Starting phenix.real_space_refine on Tue Jun 10 18:26:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi6_16887/06_2025/8oi6_16887.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi6_16887/06_2025/8oi6_16887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oi6_16887/06_2025/8oi6_16887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi6_16887/06_2025/8oi6_16887.map" model { file = "/net/cci-nas-00/data/ceres_data/8oi6_16887/06_2025/8oi6_16887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi6_16887/06_2025/8oi6_16887.cif" } resolution = 3.59 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= -0.002 sd= 0.214 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 8 5.49 5 Mg 4 5.21 5 S 83 5.16 5 C 7304 2.51 5 N 1945 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11573 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2843 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 19, 'TRANS': 344} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2767 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 18, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" 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: "B" 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: "C" 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: "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} Time building chain proxies: 8.76, per 1000 atoms: 0.76 Number of scatterers: 11573 At special positions: 0 Unit cell: (94.38, 89.54, 165.77, 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 83 16.00 P 8 15.00 Mg 4 11.99 O 2229 8.00 N 1945 7.00 C 7304 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 1.5 seconds 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 2722 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 22 sheets defined 49.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.569A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.864A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.699A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 214 removed outlier: 4.041A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.783A pdb=" N GLU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.599A pdb=" N ILE A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.050A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.007A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.531A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 93 removed outlier: 3.570A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.293A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.518A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.678A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.797A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.518A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 285 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.165A pdb=" N LYS B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.958A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.568A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.908A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.680A pdb=" N SER B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.500A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.691A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS C 87 " --> pdb=" O GLU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.810A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.507A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.549A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.733A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.430A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.501A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.916A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.585A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.567A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.652A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.585A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.746A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.513A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.851A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.550A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.658A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 285 removed outlier: 3.602A pdb=" N MET D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N CYS D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 301 through 306 removed outlier: 4.019A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 354 removed outlier: 4.011A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.565A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 9 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.839A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.171A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.667A pdb=" N PHE B 31 " --> pdb=" O CYS B 17 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.698A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.574A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.654A pdb=" N PHE C 31 " --> pdb=" O CYS C 17 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR C 106 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.815A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.705A pdb=" N SER C 155 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 8 through 10 removed outlier: 6.071A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 133 " --> pdb=" O VAL D 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 16 through 19 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.755A pdb=" N LYS D 68 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG D 37 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 176 through 178 removed outlier: 5.947A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 529 hydrogen bonds defined for protein. 