Starting phenix.real_space_refine on Sat Jun 14 20:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e6n_47573/06_2025/9e6n_47573.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e6n_47573/06_2025/9e6n_47573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e6n_47573/06_2025/9e6n_47573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e6n_47573/06_2025/9e6n_47573.map" model { file = "/net/cci-nas-00/data/ceres_data/9e6n_47573/06_2025/9e6n_47573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e6n_47573/06_2025/9e6n_47573.cif" } resolution = 2.8 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= 0.027 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 36 5.49 5 Mg 6 5.21 5 S 108 5.16 5 C 10268 2.51 5 N 2871 2.21 5 O 3233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16522 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "B" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "C" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "D" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "E" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2431 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "F" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2442 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 307} Chain: "G" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 263 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "I" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 276 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "J" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 267 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "X" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 360 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.23, per 1000 atoms: 0.62 Number of scatterers: 16522 At special positions: 0 Unit cell: (119.13, 113.715, 167.865, 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 108 16.00 P 36 15.00 Mg 6 11.99 O 3233 8.00 N 2871 7.00 C 10268 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 - 3.00 Amino acid : True - 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: 4.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3812 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 18 sheets defined 50.7% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.660A pdb=" N GLU A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.524A pdb=" N CYS A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 236 removed outlier: 3.902A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 254 through 272 removed outlier: 3.891A pdb=" N LEU A 262 " --> pdb=" O GLN A 258 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.799A pdb=" N PHE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 347 through 354 removed outlier: 3.582A pdb=" N SER A 354 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 92 through 102 Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.551A pdb=" N LEU B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 140 removed outlier: 3.551A pdb=" N LEU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.561A pdb=" N VAL B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 225 through 236 removed outlier: 4.010A pdb=" N LEU B 229 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 Processing helix chain 'B' and resid 254 through 270 removed outlier: 3.941A pdb=" N LEU B 262 " --> pdb=" O GLN B 258 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP B 263 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 290 removed outlier: 4.485A pdb=" N TYR B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.564A pdb=" N GLN C 87 " --> pdb=" O GLU C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 102 removed outlier: 3.623A pdb=" N VAL C 96 " --> pdb=" O THR C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.520A pdb=" N LEU C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 140 removed outlier: 3.511A pdb=" N ASP C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.560A pdb=" N GLU C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.559A pdb=" N VAL C 200 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 225 through 236 removed outlier: 4.023A pdb=" N LEU C 229 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 254 through 270 removed outlier: 4.137A pdb=" N LEU C 262 " --> pdb=" O GLN C 258 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP C 263 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 290 removed outlier: 4.485A pdb=" N TYR C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 294 No H-bonds generated for 'chain 'C' and resid 292 through 294' Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 