Starting phenix.real_space_refine on Sun Aug 24 13:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8btg_16229/08_2025/8btg_16229_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8btg_16229/08_2025/8btg_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_2025/8btg_16229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2025/8btg_16229.map" model { file = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2025/8btg_16229_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8btg_16229/08_2025/8btg_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 4.52, per 1000 atoms: 0.22 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: 1.77 Conformation dependent library (CDL) restraints added in 615.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.45 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: 3.73 Time building geometry restraints manager: 2.23 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: 2336 0.046 - 0.092: 662 0.092 - 0.138: 175 0.138 - 0.183: 23 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: 2.420 Set stop_for_unknowns flag: 0.010 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: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.590 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5741 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= 0.633 Angle : 0.712 19.466 28463 Z= 0.446 Chirality : 0.046 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 aren 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 covalent geometry : bond 0.00418 (20844) covalent geometry : angle 0.71246 (28463) hydrogen bonds : bond 0.06887 ( 1167) hydrogen bonds : angle 4.34975 ( 3349) Misc. bond : bond 0.85328 ( 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 : 0.466 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: 0.1387 time to fit residues: 15.0262 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 : 0.755 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 217 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 = 0.112431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.074429 restraints weight = 93876.112| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 6.58 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20845 Z= 0.207 Angle : 0.608 11.336 28463 Z= 0.322 Chirality : 0.045 0.197 3198 Planarity : 0.005 0.069 3414 Dihedral : 18.798 142.789 3483 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.39 % Allowed : 6.01 % Favored : 93.59 % 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 aren not related in a simple way. whole: 1.50 (0.18), residues: 2311 helix: 1.55 (0.14), residues: 1511 sheet: 0.89 (0.36), residues: 217 loop : -0.31 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 249 TYR 0.025 0.002 TYR G 167 PHE 0.019 0.002 PHE E 189 TRP 0.005 0.001 TRP C 267 HIS 0.005 0.001 HIS G 171 Details of bonding type rmsd covalent geometry : bond 0.00460 (20844) covalent geometry : angle 0.60826 (28463) hydrogen bonds : bond 0.03624 ( 1167) hydrogen bonds : angle 3.98589 ( 3349) Misc. bond : bond 0.00178 ( 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 52 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 MET cc_start: 0.6436 (mpp) cc_final: 0.6165 (mpp) REVERT: B 422 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5349 (pp20) REVERT: C 391 MET cc_start: 0.3486 (tmm) cc_final: 0.1570 (ttp) REVERT: D 301 MET cc_start: 0.9224 (mmt) cc_final: 0.8855 (mmt) REVERT: D 391 MET cc_start: 0.5803 (tpt) cc_final: 0.4993 (tmm) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1085 time to fit residues: 9.7752 Evaluate side-chains 48 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 68 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 81 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 219 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 306 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.116281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.079866 restraints weight = 98186.424| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.95 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20845 Z= 0.119 Angle : 0.535 8.171 28463 Z= 0.285 Chirality : 0.042 0.182 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.511 143.301 3483 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.73 % Allowed : 8.22 % 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 aren not related in a simple way. whole: 1.80 (0.18), residues: 2311 helix: 1.76 (0.14), residues: 1512 sheet: 1.05 (0.36), residues: 217 loop : -0.15 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 249 TYR 0.014 0.001 TYR F 303 PHE 0.015 0.001 PHE G 189 TRP 0.004 0.001 TRP D 267 HIS 0.004 0.001 HIS B 414 Details of bonding type rmsd covalent geometry : bond 0.00254 (20844) covalent geometry : angle 0.53507 (28463) hydrogen bonds : bond 0.03115 ( 1167) hydrogen bonds : angle 