1329 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: 3.70 Time building geometry restraints manager: 3.67 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: 3734 1.34 - 1.46: 2694 1.46 - 1.58: 5233 1.58 - 1.70: 18 1.70 - 1.82: 143 Bond restraints: 11822 Sorted by residual: bond pdb=" N HYP I 6 " pdb=" CD HYP I 6 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" N HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.35e+02 bond pdb=" N HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.473 1.635 -0.162 1.40e-02 5.10e+03 1.33e+02 bond pdb=" CG HYP H 6 " pdb=" CD HYP H 6 " ideal model delta sigma weight residual 1.530 1.371 0.159 2.00e-02 2.50e+03 6.30e+01 bond pdb=" CG HYP J 6 " pdb=" CD HYP J 6 " ideal model delta sigma weight residual 1.530 1.372 0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 11817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 15688 1.80 - 3.60: 254 3.60 - 5.39: 66 5.39 - 7.19: 30 7.19 - 8.99: 7 Bond angle restraints: 16045 Sorted by residual: angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 107.42 -4.42 1.10e+00 8.26e-01 1.61e+01 angle pdb=" N HYP H 6 " pdb=" CD HYP H 6 " pdb=" CG HYP H 6 " ideal model delta sigma weight residual 103.20 109.04 -5.84 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 116.88 -6.38 1.70e+00 3.46e-01 1.41e+01 angle pdb=" N HYP J 6 " pdb=" CA HYP J 6 " pdb=" CB HYP J 6 " ideal model delta sigma weight residual 103.00 106.86 -3.86 1.10e+00 8.26e-01 1.23e+01 angle pdb=" N HYP I 6 " pdb=" CA HYP I 6 " pdb=" CB HYP I 6 " ideal model delta sigma weight residual 103.00 106.84 -3.84 1.10e+00 8.26e-01 1.22e+01 ... (remaining 16040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.98: 6878 33.98 - 67.96: 224 67.96 - 101.94: 17 101.94 - 135.92: 4 135.92 - 169.90: 3 Dihedral angle restraints: 7126 sinusoidal: 2885 harmonic: 4241 Sorted by residual: dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 130.10 169.90 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 131.78 168.22 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 137.14 162.86 1 2.00e+01 2.50e-03 4.69e+01 ... (remaining 7123 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1562 0.061 - 0.122: 226 0.122 - 0.184: 4 0.184 - 0.245: 0 0.245 - 0.306: 3 Chirality restraints: 1795 Sorted by residual: chirality pdb=" CA HYP I 6 " pdb=" N HYP I 6 " pdb=" C HYP I 6 " pdb=" CB HYP I 6 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA HYP J 6 " pdb=" N HYP J 6 " pdb=" C HYP J 6 " pdb=" CB HYP J 6 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA HYP H 6 " pdb=" N HYP H 6 " pdb=" C HYP H 6 " pdb=" CB HYP H 6 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1792 not shown) Planarity restraints: 2037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 117 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" CD GLU A 117 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 117 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 117 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 166 " -0.011 2.00e-02 2.50e+03 1.15e-02 2.63e+00 pdb=" CG TYR C 166 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR C 166 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 166 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 166 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 166 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 166 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 366 " -0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO B 367 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 367 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 367 " -0.022 5.00e-02 4.00e+02 ... (remaining 2034 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 45 2.43 - 3.04: 7139 3.04 - 3.66: 17282 3.66 - 4.28: 26390 4.28 - 4.90: 43999 Nonbonded interactions: 94855 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.808 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.810 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.820 3.620 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.126 2.170 nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.137 2.170 ... (remaining 94850 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 6 through 362 or resid 401 through 402)) selection = (chain 'B' and (resid 6 through 362 or resid 401 through 402)) selection = (chain 'C' and (resid 6 through 362 or resid 401 through 402)) selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.530 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.290 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 0.163 11828 Z= 0.303 Angle : 0.648 10.099 16063 Z= 0.305 Chirality : 0.043 0.306 1795 Planarity : 0.003 0.040 2031 Dihedral : 16.973 169.900 4386 