Starting phenix.real_space_refine on Fri Aug 7 07:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8btg_16229/08_2026/8btg_16229_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8btg_16229/08_2026/8btg_16229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2026/8btg_16229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2026/8btg_16229.map" model { file = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2026/8btg_16229_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2026/8btg_16229_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.034 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 86 5.49 5 Mg 7 5.21 5 S 35 5.16 5 C 12643 2.51 5 N 3564 2.21 5 O 3995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20330 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2679 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "B" Number of atoms: 2687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2687 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "D" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "E" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "F" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "G" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2680 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "X" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 482 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "Y" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 858 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" 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: 4.69, per 1000 atoms: 0.23 Number of scatterers: 20330 At special positions: 0 Unit cell: (115.776, 135.072, 172.592, 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 35 16.00 P 86 15.00 Mg 7 11.99 O 3995 8.00 N 3564 7.00 C 12643 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 765.5 milliseconds 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4468 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 7 sheets defined 67.8% alpha, 6.3% beta 18 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 156 through 172 Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.807A pdb=" N ASN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.510A pdb=" N LEU A 219 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 277 through 293 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 311 through 330 Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 380 through 398 Proline residue: A 386 - end of helix Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 413 through 429 removed outlier: 3.506A pdb=" N VAL A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 446 removed outlier: 3.632A pdb=" N GLN A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 182 through 196 Processing helix chain 'B' and resid 197 through 206 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 222 through 239 Processing helix chain 'B' and resid 258 through 266 Processing helix chain 'B' and resid 277 through 293 Processing helix chain 'B' and resid 297 through 308 removed outlier: 3.682A pdb=" N MET B 301 " --> pdb=" O PRO B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 330 removed outlier: 3.608A pdb=" N LEU B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 380 through 398 Proline residue: B 386 - end of helix Processing helix chain 'B' and resid 401 through 408 Processing helix chain 'B' and resid 413 through 429 Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'C' and resid 126 through 139 Processing helix chain 'C' and resid 156 through 172 Processing helix chain 'C' and resid 182 through 196 Processing helix chain 'C' and resid 197 through 207 removed outlier: 3.608A pdb=" N PHE C 201 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN C 207 " --> pdb=" O ASN C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 222 through 239 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.506A pdb=" N ILE C 254 " --> pdb=" O PRO C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 277 through 293 Processing helix chain 'C' and resid 297 through 308 Processing helix chain 'C' and resid 311 through 329 removed outlier: 3.626A pdb=" N LEU C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'C' and resid 355 through 367 Processing helix chain 'C' and resid 380 through 398 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 401 through 409 Processing helix chain 'C' and resid 413 through 429 Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'D' and resid 126 through 139 Processing helix chain 'D' and resid 156 through 172 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 197 through 207 removed outlier: 3.957A pdb=" N ASN D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 220 Processing helix chain 'D' and resid 222 through 239 Processing helix chain 'D' and resid 258 through 268 removed outlier: 4.362A pdb=" N GLY D 268 " --> pdb=" O ARG D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 293 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 311 through 330 removed outlier: 3.759A pdb=" N GLY D 317 " --> pdb=" O ARG D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 355 through 367 Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.961A pdb=" N PHE D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS D 375 " --> pdb=" O LEU