3.74665 ( 3349) Misc. bond : bond 0.00518 ( 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 60 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.737 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: symmetry clash REVERT: A 391 MET cc_start: 0.3744 (mmt) cc_final: 0.3099 (tmm) REVERT: B 205 TYR cc_start: 0.8824 (m-80) cc_final: 0.8523 (m-10) REVERT: B 397 MET cc_start: 0.5639 (mpp) cc_final: 0.5340 (mpp) REVERT: B 422 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5271 (pp20) REVERT: C 391 MET cc_start: 0.2950 (tmm) cc_final: 0.2406 (ppp) REVERT: D 301 MET cc_start: 0.9183 (mmt) cc_final: 0.8741 (mmt) REVERT: D 391 MET cc_start: 0.5994 (tpt) cc_final: 0.5091 (tmm) outliers start: 15 outliers final: 9 residues processed: 56 average time/residue: 0.1314 time to fit residues: 12.6451 Evaluate side-chains 54 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 388 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 151 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 40.0000 chunk 92 optimal weight: 0.0570 chunk 162 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 26 optimal weight: 50.0000 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.110441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073311 restraints weight = 95263.684| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 7.59 r_work: 0.2863 rms_B_bonded: 6.87 restraints_weight: 2.0000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20845 Z= 0.260 Angle : 0.620 9.600 28463 Z= 0.327 Chirality : 0.045 0.179 3198 Planarity : 0.004 0.061 3414 Dihedral : 18.583 143.266 3483 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.17 % Allowed : 9.88 % Favored : 88.95 % 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 aren not related in a simple way. whole: 1.70 (0.18), residues: 2311 helix: 1.70 (0.14), residues: 1505 sheet: 0.94 (0.36), residues: 220 loop : -0.21 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 260 TYR 0.020 0.002 TYR G 144 PHE 0.023 0.002 PHE F 148 TRP 0.009 0.001 TRP E 267 HIS 0.006 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00581 (20844) covalent geometry : angle 0.61989 (28463) hydrogen bonds : bond 0.03859 ( 1167) hydrogen bonds : angle 3.94563 ( 3349) Misc. bond : bond 0.00259 ( 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 65 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 41 time to evaluate : 0.655 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: 0.3941 (mmt) cc_final: 0.3199 (tmm) REVERT: B 397 MET cc_start: 0.6239 (mpp) cc_final: 0.5947 (mpp) REVERT: B 422 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5567 (pp20) REVERT: C 391 MET cc_start: 0.3474 (tmm) cc_final: 0.2859 (ppp) REVERT: D 301 MET cc_start: 0.9366 (mmt) cc_final: 0.8902 (mmt) REVERT: F 110 MET cc_start: 0.7973 (pmm) cc_final: 0.7664 (pmm) outliers start: 24 outliers final: 9 residues processed: 62 average time/residue: 0.1152 time to fit residues: 12.3978 Evaluate side-chains 52 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 199 VAL Chi-restraints excluded: chain D residue 436 GLN 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 161 MET 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: 1.9990 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 230 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4253 r_free = 0.4253 target = 0.114379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076570 restraints weight = 96390.861| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 5.46 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20845 Z= 0.113 Angle : 0.528 7.758 28463 Z= 0.282 Chirality : 0.042 0.180 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.360 144.419 3483 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.88 % Allowed : 10.66 % Favored : 88.46 % 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 aren not related in a simple way. whole: 1.97 (0.18), residues: 2311 helix: 1.91 (0.14), residues: 1502 sheet: 1.20 (0.37), residues: 217 loop : -0.13 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 249 TYR 0.018 0.001 TYR G 144 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 covalent geometry : bond 0.00240 (20844) covalent geometry : angle 0.52783 (28463) hydrogen bonds : bond 0.03018 ( 1167) hydrogen bonds : angle 3.67363 ( 3349) Misc. bond : bond 0.00320 ( 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 61 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.734 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 110 MET cc_start: 0.8918 (pmm) cc_final: 0.8692 (pmm) REVERT: B 205 TYR cc_start: 0.8941 (m-80) cc_final: 0.8330 (m-10) REVERT: B 397 MET cc_start: 0.6489 (mpp) cc_final: 0.6258 (mpp) REVERT: B 422 GLU cc_start: 0.6149 (OUTLIER) cc_final: 0.5382 (pp20) REVERT: C 391 MET cc_start: 0.3417 (tmm) cc_final: 0.2791 (ppp) REVERT: D 301 MET