346 through 354 removed outlier: 3.740A pdb=" N MET C 350 " --> pdb=" O GLY C 346 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 354 " --> pdb=" O MET C 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 113 Processing helix chain 'D' and resid 114 through 121 removed outlier: 3.512A pdb=" N LEU D 118 " --> pdb=" O PRO D 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 140 Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.721A pdb=" N GLU D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.763A pdb=" N VAL D 200 " --> pdb=" O HIS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 225 through 237 removed outlier: 3.957A pdb=" N LEU D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 254 through 272 removed outlier: 3.906A pdb=" N LEU D 262 " --> pdb=" O GLN D 258 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.717A pdb=" N PHE D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 295 through 318 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.556A pdb=" N MET D 350 " --> pdb=" O GLY D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.587A pdb=" N GLN E 87 " --> pdb=" O GLU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.622A pdb=" N VAL E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 114 through 120 removed outlier: 3.640A pdb=" N LEU E 118 " --> pdb=" O PRO E 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 119 " --> pdb=" O ARG E 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU E 120 " --> pdb=" O LYS E 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 114 through 120' Processing helix chain 'E' and resid 125 through 140 removed outlier: 3.519A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 190 through 202 removed outlier: 3.500A pdb=" N VAL E 200 " --> pdb=" O HIS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 225 through 237 removed outlier: 3.911A pdb=" N LEU E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN E 234 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 254 through 270 removed outlier: 3.965A pdb=" N LEU E 262 " --> pdb=" O GLN E 258 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP E 263 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 292 through 294 No H-bonds generated for 'chain 'E' and resid 292 through 294' Processing helix chain 'E' and resid 295 through 318 Processing helix chain 'E' and resid 346 through 354 removed outlier: 3.523A pdb=" N MET E 350 " --> pdb=" O GLY E 346 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 92 through 102 removed outlier: 3.625A pdb=" N VAL F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 113 Processing helix chain 'F' and resid 114 through 120 removed outlier: 4.031A pdb=" N LEU F 118 " --> pdb=" O PRO F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 140 removed outlier: 3.505A pdb=" N GLU F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 164 through 172 Processing helix chain 'F' and resid 190 through 202 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 225 through 237 removed outlier: 3.785A pdb=" N LEU F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 254 through 272 removed outlier: 4.007A pdb=" N LEU F 262 " --> pdb=" O GLN F 258 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU F 271 " --> pdb=" O GLN F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 290 removed outlier: 4.403A pdb=" N TYR F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE F 290 " --> pdb=" O TYR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 318 Processing helix chain 'F' and resid 347 through 354 Processing helix chain 'G' and resid 124 through 137 removed outlier: 3.652A pdb=" N TYR G 129 " --> pdb=" O LYS G 125 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 137 Processing helix chain 'I' and resid 123 through 137 removed outlier: 3.565A pdb=" N GLU I 130 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 137 removed outlier: 3.515A pdb=" N LYS J 133 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 136 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 391 through 393 removed outlier: 6.853A pdb=" N ARG A 357 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 184 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE A 277 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR A 324 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL A 279 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU A 216 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP A 280 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE A 218 " --> pdb=" O ASP A 280 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 248 