D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'D' and resid 380 through 397 Proline residue: D 386 - end of helix Processing helix chain 'D' and resid 401 through 409 Processing helix chain 'D' and resid 413 through 429 removed outlier: 3.592A pdb=" N VAL D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 removed outlier: 3.895A pdb=" N LYS D 446 " --> pdb=" O LYS D 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 139 Processing helix chain 'E' and resid 156 through 172 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 197 through 207 removed outlier: 3.925A pdb=" N ASN E 207 " --> pdb=" O ASN E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'E' and resid 222 through 239 removed outlier: 3.502A pdb=" N GLN E 226 " --> pdb=" O LYS E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.622A pdb=" N ILE E 254 " --> pdb=" O PRO E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 266 Processing helix chain 'E' and resid 277 through 293 Processing helix chain 'E' and resid 297 through 308 Processing helix chain 'E' and resid 312 through 330 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'E' and resid 355 through 367 Processing helix chain 'E' and resid 370 through 374 removed outlier: 4.031A pdb=" N PHE E 374 " --> pdb=" O LEU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 398 Proline residue: E 386 - end of helix Processing helix chain 'E' and resid 401 through 409 Processing helix chain 'E' and resid 413 through 429 removed outlier: 3.641A pdb=" N VAL E 417 " --> pdb=" O ASP E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 432 through 445 Processing helix chain 'F' and resid 116 through 120 Processing helix chain 'F' and resid 126 through 139 Processing helix chain 'F' and resid 156 through 172 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 197 through 206 removed outlier: 3.688A pdb=" N PHE F 201 " --> pdb=" O LYS F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 Processing helix chain 'F' and resid 222 through 239 Processing helix chain 'F' and resid 250 through 254 removed outlier: 3.679A pdb=" N ILE F 254 " --> pdb=" O PRO F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 266 removed outlier: 3.543A pdb=" N GLU F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 293 Processing helix chain 'F' and resid 297 through 308 removed outlier: 3.557A pdb=" N MET F 301 " --> pdb=" O PRO F 297 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE F 308 " --> pdb=" O ILE F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 330 Processing helix chain 'F' and resid 334 through 342 Processing helix chain 'F' and resid 355 through 367 Processing helix chain 'F' and resid 380 through 398 Proline residue: F 386 - end of helix Processing helix chain 'F' and resid 401 through 409 Processing helix chain 'F' and resid 413 through 429 Processing helix chain 'F' and resid 432 through 446 removed outlier: 4.122A pdb=" N LYS F 446 " --> pdb=" O LYS F 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 139 Processing helix chain 'G' and resid 156 through 172 Processing helix chain 'G' and resid 182 through 195 Processing helix chain 'G' and resid 197 through 207 removed outlier: 3.926A pdb=" N ASN G 207 " --> pdb=" O ASN G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 222 through 239 removed outlier: 3.503A pdb=" N GLN G 226 " --> pdb=" O LYS G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 254 removed outlier: 3.621A pdb=" N ILE G 254 " --> pdb=" O PRO G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 266 Processing helix chain 'G' and resid 277 through 293 Processing helix chain 'G' and resid 297 through 308 Processing helix chain 'G' and resid 312 through 330 Processing helix chain 'G' and resid 334 through 342 Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'G' and resid 380 through 398 Proline residue: G 386 - end of helix Processing helix chain 'G' and resid 401 through 409 Processing helix chain 'G' and resid 413 through 429 removed outlier: 3.648A pdb=" N VAL G 417 " --> pdb=" O ASP G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 446 removed outlier: 3.883A pdb=" N LYS G 446 " --> pdb=" O LYS G 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 181 removed outlier: 8.058A pdb=" N THR A 271 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A 148 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A 273 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N TYR A 150 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 177 through 181 removed outlier: 6.286A pdb=" N LEU B 147 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER B 247 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 149 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 181 removed outlier: 6.786A pdb=" N VAL C 178 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP C 214 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 180 " --> pdb=" O ASP C 214 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU C 211 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N SER C 246 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 213 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR C 271 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N PHE C 148 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 177 through 181 removed outlier: 