cc_start: 0.9287 (mmt) cc_final: 0.8925 (mmt) REVERT: F 110 MET cc_start: 0.7904 (pmm) cc_final: 0.7556 (pmm) REVERT: G 167 TYR cc_start: 0.9383 (t80) cc_final: 0.9156 (t80) outliers start: 18 outliers final: 10 residues processed: 59 average time/residue: 0.1178 time to fit residues: 12.1702 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 392 TYR Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 110 MET 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 361 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 14 optimal weight: 0.0970 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4259 r_free = 0.4259 target = 0.114565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.076610 restraints weight = 95990.056| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 5.60 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20845 Z= 0.108 Angle : 0.510 8.023 28463 Z= 0.271 Chirality : 0.041 0.173 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.195 144.082 3483 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.27 % Allowed : 10.61 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.07 (0.18), residues: 2311 helix: 1.96 (0.14), residues: 1505 sheet: 1.31 (0.37), residues: 217 loop : -0.05 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 249 TYR 0.018 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 covalent geometry : bond 0.00227 (20844) covalent geometry : angle 0.50967 (28463) hydrogen bonds : bond 0.02867 ( 1167) hydrogen bonds : angle 3.57076 ( 3349) Misc. bond : bond 0.00327 ( 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 69 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 43 time to evaluate : 0.472 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: symmetry clash REVERT: A 391 MET cc_start: 0.3563 (mmt) cc_final: 0.2720 (tmm) REVERT: B 110 MET cc_start: 0.8931 (pmm) cc_final: 0.8493 (pmm) REVERT: B 205 TYR cc_start: 0.8914 (m-80) cc_final: 0.8354 (m-10) REVERT: B 397 MET cc_start: 0.6940 (mpp) cc_final: 0.6710 (mpp) REVERT: B 422 GLU cc_start: 0.6326 (OUTLIER) cc_final: 0.5589 (pp20) REVERT: C 391 MET cc_start: 0.3623 (tmm) cc_final: 0.2994 (ppp) REVERT: D 301 MET cc_start: 0.9232 (mmt) cc_final: 0.8859 (mmt) REVERT: F 110 MET cc_start: 0.7937 (pmm) cc_final: 0.7571 (pmm) REVERT: G 167 TYR cc_start: 0.9398 (t80) cc_final: 0.9151 (t80) outliers start: 26 outliers final: 13 residues processed: 66 average time/residue: 0.1237 time to fit residues: 13.6466 Evaluate side-chains 57 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 199 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 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 Chi-restraints excluded: chain G residue 408 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 145 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 224 optimal weight: 50.0000 chunk 66 optimal weight: 0.4980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4257 r_free = 0.4257 target = 0.114387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.076424 restraints weight = 96636.924| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 5.73 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20845 Z= 0.111 Angle : 0.509 7.203 28463 Z= 0.270 Chirality : 0.041 0.176 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.118 144.088 3483 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.17 % Allowed : 11.00 % 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 aren not related in a simple way. whole: 2.14 (0.18), residues: 2311 helix: 2.00 (0.14), residues: 1503 sheet: 1.37 (0.38), residues: 217 loop : -0.03 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 387 TYR 0.017 0.001 TYR F 303 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 covalent geometry : bond 0.00238 (20844) covalent geometry : angle 0.50864 (28463) hydrogen bonds : bond 0.02832 ( 1167) hydrogen bonds : angle 3.53350 ( 3349) Misc. bond : bond 0.00304 ( 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 66 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 42 time to evaluate : 0.720 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: symmetry clash revert: symmetry clash REVERT: A 391 MET cc_start: 0.3742 (mmt) cc_final: 0.3506 (mmt) REVERT: B 110 MET cc_start: 0.9022 (pmm) cc_final: 0.8588 (pmm) REVERT: B 205 TYR cc_start: 0.8911 (m-80) cc_final: 0.8352 (m-10) REVERT: B 397 MET cc_start: 0.7030 (mpp) cc_final: 0.6804 (mpp) REVERT: B 422 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5610 (pp20) REVERT: C 391 MET cc_start: 0.3687 (tmm) cc_final: 0.3048 (ppp) REVERT: D 301 MET cc_start: 0.9222 (mmt) cc_final: 0.8845 (mmt) REVERT: F 110 MET cc_start: 0.7916 (pmm) cc_final: 0.7532 (pmm) REVERT: G 167 TYR cc_start: 0.9405 (t80) cc_final: 0.9147 (t80) outliers start: 24 outliers final: 17 residues processed: 63 average time/residue: 0.1158 time to fit