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 329 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AA5, first strand: chain 'B' and resid 391 through 393 removed outlier: 6.854A pdb=" N ARG B 357 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR B 181 " --> pdb=" O VAL B 323 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ASN B 325 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 183 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER B 275 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL B 322 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 277 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR B 324 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL B 279 " --> pdb=" O THR B 324 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LYS B 214 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU B 276 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 327 through 329 Processing sheet with id=AA7, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 393 removed outlier: 6.637A pdb=" N ARG C 357 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N THR C 181 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN C 325 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 183 " --> pdb=" O ASN C 325 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER C 275 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL C 322 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 277 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N THR C 324 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL C 279 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS C 214 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 276 " --> pdb=" O LYS C 214 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 327 through 329 Processing sheet with id=AB1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AB2, first strand: chain 'D' and resid 391 through 393 removed outlier: 6.751A pdb=" N ARG D 357 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY D 185 " --> pdb=" O ASN D 325 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 320 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LYS D 214 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE D 277 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU D 216 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL D 279 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE D 218 " --> pdb=" O VAL D 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 329 Processing sheet with id=AB4, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AB5, first strand: chain 'E' and resid 391 through 393 removed outlier: 6.758A pdb=" N ARG E 357 " --> pdb=" O VAL E 373 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR E 181 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN E 325 " --> pdb=" O THR E 181 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU E 183 " --> pdb=" O ASN E 325 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SER E 275 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL E 322 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE E 277 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR E 324 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL E 279 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LYS E 214 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU E 276 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 327 through 329 Processing sheet with id=AB7, first strand: chain 'F' and resid 159 through 160 Processing sheet with id=AB8, first strand: chain 'F' and resid 247 through 251 removed outlier: 5.284A pdb=" N LYS F 214 " --> pdb=" O PHE F 274 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 276 " --> pdb=" O LYS F 214 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N SER F 275 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL F 322 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE F 277 " --> pdb=" O VAL F 322 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR F 324 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL F 279 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG F 357 " --> pdb=" O VAL F 373 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 327 through 329 removed outlier: 3.540A pdb=" N VAL F 328 " --> pdb=" O LYS F 343 " (cutoff:3.500A) 796 hydrogen bonds defined for protein. 