6.348A pdb=" N VAL D 178 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ASP D 214 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 180 " --> pdb=" O ASP D 214 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU D 147 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N SER D 247 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 149 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N THR D 271 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE D 148 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE D 273 " --> pdb=" O PHE D 148 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N TYR D 150 " --> pdb=" O ILE D 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 177 through 181 removed outlier: 7.901A pdb=" N THR E 271 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE E 148 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE E 273 " --> pdb=" O PHE E 148 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N TYR E 150 " --> pdb=" O ILE E 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 177 through 181 removed outlier: 6.456A pdb=" N VAL F 178 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP F 214 " --> pdb=" O VAL F 178 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU F 180 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU F 211 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER F 246 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE F 213 " --> pdb=" O SER F 246 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE F 148 " --> pdb=" O THR F 271 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE F 273 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR F 150 " --> pdb=" O ILE F 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 177 through 181 removed outlier: 7.902A pdb=" N THR G 271 " --> pdb=" O PRO G 146 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N PHE G 148 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE G 273 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR G 150 " --> pdb=" O ILE G 273 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 3.58 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4771 1.33 - 1.45: 4198 1.45 - 1.57: 11642 1.57 - 1.69: 163 1.69 - 1.80: 70 Bond restraints: 20844 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.90e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.88e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.35e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C8 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 20839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 28351 3.89 - 7.79: 100 7.79 - 11.68: 8 11.68 - 15.57: 0 15.57 - 19.47: 4 Bond angle restraints: 28463 Sorted by residual: angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 120.40 19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 120.35 16.48 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 120.38 16.45 1.00e+00 1.00e+00 2.71e+02 angle pdb=" C5 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N3 ATP B 501 " ideal model delta sigma weight residual 126.80 118.63 8.17 1.00e+00 1.00e+00 6.68e+01 ... (remaining 28458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.25: 11751 28.25 - 56.50: 821 56.50 - 84.76: 122 84.76 - 113.01: 6 113.01 - 141.26: 1 Dihedral angle restraints: 12701 sinusoidal: 5845 harmonic: 6856 Sorted by residual: dihedral pdb=" CA ASP E 214 " pdb=" C ASP E 214 " pdb=" N ASP E 215 " pdb=" CA ASP E 215 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ASP G 214 " pdb=" C ASP G 214 " pdb=" N ASP G 215 " pdb=" CA ASP G 215 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ILE C 312 " pdb=" C ILE C 312 " pdb=" N ARG C 313 " pdb=" CA ARG C 313 " ideal model delta harmonic sigma weight residual 180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 12698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2287 0.046 - 0.092: 701 0.092 - 0.138: 184 0.138 - 0.183: 24 0.183 - 0.229: 2 Chirality restraints: 3198 Sorted by residual: chirality pdb=" CA ILE C 312 " pdb=" N ILE C 312 " pdb=" C ILE C 312 " pdb=" CB ILE C 312 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASN E 368 " pdb=" N ASN E 368 " pdb=" C ASN E 368 " pdb=" CB ASN E 368 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ASN F 368 " pdb=" N ASN F 368 " pdb=" C ASN F 368 " pdb=" CB ASN F 368 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 3195 not shown) Planarity restraints: 3414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 274 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO D 275 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 275 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 275 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 402 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO B 403 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 403 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 403 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 274 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.14e+00 pdb=" N PRO C 275 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 275 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 275 " -0.034 5.00e-02 4.00e+02 ... (remaining 3411 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 3 1.83 - 2.60: 302 2.60 - 3.37: 27821 3.37 - 4.13: 50822 4.13 - 4.90: 