residues: 12.5218 Evaluate side-chains 60 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 42 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 D residue 444 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 421 HIS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 361 ARG Chi-restraints excluded: chain G residue 396 GLU Chi-restraints excluded: chain G residue 408 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 88 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 9 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 102 optimal weight: 0.0070 chunk 211 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** 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 = 0.4231 r_free = 0.4231 target = 0.113090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074827 restraints weight = 96988.185| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.32 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20845 Z= 0.194 Angle : 0.559 10.402 28463 Z= 0.294 Chirality : 0.043 0.213 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.203 144.038 3483 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.37 % Allowed : 10.76 % 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 aren not related in a simple way. whole: 2.08 (0.18), residues: 2311 helix: 1.97 (0.14), residues: 1503 sheet: 1.19 (0.37), residues: 220 loop : -0.03 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 194 TYR 0.018 0.001 TYR F 303 PHE 0.019 0.002 PHE F 148 TRP 0.007 0.001 TRP E 267 HIS 0.006 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00433 (20844) covalent geometry : angle 0.55927 (28463) hydrogen bonds : bond 0.03207 ( 1167) hydrogen bonds : angle 3.67067 ( 3349) Misc. bond : bond 0.00256 ( 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 68 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 40 time to evaluate : 0.531 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: symmetry clash REVERT: A 391 MET cc_start: 0.3942 (mmt) cc_final: 0.3185 (tmm) REVERT: B 110 MET cc_start: 0.9004 (pmm) cc_final: 0.8581 (pmm) REVERT: B 397 MET cc_start: 0.6628 (mpp) cc_final: 0.6400 (mpp) REVERT: C 391 MET cc_start: 0.3377 (tmm) cc_final: 0.2750 (ppp) REVERT: D 301 MET cc_start: 0.9307 (mmt) cc_final: 0.8889 (mmt) REVERT: F 110 MET cc_start: 0.8066 (pmm) cc_final: 0.7664 (pmm) REVERT: F 256 THR cc_start: 0.9163 (OUTLIER) cc_final: 0.8756 (p) REVERT: G 167 TYR cc_start: 0.9395 (t80) cc_final: 0.9146 (t80) outliers start: 28 outliers final: 19 residues processed: 65 average time/residue: 0.1113 time to fit residues: 12.5277 Evaluate side-chains 60 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 40 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR 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 D residue 444 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 178 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 396 GLU Chi-restraints excluded: chain G residue 421 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 14 optimal weight: 0.0060 chunk 202 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 118 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** 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 = 0.4255 r_free = 0.4255 target = 0.114177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076161 restraints weight = 95859.452| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 5.88 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 20845 Z= 0.105 Angle : 0.515 9.198 28463 Z= 0.272 Chirality : 0.042 0.186 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.075 144.541 3483 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.98 % Allowed : 11.25 % 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 aren not related in a simple way. whole: 2.16 (0.18), residues: 2311 helix: 2.00 (0.14), residues: 1511 sheet: 1.39 (0.38), residues: 217 loop : 0.03 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 194 TYR 0.019 0.001 TYR A 392 PHE 0.013 0.001 PHE G 189 TRP 0.004 0.000 TRP C 267 HIS 0.004 0.001 HIS G 437 Details of bonding type rmsd covalent geometry : bond 0.00221 (20844) covalent geometry : angle 0.51517 (28463) hydrogen bonds : bond 0.02839 ( 1167) hydrogen bonds : angle 3.53716 ( 3349) Misc. bond : bond 0.00316 ( 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 61 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.770 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: 0.3825 (mmt) cc_final: 0.3026 (tmm) REVERT: B 110 MET cc_start: 0.9011 (pmm) cc_final: 0.8607 (pmm) REVERT: B 205 TYR cc_start: 0.8899 (m-80) cc_final: 0.8335 (m-10) REVERT: B 397 MET cc_start: 0.7237 (mpp) cc_final: 0.7008 (mpp) REVERT: B 422 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5890 (pp20) REVERT: C 391 MET cc_start: 0.3930 (tmm) cc_final: 0.3252 (ppp) REVERT: D 301 MET cc_start: 0.9246 (mmt) cc_final: 0.8873 (mmt) REVERT: F 110 MET cc_start: 0.7992 (pmm) cc_final: 0.7601 (pmm) REVERT: G 167 TYR cc_start: 0.9414 (t80) cc_final: 0.9145 (t80) outliers start: 20 outliers final: 14 residues processed: 60 average time/residue: 0.1051 time to fit residues: 11.3731 Evaluate side-chains 56 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR 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 417 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 444 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 421 HIS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 408 GLU Chi-restraints excluded: chain G residue 421 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 29 optimal weight: 0.4980 chunk 31 optimal weight: 40.0000 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 204 optimal weight: 10.0000 chunk 113 optimal weight: 0.0040 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 GLN ** 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 = 0.4243 r_free = 0.4243 target = 0.113532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075504 restraints weight = 96990.937| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 5.68 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20845 Z= 0.146 Angle : 0.526 8.845 28463 Z= 0.278 Chirality : 0.042 0.189 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.064 144.361 3483 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.98 % Allowed : 11.20 % 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 aren not related in a simple way. whole: 2.16 (0.18), residues: 2311 helix: 2.00 (0.14), residues: 1511 sheet: 1.30 (0.38), residues: 219 loop : 0.06 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 194 TYR 0.028 0.001 TYR G 392 PHE 0.016 0.001 PHE F 148 TRP 0.004 0.001 TRP C 267 HIS 0.004 0.001 HIS A 171 Details of bonding type rmsd covalent geometry : bond 0.00322 (20844) covalent geometry : angle 0.52595 (28463) hydrogen bonds : bond 0.02996 ( 1167) hydrogen bonds : angle 3.56846 ( 3349) Misc. bond : bond 0.00278 ( 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 61 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.628 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: 0.3863 (mmt) cc_final: 0.3116 (tmm) REVERT: B 110 MET cc_start: 0.9007 (pmm) cc_final: 0.8617 (pmm) REVERT: B 205 TYR cc_start: 0.8920 (m-80) cc_final: 0.8365 (m-10) REVERT: B 273 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8831 (mm) REVERT: B 397 MET cc_start: 0.6861 (mpp) cc_final: 0.6640 (mpp) REVERT: C 391 MET cc_start: 0.3707 (tmm) cc_final: 0.3038 (ppp) REVERT: D 301 MET cc_start: 0.9279 (mmt) cc_final: 0.8973 (mmt) REVERT: F 110 MET cc_start: 0.8089 (pmm) cc_final: 0.7698 (pmm) REVERT: F 256 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8743 (p) REVERT: G 167 TYR cc_start: 0.9406 (t80) cc_final: 0.9174 (t80) outliers start: 20 outliers final: 18 residues processed: 59 average time/residue: 0.1006 time to fit residues: 10.6959 Evaluate side-chains 61 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR 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 417 VAL Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 444 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 178 VAL Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 421 HIS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 408 GLU Chi-restraints excluded: chain G residue 421 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 101 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 131 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 193 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 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 = 0.4230 r_free = 0.4230 target = 0.112838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.074802 restraints weight = 97439.058| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.37 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20845 Z= 0.163 Angle : 0.541 8.816 28463 Z= 0.285 Chirality : 0.042 0.183 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.111 144.617 3483 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.88 % Allowed : 11.34 % 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 aren not related in a simple way. whole: 2.10 (0.18), residues: 2311 helix: 1.95 (0.14), residues: 1511 sheet: 1.24 (0.38), residues: 219 loop : 0.05 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 194 TYR 0.027 0.001 TYR G 392 PHE 0.017 0.001 PHE F 148 TRP 0.006 0.001 TRP E 267 HIS 0.005 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00363 (20844) covalent geometry : angle 0.54106 (28463) hydrogen bonds : bond 0.03142 ( 1167) hydrogen bonds : angle 3.64415 ( 3349) Misc. bond : bond 0.00242 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5546.93 seconds wall clock time: 95 minutes 32.41 seconds (5732.41 seconds total)