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 0.24 % Allowed : 17.74 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1418 helix: 0.06 (0.22), residues: 538 sheet: 0.56 (0.37), residues: 212 loop : 0.49 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 86 HIS 0.011 0.001 HIS B 371 PHE 0.008 0.001 PHE A 124 TYR 0.028 0.001 TYR C 166 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.01252 ( 6) link_TRANS : angle 2.98562 ( 18) hydrogen bonds : bond 0.30317 ( 525) hydrogen bonds : angle 8.74333 ( 1329) covalent geometry : bond 0.00523 (11822) covalent geometry : angle 0.64020 (16045) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 88 average time/residue: 0.1975 time to fit residues: 27.3240 Evaluate side-chains 84 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain H residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 225 GLN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS D 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.072954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.061999 restraints weight = 33810.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064157 restraints weight = 17398.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.065586 restraints weight = 10806.452| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11828 Z= 0.269 Angle : 0.691 7.003 16063 Z= 0.337 Chirality : 0.047 0.175 1795 Planarity : 0.004 0.038 2031 Dihedral : 11.989 176.450 1673 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 2.28 % Allowed : 16.60 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1418 helix: 0.19 (0.22), residues: 581 sheet: 0.45 (0.34), residues: 250 loop : 0.54 (0.26), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 1 HIS 0.005 0.002 HIS B 101 PHE 0.018 0.002 PHE C 352 TYR 0.017 0.002 TYR B 143 ARG 0.003 0.001 ARG A 183 Details of bonding type rmsd link_TRANS : bond 0.00530 ( 6) link_TRANS : angle 0.89185 ( 18) hydrogen bonds : bond 0.05094 ( 525) hydrogen bonds : angle 5.82805 ( 1329) covalent geometry : bond 0.00622 (11822) covalent geometry : angle 0.69055 (16045) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 1.460 Fit side-chains REVERT: A 80 ASP cc_start: 0.7982 (t0) cc_final: 0.7651 (t0) REVERT: B 123 MET cc_start: 0.8287 (mmm) cc_final: 0.7967 (mmt) REVERT: B 314 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: C 330 ILE cc_start: 0.9512 (OUTLIER) cc_final: 0.9206 (tp) REVERT: D 355 MET cc_start: 0.7593 (pmm) cc_final: 0.7284 (pmm) outliers start: 28 outliers final: 13 residues processed: 102 average time/residue: 0.1885 time to fit residues: 31.1578 Evaluate side-chains 91 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 80 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.074564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.063607 restraints weight = 33930.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.065824 restraints weight = 17162.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.067307 restraints weight = 10551.685| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11828 Z= 0.119 Angle : 0.565 7.204 16063 Z= 0.265 Chirality : 0.044 0.199 1795 Planarity : 0.004 0.035 2031 Dihedral : 10.908 160.173 1668 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.83 % Favored : 98.10 % Rotamer: Outliers : 1.63 % Allowed : 17.66 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1418 helix: 0.51 (0.22), residues: 582 sheet: 0.42 (0.34), residues: 253 loop : 0.67 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.003 0.001 HIS D 87 PHE 0.013 0.001 PHE D 31 TYR 0.015 0.001 TYR B 143 ARG 0.002 0.000 ARG C 116 Details of bonding type rmsd link_TRANS : bond 0.00180 ( 6) link_TRANS : angle 0.37377 ( 18) hydrogen bonds : bond 0.03463 ( 525) hydrogen bonds : angle 5.22826 ( 1329) covalent geometry : bond 0.00268 (11822) covalent geometry : angle 0.56475 (16045) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.313 Fit side-chains REVERT: A 80 ASP cc_start: 0.7995 (t0) cc_final: 0.7535 (t0) REVERT: B 314 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: C 82 MET cc_start: 0.8438 (tpt) cc_final: 0.8197 (tpt) REVERT: C 132 MET cc_start: 0.8218 (tmm) cc_final: 0.8017 (tmm) outliers start: 20 outliers final: 9 residues processed: 100 average time/residue: 0.1965 time to fit residues: 31.3588 Evaluate side-chains 89 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 12 ASN ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.072658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.061911 restraints weight = 34349.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.064005 restraints weight = 17589.