91161 Nonbonded interactions: 170109 Sorted by model distance: nonbonded pdb=" NH2 ARG G 194 " pdb=" O2 DT Y 1 " model vdw 1.067 3.120 nonbonded pdb=" NH2 ARG G 194 " pdb=" C2 DT Y 1 " model vdw 1.251 3.340 nonbonded pdb=" NH2 ARG G 194 " pdb=" N3 DT Y 1 " model vdw 1.536 3.200 nonbonded pdb=" OD1 ASP A 215 " pdb="MG MG A 500 " model vdw 1.962 2.170 nonbonded pdb="MG MG C 500 " pdb=" O2G ATP C 501 " model vdw 1.994 2.170 ... (remaining 170104 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 109 through 344 or resid 351 through 446)) selection = (chain 'B' and (resid 109 through 344 or resid 351 through 446)) selection = (chain 'C' and (resid 109 through 344 or resid 351 through 446)) selection = (chain 'D' and (resid 109 through 344 or resid 351 through 446)) selection = (chain 'E' and (resid 109 through 344 or resid 351 through 446)) selection = (chain 'F' and (resid 109 through 344 or resid 351 through 446)) selection = (chain 'G' and (resid 109 through 344 or resid 351 through 446)) } 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: 2.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.550 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5800 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 : 0.007 0.853 20845 Z= 0.657 Angle : 0.736 19.466 28463 Z= 0.500 Chirality : 0.047 0.229 3198 Planarity : 0.004 0.067 3414 Dihedral : 18.070 141.262 8233 Min Nonbonded Distance : 1.067 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.18), residues: 2311 helix: 1.23 (0.14), residues: 1503 sheet: 0.85 (0.37), residues: 199 loop : -0.44 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 206 TYR 0.017 0.002 TYR C 144 PHE 0.018 0.002 PHE E 189 TRP 0.009 0.001 TRP C 267 HIS 0.009 0.001 HIS F 421 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.29 (20844) covalent geometry : angle 0.73599 / 0.50 (28463) hydrogen bonds : bond 0.06887 / 5.08 ( 1167) hydrogen bonds : angle 4.34975 / 3.17 ( 3349) Misc. bond : bond 0.85328 / 44.91 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 391 MET cc_start: 0.4435 (tpt) cc_final: 0.3791 (tmm) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.1572 time to fit residues: 17.0763 Evaluate side-chains 46 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.2980 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 30.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 433 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.112385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.073226 restraints weight = 95256.766| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 6.37 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20845 Z= 0.208 Angle : 0.633 10.073 28463 Z= 0.336 Chirality : 0.046 0.249 3198 Planarity : 0.005 0.062 3414 Dihedral : 18.763 142.043 3483 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.49 % Allowed : 6.01 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.18), residues: 2311 helix: 1.50 (0.14), residues: 1511 sheet: 1.03 (0.38), residues: 195 loop : -0.31 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG G 194 TYR 0.031 0.002 TYR G 167 PHE 0.019 0.001 PHE E 189 TRP 0.005 0.001 TRP C 267 HIS 0.006 0.001 HIS G 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (20844) covalent geometry : angle 0.63277 / 0.34 (28463) hydrogen bonds : bond 0.03833 / 2.63 ( 1167) hydrogen bonds : angle 4.02609 / 2.93 ( 3349) Misc. bond : bond 0.00032 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 TYR cc_start: 0.8866 (m-80) cc_final: 0.8426 (m-10) REVERT: B 397 MET cc_start: 0.6266 (mpp) cc_final: 0.5988 (mpp) REVERT: B 422 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5541 (pp20) REVERT: C 391 MET cc_start: 0.3468 (tmm) cc_final: 0.1935 (ttp) REVERT: D 301 MET cc_start: 0.9230 (mmm) cc_final: 0.8890 (mmt) REVERT: D 391 MET cc_start: 0.5797 (tpt) cc_final: 0.5016 (tmm) outliers start: 10 outliers final: 6 residues processed: 53 average time/residue: 0.1278 time to fit residues: 11.8574 Evaluate side-chains 51 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 304 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 0.0070 chunk 57 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN G 436 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.112929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.076765 restraints weight = 94044.926| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 6.15 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20845 Z= 0.121 Angle : 0.552 9.446 28463 Z= 0.295 Chirality : 0.044 0.205 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.642 142.466 3483 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.59 % Allowed : 8.36 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2311 helix: 1.70 (0.14), residues: 1504 sheet: 1.01 (0.36), residues: 217 loop : -0.17 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 249 TYR 0.016 0.001 TYR G 167 PHE 0.015 0.001 PHE G 189 TRP 0.004 0.000 TRP D 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (20844) covalent geometry : angle 0.55157 / 0.29 (28463) hydrogen bonds : bond 0.03304 / 2.25 ( 1167) hydrogen bonds : angle 3.80245 / 2.74 ( 3349) Misc. bond : bond 0.01130 / 0.59 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.3602 (mmt) cc_final: 0.3026 (tmm) REVERT: B 205 TYR cc_start: 0.8792 (m-80) cc_final: 0.8398 (m-10) REVERT: B 397 MET cc_start: 0.5242 (mpp) cc_final: 0.4847 (mpp) REVERT: B 422 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5123 (pp20) REVERT: C 391 MET cc_start: 0.2824 (tmm) cc_final: 0.2279 (ppp) REVERT: D 301 MET cc_start: 0.9172 (mmt) cc_final: 0.8729 (mmt) REVERT: D 391 MET cc_start: 0.6017 (tpt) cc_final: 0.5095 (tmm) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 0.1380 time to fit residues: 13.1460 Evaluate side-chains 51 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 436 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 151 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 92 optimal weight: 0.0050 chunk 162 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 26 optimal weight: 40.0000 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 165 optimal weight: 7.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.116414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.082411 restraints weight = 97477.821| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 6.02 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20845 Z= 0.110 Angle : 0.534 8.641 28463 Z= 0.285 Chirality : 0.043 0.195 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.484 142.855 3483 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.83 % Allowed : 9.00 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.18), residues: 2311 helix: 1.79 (0.14), residues: 1502 sheet: 1.13 (0.37), residues: 217 loop : -0.13 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 249 TYR 0.011 0.001 TYR G 144 PHE 0.015 0.001 PHE G 189 TRP 0.003 0.000 TRP C 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (20844) covalent geometry : angle 0.53356 / 0.28 (28463) hydrogen bonds : bond 0.03175 / 2.13 ( 1167) hydrogen bonds : angle 3.73710 / 2.70 ( 3349) Misc. bond : bond 0.00516 / 0.27 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 45 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.3634 (mmt) cc_final: 0.3118 (tmm) REVERT: B 205 TYR cc_start: 0.8777 (m-80) cc_final: 0.8388 (m-10) REVERT: B 397 MET cc_start: 0.4891 (mpp) cc_final: 0.4578 (mpp) REVERT: B 422 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5178 (pp20) REVERT: C 391 MET cc_start: 0.2511 (tmm) cc_final: 0.1996 (ppp) REVERT: D 301 MET cc_start: 0.9161 (mmt) cc_final: 0.8676 (mmt) REVERT: D 391 MET cc_start: 0.6105 (tpt) cc_final: 0.5044 (tmm) REVERT: F 301 MET cc_start: 0.9142 (mtp) cc_final: 0.8909 (ptp) outliers start: 17 outliers final: 8 residues processed: 59 average time/residue: 0.1371 time to fit residues: 13.9388 Evaluate side-chains 53 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 361 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 85 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.111744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.076083 restraints weight = 94550.265| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 7.28 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20845 Z= 0.173 Angle : 0.568 8.240 28463 Z= 0.300 Chirality : 0.044 0.202 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.459 143.408 3483 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.12 % Allowed : 9.98 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.18), residues: 2311 helix: 1.90 (0.14), residues: 1503 sheet: 1.09 (0.37), residues: 218 loop : -0.13 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.023 0.001 TYR G 144 PHE 0.022 0.002 PHE F 148 TRP 0.005 0.001 TRP E 267 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (20844) covalent geometry : angle 0.56847 / 0.30 (28463) hydrogen bonds : bond 0.03384 / 2.31 ( 1167) hydrogen bonds : angle 3.75312 / 2.71 ( 3349) Misc. bond : bond 0.00249 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 TYR cc_start: 0.8923 (m-80) cc_final: 0.8479 (m-10) REVERT: B 397 MET cc_start: 0.5341 (mpp) cc_final: 0.5082 (mpp) REVERT: B 422 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5316 (pp20) REVERT: C 391 MET cc_start: 0.2707 (tmm) cc_final: 0.2127 (ppp) REVERT: D 301 MET cc_start: 0.9232 (mmt) cc_final: 0.8778 (mmt) REVERT: F 110 MET cc_start: 0.7952 (pmm) cc_final: 0.7630 (pmm) REVERT: G 144 TYR cc_start: 0.9095 (m-80) cc_final: 0.8855 (m-10) outliers start: 23 outliers final: 10 residues processed: 64 average time/residue: 0.1396 time to fit residues: 15.3774 Evaluate side-chains 54 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 361 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 9.9990 chunk 199 optimal weight: 9.9990 chunk 142 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 57 optimal weight: 0.0670 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079140 restraints weight = 97073.613| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 5.04 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20845 Z= 0.105 Angle : 0.527 7.963 28463 Z= 0.280 Chirality : 0.043 0.190 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.340 143.101 3483 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.08 % Allowed : 10.76 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.18), residues: 2311 helix: 1.92 (0.14), residues: 1503 sheet: 1.27 (0.37), residues: 217 loop : -0.06 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 387 TYR 0.028 0.001 TYR G 167 PHE 0.014 0.001 PHE G 189 TRP 0.003 0.000 TRP D 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.11 (20844) covalent geometry : angle 0.52655 / 0.28 (28463) hydrogen bonds : bond 0.03008 / 2.03 ( 1167) hydrogen bonds : angle 3.63677 / 2.62 ( 3349) Misc. bond : bond 0.00360 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 43 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.3360 (mmt) cc_final: 0.2625 (tmm) REVERT: B 205 TYR cc_start: 0.8813 (m-80) cc_final: 0.8489 (m-10) REVERT: B 397 MET cc_start: 0.6050 (mpp) cc_final: 0.5798 (mpp) REVERT: B 422 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.5507 (pp20) REVERT: C 391 MET cc_start: 0.3092 (tmm) cc_final: 0.2507 (ppp) REVERT: D 301 MET cc_start: 0.9223 (mmt) cc_final: 0.8846 (mmt) REVERT: F 110 MET cc_start: 0.7887 (pmm) cc_final: 0.7560 (pmm) outliers start: 22 outliers final: 11 residues processed: 62 average time/residue: 0.1388 time to fit residues: 14.8839 Evaluate side-chains 54 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 145 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 56 optimal weight: 0.0170 chunk 203 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 224 optimal weight: 0.0070 chunk 66 optimal weight: 0.4980 overall best weight: 1.3040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.112332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.076665 restraints weight = 94532.543| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 7.18 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20845 Z= 0.127 Angle : 0.530 8.583 28463 Z= 0.280 Chirality : 0.043 0.177 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.301 143.525 3483 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.03 % Allowed : 11.10 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.18), residues: 2311 helix: 1.97 (0.14), residues: 1505 sheet: 1.34 (0.37), residues: 217 loop : -0.02 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 194 TYR 0.024 0.001 TYR G 144 PHE 0.015 0.001 PHE G 189 TRP 0.002 0.000 TRP C 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (20844) covalent geometry : angle 0.53005 / 0.28 (28463) hydrogen bonds : bond 0.03026 / 2.06 ( 1167) hydrogen bonds : angle 3.61537 / 2.60 ( 3349) Misc. bond : bond 0.00326 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.2978 (mmt) cc_final: 0.2405 (tmm) REVERT: B 205 TYR cc_start: 0.8875 (m-80) cc_final: 0.8349 (m-10) REVERT: B 397 MET cc_start: 0.5159 (mpp) cc_final: 0.4955 (mpp) REVERT: B 422 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5077 (pp20) REVERT: C 391 MET cc_start: 0.2736 (tmm) cc_final: 0.2108 (ppp) REVERT: D 301 MET cc_start: 0.9216 (mmt) cc_final: 0.8716 (mmt) REVERT: D 391 MET cc_start: 0.5642 (tpt) cc_final: 0.4374 (tmm) REVERT: F 110 MET cc_start: 0.8021 (pmm) cc_final: 0.7670 (pmm) REVERT: G 144 TYR cc_start: 0.9154 (m-80) cc_final: 0.8812 (m-10) outliers start: 21 outliers final: 11 residues processed: 60 average time/residue: 0.1302 time to fit residues: 13.8196 Evaluate side-chains 54 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 88 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 193 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 211 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.110782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.071157 restraints weight = 94324.674| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 6.14 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20845 Z= 0.227 Angle : 0.597 10.509 28463 Z= 0.313 Chirality : 0.045 0.215 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.405 143.848 3483 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.78 % Allowed : 11.49 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.18), residues: 2311 helix: 1.93 (0.14), residues: 1505 sheet: 1.14 (0.37), residues: 220 loop : -0.05 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.021 0.002 TYR F 303 PHE 0.021 0.002 PHE F 148 TRP 0.009 0.001 TRP E 267 HIS 0.005 0.001 HIS F 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (20844) covalent geometry : angle 0.59692 / 0.31 (28463) hydrogen bonds : bond 0.03485 / 2.39 ( 1167) hydrogen bonds : angle 3.75390 / 2.71 ( 3349) Misc. bond : bond 0.00281 / 0.15 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.3637 (mmt) cc_final: 0.2824 (tmm) REVERT: B 397 MET cc_start: 0.7019 (mpp) cc_final: 0.6774 (mpp) REVERT: B 422 GLU cc_start: 0.6170 (OUTLIER) cc_final: 0.5437 (pp20) REVERT: C 391 MET cc_start: 0.3735 (tmm) cc_final: 0.3097 (ppp) REVERT: D 301 MET cc_start: 0.9282 (mmt) cc_final: 0.8826 (mmt) REVERT: D 391 MET cc_start: 0.5588 (tpt) cc_final: 0.4533 (tmm) REVERT: F 110 MET cc_start: 0.8014 (pmm) cc_final: 0.7664 (pmm) REVERT: G 301 MET cc_start: 0.8519 (ttt) cc_final: 0.8277 (tpt) outliers start: 16 outliers final: 12 residues processed: 53 average time/residue: 0.1317 time to fit residues: 12.6034 Evaluate side-chains 53 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 408 GLU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 396 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 14 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 156 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 174 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.114531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.076965 restraints weight = 95578.795| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 