2235 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: 5.19 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5019 1.33 - 1.45: 2127 1.45 - 1.57: 9419 1.57 - 1.69: 65 1.69 - 1.81: 168 Bond restraints: 16798 Sorted by residual: bond pdb=" C ASN J 141 " pdb=" N LYS J 142 " ideal model delta sigma weight residual 1.332 1.414 -0.082 1.35e-02 5.49e+03 3.66e+01 bond pdb=" C LYS J 142 " pdb=" N VAL J 143 " ideal model delta sigma weight residual 1.328 1.265 0.063 1.19e-02 7.06e+03 2.79e+01 bond pdb=" N LYS J 144 " pdb=" CA LYS J 144 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.09e-02 8.42e+03 9.99e+00 bond pdb=" N VAL J 147 " pdb=" CA VAL J 147 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.22e-02 6.72e+03 9.36e+00 bond pdb=" N SER K 150 " pdb=" CA SER K 150 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.72e+00 ... (remaining 16793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 22377 1.73 - 3.45: 323 3.45 - 5.18: 31 5.18 - 6.90: 4 6.90 - 8.63: 10 Bond angle restraints: 22745 Sorted by residual: angle pdb=" N LEU K 124 " pdb=" CA LEU K 124 " pdb=" C LEU K 124 " ideal model delta sigma weight residual 111.75 119.86 -8.11 1.28e+00 6.10e-01 4.02e+01 angle pdb=" N VAL J 138 " pdb=" CA VAL J 138 " pdb=" C VAL J 138 " ideal model delta sigma weight residual 108.17 115.69 -7.52 1.40e+00 5.10e-01 2.88e+01 angle pdb=" N TYR K 129 " pdb=" CA TYR K 129 " pdb=" C TYR K 129 " ideal model delta sigma weight residual 111.36 105.74 5.62 1.09e+00 8.42e-01 2.66e+01 angle pdb=" N GLN J 137 " pdb=" CA GLN J 137 " pdb=" C GLN J 137 " ideal model delta sigma weight residual 111.54 118.51 -6.97 1.36e+00 5.41e-01 2.63e+01 angle pdb=" N TYR J 136 " pdb=" CA TYR J 136 " pdb=" C TYR J 136 " ideal model delta sigma weight residual 113.61 121.12 -7.51 1.50e+00 4.44e-01 2.51e+01 ... (remaining 22740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9290 17.97 - 35.93: 739 35.93 - 53.90: 201 53.90 - 71.86: 53 71.86 - 89.83: 18 Dihedral angle restraints: 10301 sinusoidal: 4364 harmonic: 5937 Sorted by residual: dihedral pdb=" N GLN J 137 " pdb=" C GLN J 137 " pdb=" CA GLN J 137 " pdb=" CB GLN J 137 " ideal model delta harmonic sigma weight residual 122.80 132.79 -9.99 0 2.50e+00 1.60e-01 1.60e+01 dihedral pdb=" C GLN J 137 " pdb=" N GLN J 137 " pdb=" CA GLN J 137 " pdb=" CB GLN J 137 " ideal model delta harmonic sigma weight residual -122.60 -132.37 9.77 0 2.50e+00 1.60e-01 1.53e+01 dihedral pdb=" CG ARG B 228 " pdb=" CD ARG B 228 " pdb=" NE ARG B 228 " pdb=" CZ ARG B 228 " ideal model delta sinusoidal sigma weight residual 90.00 134.85 -44.85 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 10298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2342 0.075 - 0.151: 225 0.151 - 0.226: 10 0.226 - 0.301: 1 0.301 - 0.376: 3 Chirality restraints: 2581 Sorted by residual: chirality pdb=" CA GLN J 137 " pdb=" N GLN J 137 " pdb=" C GLN J 137 " pdb=" CB GLN J 137 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA TYR J 136 " pdb=" N TYR J 136 " pdb=" C TYR J 136 " pdb=" CB TYR J 136 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA TYR K 129 " pdb=" N TYR K 129 " pdb=" C TYR K 129 " pdb=" CB TYR K 129 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 2578 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 128 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C ILE K 128 " -0.025 2.00e-02 2.50e+03 pdb=" O ILE K 128 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR K 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 187 " 0.006 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE C 187 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE C 187 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE C 187 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 187 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 187 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 335 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C MET D 335 " -0.023 2.00e-02 2.50e+03 pdb=" O MET D 335 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA D 336 " 0.008 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 118 2.56 - 3.15: 12685 3.15 - 3.73: 24926 3.73 - 4.32: 36117 4.32 - 4.90: 59624 Nonbonded interactions: 133470 Sorted by model distance: nonbonded pdb=" OG SER B 192 " pdb="MG MG B 502 " model vdw 1.976 2.170 nonbonded pdb=" O1G ATP A 501 " pdb="MG MG A 502 " model vdw 2.006 2.170 nonbonded pdb=" OG SER D 192 " pdb="MG MG D 502 " model vdw 2.014 2.170 nonbonded pdb=" OG SER C 192 " pdb="MG MG C 502 " model vdw 2.018 2.170 nonbonded pdb=" O1G ATP D 501 " pdb="MG MG D 502 " model vdw 2.020 2.170 ... (remaining 133465 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 81 through 400 or resid 501 through 502)) selection = chain 'B' selection = (chain 'C' and (resid 81 through 400 or resid 501 through 502)) selection = (chain 'D' and (resid 81 through 400 or resid 501 through 502)) selection = chain 