angle pdb=" N ASP F 382 " pdb=" CA ASP F 382 " pdb=" C ASP F 382 " ideal model delta sigma weight residual 114.31 109.48 4.83 1.29e+00 6.01e-01 1.40e+01 angle pdb=" N GLU A 122 " pdb=" CA GLU A 122 " pdb=" C GLU A 122 " ideal model delta sigma weight residual 111.71 107.41 4.30 1.15e+00 7.56e-01 1.40e+01 ... (remaining 28961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 12718 35.65 - 71.31: 149 71.31 - 106.96: 4 106.96 - 142.61: 1 142.61 - 178.27: 4 Dihedral angle restraints: 12876 sinusoidal: 5262 harmonic: 7614 Sorted by residual: dihedral pdb=" O1B AGS E 501 " pdb=" O3B AGS E 501 " pdb=" PB AGS E 501 " pdb=" PG AGS E 501 " ideal model delta sinusoidal sigma weight residual 68.91 -112.82 -178.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS F 501 " pdb=" O3A AGS F 501 " pdb=" PA AGS F 501 " pdb=" PB AGS F 501 " ideal model delta sinusoidal sigma weight residual -67.73 106.47 -174.20 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS B 501 " pdb=" O3B AGS B 501 " pdb=" PB AGS B 501 " pdb=" PG AGS B 501 " ideal model delta sinusoidal sigma weight residual 68.91 -88.57 157.48 1 3.00e+01 1.11e-03 2.05e+01 ... (remaining 12873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2404 0.044 - 0.088: 561 0.088 - 0.132: 237 0.132 - 0.175: 33 0.175 - 0.219: 11 Chirality restraints: 3246 Sorted by residual: chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ARG A 124 " pdb=" N ARG A 124 " pdb=" C ARG A 124 " pdb=" CB ARG A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3243 not shown) Planarity restraints: 3599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 373 " -0.016 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C GLU A 373 " 0.058 2.00e-02 2.50e+03 pdb=" O GLU A 373 " -0.021 2.00e-02 2.50e+03 pdb=" N SER A 374 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 145 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C SER B 145 " 0.039 2.00e-02 2.50e+03 pdb=" O SER B 145 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE B 146 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 122 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C GLU A 122 " -0.036 2.00e-02 2.50e+03 pdb=" O GLU A 122 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS A 123 " 0.012 2.00e-02 2.50e+03 ... (remaining 3596 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 159 2.56 - 3.14: 16967 3.14 - 3.73: 33544 3.73 - 4.31: 47227 4.31 - 4.90: 78111 Nonbonded interactions: 176008 Sorted by model distance: nonbonded pdb=" O3B AGS B 501 " pdb="MG MG B 502 " model vdw 1.973 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 502 " model vdw 1.979 2.170 nonbonded pdb=" O2G AGS E 501 " pdb="MG MG E 502 " model vdw 1.984 2.170 nonbonded pdb=" O2B AGS F 501 " pdb="MG MG F 502 " model vdw 1.993 2.170 nonbonded pdb=" OE2 GLU C 227 " pdb="MG MG C 502 " model vdw 2.005 2.170 ... (remaining 176003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 432) selection = (chain 'C' and resid 1 through 432) selection = (chain 'D' and resid 1 through 432) selection = (chain 'E' and resid 1 through 432) selection = (chain 'F' and resid 1 through 432) } 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: 1.510 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: 0.020 Extract box with map and model: 8.340 Check model and map are aligned: 0.300 Set scattering table: 0.230 Process input model: 51.780 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.110 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:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: