Starting phenix.real_space_refine on Tue Jun 17 19:03:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8btg_16229/06_2025/8btg_16229_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8btg_16229/06_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_16229/06_2025/8btg_16229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8btg_16229/06_2025/8btg_16229.map" model { file = "/net/cci-nas-00/data/ceres_data/8btg_16229/06_2025/8btg_16229_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8btg_16229/06_2025/8btg_16229_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.84, per 1000 atoms: 0.68 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: 5.54 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 7.69 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: 6.64 Time building geometry restraints manager: 6.49 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 54.450 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.100 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.080 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (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 TRP 0.009 0.001 TRP C 267 HIS 0.009 0.001 HIS F 421 PHE 0.018 0.002 PHE E 189 TYR 0.017 0.002 TYR C 144 ARG 0.009 0.000 ARG C 206 Details of bonding type rmsd hydrogen bonds : bond 0.06887 ( 1167) hydrogen bonds : angle 4.34975 ( 3349) covalent geometry : bond 0.00418 (20844) covalent geometry : angle 0.71246 (28463) 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 : 2.327 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: 0.3897 time to fit residues: 42.3051 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 : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 215 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 HIS ** 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 224 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.111413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.072451 restraints weight = 94924.684| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 6.26 r_work: 0.2952 rms_B_bonded: 6.16 restraints_weight: 2.0000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20845 Z= 0.230 Angle : 0.632 9.722 28463 Z= 0.334 Chirality : 0.045 0.194 3198 Planarity : 0.005 0.064 3414 Dihedral : 18.874 143.085 3483 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.44 % Allowed : 6.41 % Favored : 93.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2311 helix: 1.54 (0.14), residues: 1502 sheet: 0.83 (0.36), residues: 217 loop : -0.34 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 267 HIS 0.005 0.001 HIS G 171 PHE 0.021 0.002 PHE E 189 TYR 0.023 0.002 TYR G 167 ARG 0.007 0.001 ARG A 286 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 1167) hydrogen bonds : angle 4.03250 ( 3349) covalent geometry : bond 0.00514 (20844) covalent geometry : angle 0.63225 (28463) Misc. bond : bond 0.00318 ( 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: 9 poor density : 43 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 397 MET cc_start: 0.6060 (mpp) cc_final: 0.5749 (mpp) REVERT: B 422 GLU cc_start: 0.6194 (OUTLIER) cc_final: 0.5500 (pp20) REVERT: C 391 MET cc_start: 0.3271 (tmm) cc_final: 0.1370 (ttp) REVERT: D 301 MET cc_start: 0.9331 (mmt) cc_final: 0.9039 (mmt) REVERT: D 391 MET cc_start: 0.6017 (tpt) cc_final: 0.5277 (tmm) outliers start: 9 outliers final: 4 residues processed: 52 average time/residue: 0.2786 time to fit residues: 25.9219 Evaluate side-chains 46 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 2.121 ------------------------------------------------------------------------------- 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 122 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 202 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 224 optimal weight: 40.0000 chunk 115 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 HIS ** B 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 ASN ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.110771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.073915 restraints weight = 94221.521| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 7.17 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20845 Z= 0.211 Angle : 0.584 8.361 28463 Z= 0.310 Chirality : 0.044 0.195 3198 Planarity : 0.004 0.062 3414 Dihedral : 18.626 143.763 3483 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.03 % Allowed : 9.00 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.18), residues: 2311 helix: 1.73 (0.14), residues: 1505 sheet: 0.92 (0.36), residues: 219 loop : -0.22 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 267 HIS 0.004 0.001 HIS A 171 PHE 0.018 0.002 PHE G 189 TYR 0.023 0.002 TYR G 144 ARG 0.006 0.001 ARG E 249 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 1167) hydrogen bonds : angle 3.88590 ( 3349) covalent geometry : bond 0.00470 (20844) covalent geometry : angle 0.58432 (28463) Misc. bond : bond 0.00410 ( 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 62 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 41 time to evaluate : 2.168 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: 0.3649 (mmt) cc_final: 0.3018 (tmm) REVERT: B 397 MET cc_start: 0.5568 (mpp) cc_final: 0.5322 (mpp) REVERT: B 422 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5272 (pp20) REVERT: C 391 MET cc_start: 0.3041 (tmm) cc_final: 0.2381 (ppp) REVERT: D 301 MET cc_start: 0.9262 (mmt) cc_final: 0.8833 (mmt) REVERT: D 391 MET cc_start: 0.5908 (tpt) cc_final: 0.4877 (tmm) REVERT: F 110 MET cc_start: 0.8072 (pmm) cc_final: 0.7724 (pmm) REVERT: G 144 TYR cc_start: 0.9081 (m-80) cc_final: 0.8753 (m-10) outliers start: 21 outliers final: 9 residues processed: 59 average time/residue: 0.2921 time to fit residues: 30.0201 Evaluate side-chains 50 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 2.151 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 11 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 147 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 chunk 123 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 52 optimal weight: 6.9990 chunk 216 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.114398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076201 restraints weight = 97056.516| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 5.38 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20845 Z= 0.130 Angle : 0.528 8.624 28463 Z= 0.283 Chirality : 0.042 0.177 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.430 143.776 3483 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.22 % Allowed : 9.93 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.18), residues: 2311 helix: 1.85 (0.14), residues: 1502 sheet: 1.12 (0.37), residues: 217 loop : -0.17 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 267 HIS 0.004 0.001 HIS A 437 PHE 0.016 0.001 PHE F 148 TYR 0.021 0.001 TYR F 303 ARG 0.004 0.000 ARG E 249 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 1167) hydrogen bonds : angle 3.71807 ( 3349) covalent geometry : bond 0.00277 (20844) covalent geometry : angle 0.52803 (28463) Misc. bond : bond 0.00321 ( 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 67 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 2.398 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: 0.8916 (m-80) cc_final: 0.8319 (m-10) REVERT: B 397 MET cc_start: 0.6463 (mpp) cc_final: 0.6237 (mpp) REVERT: B 422 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5482 (pp20) REVERT: C 391 MET cc_start: 0.3321 (tmm) cc_final: 0.2707 (ppp) REVERT: D 301 MET cc_start: 0.9281 (mmt) cc_final: 0.8954 (mmt) REVERT: F 110 MET cc_start: 0.7957 (pmm) cc_final: 0.7577 (pmm) REVERT: F 161 MET cc_start: 0.8933 (mtp) cc_final: 0.8634 (mtp) REVERT: G 144 TYR cc_start: 0.9083 (m-80) cc_final: 0.8798 (m-10) REVERT: G 167 TYR cc_start: 0.9399 (t80) cc_final: 0.9172 (t80) outliers start: 25 outliers final: 9 residues processed: 64 average time/residue: 0.3040 time to fit residues: 34.0963 Evaluate side-chains 53 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 131 optimal weight: 10.0000 chunk 216 optimal weight: 0.0060 chunk 34 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 59 optimal weight: 40.0000 chunk 23 optimal weight: 0.0980 chunk 150 optimal weight: 0.8980 chunk 236 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 196 optimal weight: 50.0000 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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** ** 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 = 0.4237 r_free = 0.4237 target = 0.111061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.071893 restraints weight = 93838.571| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 6.05 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20845 Z= 0.177 Angle : 0.548 8.804 28463 Z= 0.290 Chirality : 0.043 0.187 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.374 143.929 3483 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.27 % Allowed : 10.66 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.18), residues: 2311 helix: 1.89 (0.14), residues: 1504 sheet: 1.18 (0.37), residues: 217 loop : -0.13 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 267 HIS 0.004 0.001 HIS A 171 PHE 0.017 0.001 PHE F 148 TYR 0.019 0.001 TYR F 303 ARG 0.004 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 1167) hydrogen bonds : angle 3.70889 ( 3349) covalent geometry : bond 0.00394 (20844) covalent geometry : angle 0.54830 (28463) Misc. bond : bond 0.00307 ( 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 66 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 40 time to evaluate : 2.323 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: 0.3674 (mmt) cc_final: 0.2818 (tmm) REVERT: B 397 MET cc_start: 0.6912 (mpp) cc_final: 0.6699 (mpp) REVERT: B 422 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5536 (pp20) REVERT: C 391 MET cc_start: 0.3739 (tmm) cc_final: 0.3084 (ppp) REVERT: D 301 MET cc_start: 0.9304 (mmt) cc_final: 0.8995 (mmt) REVERT: F 110 MET cc_start: 0.8045 (pmm) cc_final: 0.7642 (pmm) REVERT: G 144 TYR cc_start: 0.9078 (m-80) cc_final: 0.8837 (m-10) REVERT: G 167 TYR cc_start: 0.9412 (t80) cc_final: 0.9189 (t80) outliers start: 26 outliers final: 16 residues processed: 62 average time/residue: 0.3094 time to fit residues: 32.7815 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 : 2.075 ------------------------------------------------------------------------------- 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 C residue 199 VAL 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 178 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 62 optimal weight: 50.0000 chunk 82 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 195 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 232 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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 ** 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 = 0.4231 r_free = 0.4231 target = 0.110468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.071211 restraints weight = 93748.142| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 5.96 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20845 Z= 0.182 Angle : 0.547 7.899 28463 Z= 0.289 Chirality : 0.042 0.175 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.337 144.540 3483 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.86 % Allowed : 10.86 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2311 helix: 1.90 (0.14), residues: 1502 sheet: 1.18 (0.37), residues: 220 loop : -0.05 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 267 HIS 0.008 0.001 HIS F 231 PHE 0.020 0.002 PHE F 148 TYR 0.019 0.001 TYR F 303 ARG 0.006 0.000 ARG G 387 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 1167) hydrogen bonds : angle 3.71102 ( 3349) covalent geometry : bond 0.00403 (20844) covalent geometry : angle 0.54667 (28463) Misc. bond : bond 0.00275 ( 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 79 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 41 time to evaluate : 2.524 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: B 397 MET cc_start: 0.7438 (mpp) cc_final: 0.7232 (mpp) REVERT: C 391 MET cc_start: 0.4008 (tmm) cc_final: 0.3320 (ppp) REVERT: D 301 MET cc_start: 0.9287 (mmt) cc_final: 0.8984 (mmt) REVERT: F 110 MET cc_start: 0.8014 (pmm) cc_final: 0.7594 (pmm) REVERT: F 227 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8388 (pp20) REVERT: F 256 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8793 (p) REVERT: G 167 TYR cc_start: 0.9410 (t80) cc_final: 0.9179 (t80) REVERT: G 308 ILE cc_start: 0.7853 (tp) cc_final: 0.7524 (pt) outliers start: 38 outliers final: 22 residues processed: 74 average time/residue: 0.2949 time to fit residues: 38.2820 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 : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 301 MET 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 C residue 153 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 436 GLN Chi-restraints excluded: chain D residue 444 GLN Chi-restraints excluded: chain E residue 308 ILE 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 208 VAL Chi-restraints excluded: chain F residue 227 GLU 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 110 MET Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 396 GLU 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 148 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 115 optimal weight: 0.0570 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 179 optimal weight: 0.0050 chunk 52 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 50.0000 overall best weight: 0.5712 ------------------------------------------------------------------------------- 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** ** 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 = 0.4252 r_free = 0.4252 target = 0.114059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076487 restraints weight = 96336.791| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 5.03 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2684 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= 0.103 Angle : 0.509 9.849 28463 Z= 0.270 Chirality : 0.041 0.178 3198 Planarity : 0.004 0.060 3414 Dihedral : 18.119 144.718 3483 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.17 % Allowed : 11.30 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.18), residues: 2311 helix: 1.97 (0.14), residues: 1502 sheet: 1.44 (0.38), residues: 215 loop : -0.05 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 267 HIS 0.004 0.001 HIS B 414 PHE 0.012 0.001 PHE G 189 TYR 0.017 0.001 TYR F 303 ARG 0.003 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 1167) hydrogen bonds : angle 3.52978 ( 3349) covalent geometry : bond 0.00214 (20844) covalent geometry : angle 0.50881 (28463) Misc. bond : bond 0.00333 ( 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 67 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 43 time to evaluate : 2.245 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: 0.3645 (mmt) cc_final: 0.2853 (tmm) REVERT: B 205 TYR cc_start: 0.8917 (m-80) cc_final: 0.8393 (m-10) REVERT: C 391 MET cc_start: 0.3275 (tmm) cc_final: 0.2627 (ppp) REVERT: D 298 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8434 (m-40) REVERT: D 301 MET cc_start: 0.9251 (mmt) cc_final: 0.8896 (mmt) REVERT: F 110 MET cc_start: 0.8050 (pmm) cc_final: 0.7622 (pmm) REVERT: F 256 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8778 (p) REVERT: G 167 TYR cc_start: 0.9401 (t80) cc_final: 0.9182 (t80) REVERT: G 308 ILE cc_start: 0.8218 (tp) cc_final: 0.7966 (pt) outliers start: 24 outliers final: 13 residues processed: 65 average time/residue: 0.2701 time to fit residues: 31.4295 Evaluate side-chains 58 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 2.150 ------------------------------------------------------------------------------- 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 298 ASN 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 436 GLN Chi-restraints excluded: chain G residue 408 GLU Chi-restraints excluded: chain G residue 421 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 142 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 201 optimal weight: 0.0170 chunk 202 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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** ** 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 = 0.4249 r_free = 0.4249 target = 0.111140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.073302 restraints weight = 97463.080| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.72 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 20845 Z= 0.108 Angle : 0.507 8.964 28463 Z= 0.269 Chirality : 0.041 0.209 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.044 144.356 3483 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.32 % Allowed : 11.30 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.18), residues: 2311 helix: 1.99 (0.14), residues: 1503 sheet: 1.48 (0.38), residues: 217 loop : 0.00 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 267 HIS 0.004 0.001 HIS B 414 PHE 0.013 0.001 PHE G 189 TYR 0.023 0.001 TYR G 392 ARG 0.003 0.000 ARG G 395 Details of bonding type rmsd hydrogen bonds : bond 0.02842 ( 1167) hydrogen bonds : angle 3.50745 ( 3349) covalent geometry : bond 0.00229 (20844) covalent geometry : angle 0.50681 (28463) Misc. bond : bond 0.00314 ( 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 70 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 43 time to evaluate : 2.351 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: 0.3754 (mmt) cc_final: 0.2857 (tmm) REVERT: B 205 TYR cc_start: 0.8903 (m-80) cc_final: 0.8401 (m-10) REVERT: C 391 MET cc_start: 0.3835 (tmm) cc_final: 0.3134 (ppp) REVERT: D 298 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8358 (m-40) REVERT: D 301 MET cc_start: 0.9201 (mmt) cc_final: 0.8816 (mmt) REVERT: F 110 MET cc_start: 0.8092 (pmm) cc_final: 0.7811 (pmm) REVERT: F 256 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8740 (p) REVERT: G 167 TYR cc_start: 0.9425 (t80) cc_final: 0.9193 (t80) REVERT: G 308 ILE cc_start: 0.7850 (tp) cc_final: 0.7588 (pt) outliers start: 27 outliers final: 17 residues processed: 68 average time/residue: 0.2703 time to fit residues: 33.0726 Evaluate side-chains 62 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 301 MET 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 298 ASN 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 408 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 174 optimal weight: 0.4980 chunk 226 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 228 optimal weight: 40.0000 chunk 171 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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** ** 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 = 0.4233 r_free = 0.4233 target = 0.113047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.074985 restraints weight = 97076.850| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 5.32 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20845 Z= 0.170 Angle : 0.535 8.632 28463 Z= 0.282 Chirality : 0.042 0.190 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.090 144.343 3483 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.12 % Allowed : 11.54 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.18), residues: 2311 helix: 2.01 (0.14), residues: 1504 sheet: 1.32 (0.38), residues: 219 loop : 0.05 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 267 HIS 0.005 0.001 HIS G 437 PHE 0.017 0.001 PHE F 148 TYR 0.023 0.001 TYR G 392 ARG 0.003 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.03049 ( 1167) hydrogen bonds : angle 3.58146 ( 3349) covalent geometry : bond 0.00377 (20844) covalent geometry : angle 0.53488 (28463) Misc. bond : bond 0.00255 ( 