'E' selection = (chain 'F' and (resid 81 through 400 or resid 501 through 502)) } ncs_group { reference = chain 'G' selection = (chain 'H' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) selection = (chain 'I' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) selection = (chain 'J' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) selection = (chain 'K' and ((resid 121 and (name N or name CA or name C or name O or name CB \ )) or resid 122 through 152)) } 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: 1.040 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 38.530 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.003 0.082 16798 Z= 0.157 Angle : 0.499 8.631 22745 Z= 0.293 Chirality : 0.044 0.376 2581 Planarity : 0.003 0.033 2873 Dihedral : 14.949 89.830 6489 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.41 % Allowed : 0.41 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.19), residues: 2063 helix: 0.67 (0.17), residues: 962 sheet: 1.28 (0.31), residues: 326 loop : -0.05 (0.24), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 105 PHE 0.024 0.001 PHE C 187 TYR 0.014 0.001 TYR I 145 ARG 0.003 0.000 ARG B 188 Details of bonding type rmsd hydrogen bonds : bond 0.23908 ( 796) hydrogen bonds : angle 7.35199 ( 2235) covalent geometry : bond 0.00280 (16798) covalent geometry : angle 0.49867 (22745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 1.728 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8913 (m110) cc_final: 0.8658 (m-40) REVERT: B 315 ASP cc_start: 0.8110 (m-30) cc_final: 0.7877 (m-30) REVERT: D 335 MET cc_start: -0.0601 (ppp) cc_final: -0.0854 (pmm) REVERT: F 89 ASN cc_start: 0.8861 (t0) cc_final: 0.8472 (t0) REVERT: G 139 ASP cc_start: 0.8147 (p0) cc_final: 0.7851 (p0) REVERT: K 127 LEU cc_start: 0.8737 (tt) cc_final: 0.8382 (tp) REVERT: K 129 TYR cc_start: 0.9023 (t80) cc_final: 0.8630 (t80) REVERT: K 139 ASP cc_start: 0.8182 (p0) cc_final: 0.7512 (p0) outliers start: 7 outliers final: 0 residues processed: 179 average time/residue: 1.4036 time to fit residues: 277.3717 Evaluate side-chains 149 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 121 optimal weight: 0.0020 chunk 188 optimal weight: 10.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.092293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.062173 restraints weight = 38465.438| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 3.58 r_work: 0.2786 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16798 Z= 0.169 Angle : 0.535 8.357 22745 Z= 0.284 Chirality : 0.043 0.148 2581 Planarity : 0.004 0.038 2873 Dihedral : 13.107 89.986 2632 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.93 % Allowed : 6.89 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.00 (0.19), residues: 2063 helix: 1.08 (0.18), residues: 950 sheet: 1.26 (0.30), residues: 326 loop : 0.02 (0.23), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 196 PHE 0.017 0.001 PHE C 187 TYR 0.010 0.001 TYR I 145 ARG 0.005 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 796) hydrogen bonds : angle 4.97736 ( 2235) covalent geometry : bond 0.00383 (16798) covalent geometry : angle 0.53509 (22745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 2.271 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8964 (m110) cc_final: 0.8530 (m-40) REVERT: B 234 GLN cc_start: 0.8621 (mt0) cc_final: 0.8104 (mt0) REVERT: B 315 ASP cc_start: 0.8185 (m-30) cc_final: 0.7870 (m-30) REVERT: B 353 SER cc_start: 0.8656 (m) cc_final: 0.8411 (m) REVERT: C 335 MET cc_start: 0.0217 (OUTLIER) cc_final: -0.0672 (pmm) REVERT: E 108 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: F 89 ASN cc_start: 0.8963 (t0) cc_final: 0.8536 (t0) REVERT: G 139 ASP cc_start: 0.8671 (p0) cc_final: 0.7966 (p0) REVERT: H 139 ASP cc_start: 0.7580 (t0) cc_final: 0.7292 (t0) REVERT: I 133 LYS cc_start: 0.8615 (tppp) cc_final: 0.8309 (ttmm) REVERT: I 137 GLN cc_start: 0.8428 (mp10) cc_final: 0.8195 (mp10) REVERT: K 122 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8692 (ttmt) REVERT: K 129 TYR cc_start: 0.9402 (t80) cc_final: 0.9040 (t80) REVERT: K 139 ASP cc_start: 0.8514 (p0) cc_final: 0.7811 (p0) outliers start: 16 outliers final: 6 residues processed: 169 average time/residue: 1.5698 time to fit residues: 292.9931 Evaluate side-chains 159 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 126 ASP Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 80 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.093285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.064092 restraints weight = 38605.775| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 3.44 r_work: 