5.35 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20845 Z= 0.106 Angle : 0.528 9.000 28463 Z= 0.280 Chirality : 0.043 0.174 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.279 143.657 3483 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.83 % Allowed : 11.34 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.18), residues: 2311 helix: 1.99 (0.14), residues: 1503 sheet: 1.42 (0.38), residues: 215 loop : -0.01 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 264 TYR 0.020 0.001 TYR G 144 PHE 0.014 0.001 PHE G 189 TRP 0.003 0.000 TRP C 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 (20844) covalent geometry : angle 0.52796 / 0.28 (28463) hydrogen bonds : bond 0.02941 / 2.00 ( 1167) hydrogen bonds : angle 3.59232 / 2.59 ( 3349) Misc. bond : bond 0.00328 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 42 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 205 TYR cc_start: 0.8902 (m-80) cc_final: 0.8323 (m-10) REVERT: B 273 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8734 (mm) REVERT: B 397 MET cc_start: 0.6449 (mpp) cc_final: 0.6214 (mpp) REVERT: B 422 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5386 (pp20) REVERT: C 391 MET cc_start: 0.3285 (tmm) cc_final: 0.2688 (ppp) REVERT: D 301 MET cc_start: 0.9271 (mmt) cc_final: 0.8879 (mmt) REVERT: D 391 MET cc_start: 0.5802 (tpt) cc_final: 0.4710 (tmm) REVERT: F 110 MET cc_start: 0.7901 (pmm) cc_final: 0.7533 (pmm) REVERT: G 144 TYR cc_start: 0.8938 (m-80) cc_final: 0.8707 (m-10) outliers start: 17 outliers final: 14 residues processed: 56 average time/residue: 0.1134 time to fit residues: 11.3825 Evaluate side-chains 58 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 46 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 113 optimal weight: 0.0070 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** 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 = 0.4233 r_free = 0.4233 target = 0.110288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.070737 restraints weight = 94414.574| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 6.01 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20845 Z= 0.206 Angle : 0.575 9.292 28463 Z= 0.302 Chirality : 0.044 0.175 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.348 144.250 3483 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.83 % Allowed : 11.25 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.18), residues: 2311 helix: 1.98 (0.14), residues: 1503 sheet: 1.19 (0.37), residues: 220 loop : -0.01 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 194 TYR 0.020 0.002 TYR F 303 PHE 0.019 0.002 PHE F 148 TRP 0.009 0.001 TRP E 267 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (20844) covalent geometry : angle 0.57490 / 0.30 (28463) hydrogen bonds : bond 0.03347 / 2.30 ( 1167) hydrogen bonds : angle 3.70270 / 2.68 ( 3349) Misc. bond : bond 0.00280 / 0.15 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4622 Ramachandran restraints generated. 2311 Oldfield, 0 Emsley, 2311 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.3492 (mmt) cc_final: 0.2615 (tmm) REVERT: B 273 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8907 (mm) REVERT: B 397 MET cc_start: 0.7012 (mpp) cc_final: 0.6782 (mpp) REVERT: B 422 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5525 (pp20) REVERT: C 391 MET cc_start: 0.3766 (tmm) cc_final: 0.3116 (ppp) REVERT: D 301 MET cc_start: 0.9269 (mmt) cc_final: 0.8795 (mmt) REVERT: D 391 MET cc_start: 0.5591 (tpt) cc_final: 0.4568 (tmm) REVERT: F 110 MET cc_start: 0.8076 (pmm) cc_final: 0.7707 (pmm) REVERT: G 308 ILE cc_start: 0.8027 (tp) cc_final: 0.7724 (pt) outliers start: 17 outliers final: 13 residues processed: 55 average time/residue: 0.1146 time to fit residues: 11.2535 Evaluate side-chains 55 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 436 GLN Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 396 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 101 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 131 optimal weight: 6.9990 chunk 199 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 193 optimal weight: 40.0000 chunk 218 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.114093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076064 restraints weight = 96651.456| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 5.17 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 20845 Z= 0.110 Angle : 0.525 8.695 28463 Z= 0.278 Chirality : 0.043 0.173 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.265 144.030 3483 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.78 % Allowed : 11.44 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.18), residues: 2311 helix: 2.02 (0.14), residues: 1503 sheet: 1.39 (0.38), residues: 217 loop : 0.01 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 264 TYR 0.019 0.001 TYR G 144 PHE 0.015 0.001 PHE G 189 TRP 0.003 0.000 TRP C 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (20844) covalent geometry : angle 0.52511 / 0.28 (28463) hydrogen bonds : bond 0.02951 / 2.01 ( 1167) hydrogen bonds : angle 3.58429 / 2.59 ( 3349) Misc. bond : bond 0.00316 / 0.17 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5582.41 seconds wall clock time: 96 minutes 19.40 seconds (5779.40 seconds total)