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 65 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 42 time to evaluate : 2.376 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: 0.3595 (mmt) cc_final: 0.2778 (tmm) REVERT: B 273 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8857 (mm) REVERT: C 391 MET cc_start: 0.3328 (tmm) cc_final: 0.2653 (ppp) REVERT: D 301 MET cc_start: 0.9297 (mmt) cc_final: 0.8972 (mmt) REVERT: F 110 MET cc_start: 0.8190 (pmm) cc_final: 0.7886 (pmm) REVERT: F 256 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8734 (p) REVERT: G 167 TYR cc_start: 0.9419 (t80) cc_final: 0.9183 (t80) REVERT: G 308 ILE cc_start: 0.8163 (tp) cc_final: 0.7904 (pt) outliers start: 23 outliers final: 19 residues processed: 64 average time/residue: 0.2873 time to fit residues: 32.9750 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 : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 298 ASN 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 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 117 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 178 optimal weight: 0.9980 chunk 115 optimal weight: 0.0030 chunk 81 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 232 optimal weight: 10.0000 chunk 231 optimal weight: 20.0000 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.113581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075396 restraints weight = 96548.112| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.61 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20845 Z= 0.117 Angle : 0.511 8.739 28463 Z= 0.270 Chirality : 0.041 0.186 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.015 144.613 3483 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.22 % Allowed : 11.54 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.18), residues: 2311 helix: 2.02 (0.14), residues: 1511 sheet: 1.42 (0.38), residues: 219 loop : 0.07 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 267 HIS 0.004 0.001 HIS G 437 PHE 0.013 0.001 PHE G 189 TYR 0.021 0.001 TYR G 392 ARG 0.003 0.000 ARG B 194 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 1167) hydrogen bonds : angle 3.51118 ( 3349) covalent geometry : bond 0.00253 (20844) covalent geometry : angle 0.51096 (28463) Misc. bond : bond 0.00296 ( 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 67 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 42 time to evaluate : 2.152 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: 0.3734 (mmt) cc_final: 0.2898 (tmm) REVERT: B 110 MET cc_start: 0.8887 (pmm) cc_final: 0.8541 (pmm) REVERT: B 205 TYR cc_start: 0.8903 (m-80) cc_final: 0.8362 (m-10) REVERT: B 273 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8804 (mm) REVERT: B 422 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5950 (pp20) REVERT: C 391 MET cc_start: 0.3815 (tmm) cc_final: 0.3100 (ppp) REVERT: D 301 MET cc_start: 0.9273 (mmt) cc_final: 0.8870 (mmt) REVERT: F 110 MET cc_start: 0.8121 (pmm) cc_final: 0.7832 (pmm) REVERT: F 256 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8743 (p) REVERT: G 167 TYR cc_start: 0.9440 (t80) cc_final: 0.9208 (t80) outliers start: 25 outliers final: 19 residues processed: 65 average time/residue: 0.2869 time to fit residues: 32.8585 Evaluate side-chains 64 residues out of total 2045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 42 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 409 PHE Chi-restraints excluded: chain B residue 422 GLU Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 298 ASN 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 308 ILE 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 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 181 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 173 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** ** A 388 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.112875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.075160 restraints weight = 96909.985| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 5.41 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20845 Z= 0.152 Angle : 0.527 9.136 28463 Z= 0.277 Chirality : 0.042 0.187 3198 Planarity : 0.004 0.059 3414 Dihedral : 18.028 144.472 3483 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.17 % Allowed : 11.49 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.18), residues: 2311 helix: 2.01 (0.14), residues: 1514 sheet: 1.34 (0.38), residues: 219 loop : 0.10 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 267 HIS 0.004 0.001 HIS F 421 PHE 0.016 0.001 PHE F 148 TYR 0.019 0.001 TYR G 392 ARG 0.003 0.000 ARG E 281 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 1167) hydrogen bonds : angle 3.56530 ( 3349) covalent geometry : bond 0.00337 (20844) covalent geometry : angle 0.52654 (28463) Misc. bond : bond 0.00270 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12764.88 seconds wall clock time: 218 minutes 39.09 seconds (13119.09 seconds total)