0.2880 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16798 Z= 0.123 Angle : 0.490 8.562 22745 Z= 0.257 Chirality : 0.041 0.157 2581 Planarity : 0.003 0.036 2873 Dihedral : 12.522 89.535 2632 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.34 % Allowed : 8.81 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 1.11 (0.19), residues: 2063 helix: 1.19 (0.18), residues: 968 sheet: 1.58 (0.31), residues: 304 loop : -0.06 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 196 PHE 0.015 0.001 PHE C 187 TYR 0.019 0.001 TYR H 129 ARG 0.006 0.000 ARG E 260 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 796) hydrogen bonds : angle 4.44119 ( 2235) covalent geometry : bond 0.00278 (16798) covalent geometry : angle 0.49016 (22745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4126 Ramachandran restraints generated. 2063 Oldfield, 0 Emsley, 2063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.861 Fit side-chains revert: symmetry clash REVERT: B 89 ASN cc_start: 0.8907 (m110) cc_final: 0.8457 (m-40) REVERT: B 152 MET cc_start: 0.7939 (tmm) cc_final: 0.7697 (tmm) REVERT: B 234 GLN cc_start: 0.8581 (mt0) cc_final: 0.7955 (mt0) REVERT: B 315 ASP cc_start: 0.8176 (m-30) cc_final: 0.7857 (m-30) REVERT: B 353 SER cc_start: 0.8671 (m) cc_final: 0.8446 (m) REVERT: C 335 MET cc_start: 0.0227 (OUTLIER) cc_final: -0.0678 (pmm) REVERT: D 268 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8860 (mtm) REVERT: D 269 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.9035 (mtt) REVERT: E 108 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: F 89 ASN cc_start: 0.8979 (t0) cc_final: 0.8547 (t0) REVERT: G 139 ASP cc_start: 0.8633 (p0) cc_final: 0.8420 (p0) REVERT: I 133 LYS cc_start: 0.8619 (tppp) cc_final: 0.8324 (ttmm) REVERT: I 137 GLN cc_start: 0.8536 (mp10) cc_final: 0.8230 (mp10) REVERT: J 121 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8882 (tptp) REVERT: K 122 LYS cc_start: 0.9179 (ttmt) cc_final: 0.8947 (ttpt) REVERT: K 129 TYR cc_start: 0.9441 (t80) cc_final: 0.9008 (t80) REVERT: K 130 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9047 (mt-10) REVERT: K 139 ASP cc_start: 0.8526 (p0) cc_final: 0.7904 (p0) outliers start: 23 outliers final: 7 residues processed: 167 average time/residue: 1.5103 time to fit residues: 277.8687 Evaluate side-chains 163 residues out of total 1714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 268 MET Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain F residue 383 CYS Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 145 TYR Chi-restraints excluded: chain K residue 123 SER Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 146 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4091 > 50: distance: 15 - 32: 6.497 distance: 23 - 44: 14.401 distance: 27 - 32: 3.859 distance: 28 - 51: 8.423 distance: 32 - 33: 13.952 distance: 33 - 34: 8.970 distance: 33 - 36: 13.647 distance: 34 - 35: 19.346 distance: 34 - 37: 36.056 distance: 37 - 38: 7.001 distance: 38 - 39: 13.225 distance: 38 - 41: 8.585 distance: 39 - 40: 12.648 distance: 39 - 44: 8.368 distance: 41 - 42: 16.328 distance: 41 - 43: 12.594 distance: 44 - 45: 6.672 distance: 45 - 46: 9.269 distance: 45 - 48: 9.593 distance: 46 - 47: 6.417 distance: 46 - 51: 3.495 distance: 48 - 49: 8.946 distance: 48 - 50: 8.145 distance: 51 - 52: 3.881 distance: 52 - 53: 5.722 distance: 52 - 55: 13.060 distance: 53 - 54: 3.229 distance: 53 - 57: 11.148 distance: 55 - 56: 8.524 distance: 57 - 58: 3.238 distance: 58 - 59: 3.269 distance: 58 - 61: 13.369 distance: 59 - 60: 9.601 distance: 59 - 66: 14.502 distance: 61 - 62: 12.176 distance: 62 - 63: 5.947 distance: 63 - 64: 10.243 distance: 63 - 65: 6.464 distance: 66 - 67: 6.534 distance: 67 - 68: 6.365 distance: 67 - 70: 4.547 distance: 68 - 74: 4.924 distance: 70 - 71: 9.250 distance: 70 - 72: 6.217 distance: 71 - 73: 9.573 distance: 74 - 75: 3.185 distance: 74 - 80: 5.426 distance: 75 - 76: 5.407 distance: 75 - 78: 9.018 distance: 76 - 81: 8.276 distance: 77 - 97: 5.685 distance: 78 - 79: 4.101 distance: 79 - 80: 8.282 distance: 81 - 82: 4.603 distance: 82 - 83: 6.370 distance: 82 - 85: 4.248 distance: 83 - 84: 7.090 distance: 83 - 89: 3.741 distance: 84 - 105: 5.085 distance: 85 - 86: 8.402 distance: 86 - 87: 4.012 distance: 86 - 88: 4.967 distance: 89 - 90: 4.907 distance: 90 - 91: 3.287 distance: 90 - 93: 3.816 distance: 93 - 94: 3.044 distance: 94 - 95: 4.582 distance: 97 - 98: 6.487 distance: 98 - 99: 6.138 distance: 98 - 101: 9.065 distance: 99 - 100: 9.159 distance: 99 - 105: 9.147 distance: 101 - 102: 11.728 distance: 101 - 103: 10.225 distance: 102 - 104: 14.263