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.065409 restraints weight = 10891.605| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11828 Z= 0.228 Angle : 0.626 6.760 16063 Z= 0.298 Chirality : 0.046 0.208 1795 Planarity : 0.004 0.038 2031 Dihedral : 10.245 147.859 1668 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.33 % Favored : 97.60 % Rotamer: Outliers : 2.85 % Allowed : 18.14 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1418 helix: 0.51 (0.23), residues: 585 sheet: 0.35 (0.34), residues: 250 loop : 0.51 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 340 HIS 0.011 0.001 HIS B 371 PHE 0.015 0.002 PHE C 352 TYR 0.015 0.001 TYR B 143 ARG 0.008 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00376 ( 6) link_TRANS : angle 0.50990 ( 18) hydrogen bonds : bond 0.03578 ( 525) hydrogen bonds : angle 5.15314 ( 1329) covalent geometry : bond 0.00533 (11822) covalent geometry : angle 0.62571 (16045) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 1.310 Fit side-chains REVERT: A 80 ASP cc_start: 0.8071 (t0) cc_final: 0.7521 (t0) REVERT: B 269 MET cc_start: 0.7827 (mtp) cc_final: 0.7558 (mtm) REVERT: B 314 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7798 (tt0) REVERT: I 5 CYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8110 (p) outliers start: 35 outliers final: 17 residues processed: 107 average time/residue: 0.1851 time to fit residues: 31.5973 Evaluate side-chains 94 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 83 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 13 optimal weight: 0.0670 chunk 36 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.073953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063038 restraints weight = 33645.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.065223 restraints weight = 17104.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.066686 restraints weight = 10580.255| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11828 Z= 0.117 Angle : 0.554 6.601 16063 Z= 0.258 Chirality : 0.044 0.199 1795 Planarity : 0.004 0.036 2031 Dihedral : 9.716 142.703 1668 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.97 % Favored : 97.95 % Rotamer: Outliers : 1.46 % Allowed : 18.80 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.23), residues: 1418 helix: 0.71 (0.23), residues: 589 sheet: 0.34 (0.34), residues: 253 loop : 0.68 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 340 HIS 0.008 0.001 HIS B 371 PHE 0.012 0.001 PHE D 31 TYR 0.007 0.001 TYR A 143 ARG 0.003 0.000 ARG D 147 Details of bonding type rmsd link_TRANS : bond 0.00196 ( 6) link_TRANS : angle 0.32619 ( 18) hydrogen bonds : bond 0.02878 ( 525) hydrogen bonds : angle 4.89839 ( 1329) covalent geometry : bond 0.00268 (11822) covalent geometry : angle 0.55426 (16045) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2836 Ramachandran restraints generated. 1418 Oldfield, 0 Emsley, 1418 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.287 Fit side-chains REVERT: A 16 MET cc_start: 0.7676 (ttm) cc_final: 0.7467 (ttm) REVERT: A 80 ASP cc_start: 0.8002 (t0) cc_final: 0.7441 (t0) REVERT: B 314 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: C 82 MET cc_start: 0.8497 (tpt) cc_final: 0.8257 (tpt) REVERT: H 5 CYS cc_start: 0.6757 (t) cc_final: 0.5822 (m) REVERT: I 5 CYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8009 (p) REVERT: J 5 CYS cc_start: 0.7702 (m) cc_final: 0.7369 (t) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 0.1798 time to fit residues: 28.2582 Evaluate side-chains 91 residues out of total 1229 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 371 HIS Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 17 CYS Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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: 62.1241 > 50: distance: 4 - 9: 25.043 distance: 9 - 10: 15.578 distance: 9 - 144: 23.957 distance: 10 - 11: 18.953 distance: 10 - 13: 17.673 distance: 11 - 12: 24.620 distance: 11 - 16: 13.469 distance: 12 - 141: 26.000 distance: 13 - 14: 11.025 distance: 13 - 15: 14.106 distance: 16 - 17: 30.055 distance: 16 - 107: 25.846 distance: 17 - 18: 58.105 distance: 18 - 19: 40.640 distance: 18 - 20: 29.302 distance: 19 - 104: 26.672 distance: 20 - 21: 12.301 distance: 21 - 22: 29.703 distance: 21 - 24: 35.703 distance: 22 - 23: 34.219 distance: 22 - 31: 42.765 distance: 23 - 128: 19.553 distance: 24 - 25: 30.770 distance: 25 - 26: 9.175 distance: 26 - 27: 4.531 distance: 27 - 28: 7.237 distance: 28 - 29: 16.531 distance: 28 - 30: 19.497 distance: 31 - 32: 24.775 distance: 31 - 37: 11.299 distance: 32 - 33: 14.609 distance: 32 - 35: 12.664 distance: 33 - 34: 12.420 distance: 33 - 38: 14.746 distance: 35 - 36: 10.236 distance: 36 - 37: 11.703 distance: 38 - 39: 11.158 distance: 39 - 40: 19.121 distance: 39 - 42: 8.338 distance: 40 - 41: 23.744 distance: 40 - 49: 14.161 distance: 42 - 43: 18.721 distance: 43 - 44: 17.294 distance: 44 - 45: 7.208 distance: 45 - 46: 9.102 distance: 46 - 47: 9.589 distance: 46 - 48: 8.365 distance: 49 - 50: 26.693 distance: 50 - 51: 21.263 distance: 50 - 53: 14.405 distance: 51 - 52: 8.920 distance: 51 - 59: 20.277 distance: 53 - 54: 16.995 distance: 54 - 55: 15.989 distance: 54 - 56: 28.459 distance: 55 - 57: 18.004 distance: 56 - 58: 6.313 distance: 57 - 58: 27.514 distance: 59 - 60: 4.273 distance: 60 - 61: 15.412 distance: 60 - 63: 12.092 distance: 61 - 62: 25.341 distance: 63 - 64: 15.469 distance: 64 - 65: 28.464 distance: 65 - 66: 19.520 distance: 65 - 67: 41.819 distance: 68 - 69: 18.466 distance: 69 - 70: 16.924 distance: 70 - 71: 15.890 distance: 70 - 72: 10.374 distance: 72 - 73: 7.019 distance: 73 - 74: 18.051 distance: 73 - 76: 16.546 distance: 74 - 75: 6.198 distance: 76 - 77: 33.118 distance: 76 - 78: 13.380 distance: 79 - 80: 6.860 distance: 80 - 81: 20.559 distance: 80 - 83: 8.965 distance: 81 - 82: 19.210 distance: 81 - 87: 18.395 distance: 83 - 84: 11.586 distance: 84 - 85: 7.895 distance: 85 - 86: 12.865