Starting phenix.real_space_refine on Fri Mar 6 13:56:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pdt_20309/03_2026/6pdt_20309_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pdt_20309/03_2026/6pdt_20309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pdt_20309/03_2026/6pdt_20309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pdt_20309/03_2026/6pdt_20309.map" model { file = "/net/cci-nas-00/data/ceres_data/6pdt_20309/03_2026/6pdt_20309_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pdt_20309/03_2026/6pdt_20309_trim.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 9888 2.51 5 N 2676 2.21 5 O 3064 1.98 5 H 15636 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31364 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7797 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 475} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'GLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D Time building chain proxies: 9.32, per 1000 atoms: 0.30 Number of scatterers: 31364 At special positions: 0 Unit cell: (95.55, 110.25, 171.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 3064 8.00 N 2676 7.00 C 9888 6.00 H 15636 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 448 " distance=2.21 Simple disulfide: pdb=" SG CYS B 248 " - pdb=" SG CYS B 448 " distance=2.21 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS C 448 " distance=2.21 Simple disulfide: pdb=" SG CYS D 248 " - pdb=" SG CYS D 448 " distance=2.21 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 851.1 milliseconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 54.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 2 through 26 Processing helix chain 'A' and resid 28 through 46 Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 124 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 186 through 190 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 263 through 265 No H-bonds generated for 'chain 'A' and resid 263 through 265' Processing helix chain 'A' and resid 269 through 278 Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 327 through 345 Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.551A pdb=" N LEU A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 394 removed outlier: 3.854A pdb=" N GLU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 422 Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 458 through 470 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 487 through 500 Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 28 through 46 Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 124 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 186 through 190 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 217 through 229 Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 269 through 278 Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 303 through 313 Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 327 through 345 Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.550A pdb=" N LEU B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 394 removed outlier: 3.854A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 422 Processing helix chain 'B' and resid 423 through 433 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 458 through 470 Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 487 through 500 Processing helix chain 'C' and resid 2 through 26 Processing helix chain 'C' and resid 28 through 46 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 124 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 186 through 190 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 217 through 229 Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'C' and resid 269 through 278 Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 303 through 313 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 327 through 345 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.549A pdb=" N LEU C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 394 removed outlier: 3.853A pdb=" N GLU C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 422 Processing helix chain 'C' and resid 423 through 433 Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 472 through 478 Processing helix chain 'C' and resid 487 through 500 Processing helix chain 'D' and resid 2 through 26 Processing helix chain 'D' and resid 28 through 46 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 124 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 217 through 229 Processing helix chain 'D' and resid 263 through 265 No H-bonds generated for 'chain 'D' and resid 263 through 265' Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 327 through 345 Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.550A pdb=" N LEU D 373 " --> pdb=" O SER D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 394 removed outlier: 3.853A pdb=" N GLU D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 422 Processing helix chain 'D' and resid 423 through 433 Processing helix chain 'D' and resid 450 through 456 Processing helix chain 'D' and resid 458 through 470 Processing helix chain 'D' and resid 472 through 478 Processing helix chain 'D' and resid 487 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.917A pdb=" N ILE A 285 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 256 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 245 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU A 261 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 19.065A pdb=" N GLU A 243 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 447 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 247 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP A 449 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 249 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 444 " --> pdb=" O HIS A 481 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LYS A 483 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 446 " --> pdb=" O LYS A 483 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 112 removed outlier: 11.594A pdb=" N LYS A 158 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A 80 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLY A 160 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 82 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR A 162 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 84 " --> pdb=" O THR A 162 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N MET A 157 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL A 212 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU A 159 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 214 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.917A pdb=" N ILE B 285 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY B 256 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 245 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU B 261 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 19.066A pdb=" N GLU B 243 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY B 447 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY B 247 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 449 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 249 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 444 " --> pdb=" O HIS B 481 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS B 483 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B 446 " --> pdb=" O LYS B 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 112 removed outlier: 11.593A pdb=" N LYS B 158 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 80 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLY B 160 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 82 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR B 162 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 84 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET B 157 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL B 212 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 159 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 214 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.916A pdb=" N ILE C 285 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 256 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 245 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU C 261 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 19.066A pdb=" N GLU C 243 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 447 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY C 247 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP C 449 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 249 " --> pdb=" O ASP C 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 444 " --> pdb=" O HIS C 481 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS C 483 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE C 446 " --> pdb=" O LYS C 483 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 104 through 112 removed outlier: 11.593A pdb=" N LYS C 158 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 80 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLY C 160 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 82 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR C 162 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 84 " --> pdb=" O THR C 162 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET C 157 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL C 212 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 159 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 214 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.917A pdb=" N ILE D 285 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY D 256 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL D 245 " --> pdb=" O MET D 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU D 261 " --> pdb=" O GLU D 243 " (cutoff:3.500A) removed outlier: 19.066A pdb=" N GLU D 243 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY D 447 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY D 247 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP D 449 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 249 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 444 " --> pdb=" O HIS D 481 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LYS D 483 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE D 446 " --> pdb=" O LYS D 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 104 through 112 removed outlier: 11.594A pdb=" N LYS D 158 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL D 80 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLY D 160 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 82 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR D 162 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 84 " --> pdb=" O THR D 162 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET D 157 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N VAL D 212 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU D 159 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 214 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.29 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.15: 15616 1.15 - 1.35: 5350 1.35 - 1.54: 10087 1.54 - 1.74: 482 1.74 - 1.94: 121 Bond restraints: 31656 Sorted by residual: bond pdb=" NE ARG D 412 " pdb=" HE ARG D 412 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" NE2 GLN B 20 " pdb="HE22 GLN B 20 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" NE ARG A 412 " pdb=" HE ARG A 412 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" NE2 GLN C 20 " pdb="HE22 GLN C 20 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" NE ARG D 396 " pdb=" HE ARG D 396 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.37e+01 ... (remaining 31651 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.07: 57288 10.07 - 20.14: 44 20.14 - 30.21: 4 30.21 - 40.28: 28 40.28 - 50.35: 16 Bond angle restraints: 57380 Sorted by residual: angle pdb=" C VAL D 69 " pdb=" N THR D 70 " pdb=" CA THR D 70 " ideal model delta sigma weight residual 122.68 154.46 -31.78 1.47e+00 4.63e-01 4.67e+02 angle pdb=" C VAL B 69 " pdb=" N THR B 70 " pdb=" CA THR B 70 " ideal model delta sigma weight residual 122.68 154.45 -31.77 1.47e+00 4.63e-01 4.67e+02 angle pdb=" C VAL C 69 " pdb=" N THR C 70 " pdb=" CA THR C 70 " ideal model delta sigma weight residual 122.68 154.43 -31.75 1.47e+00 4.63e-01 4.67e+02 angle pdb=" C VAL A 69 " pdb=" N THR A 70 " pdb=" CA THR A 70 " ideal model delta sigma weight residual 122.68 154.42 -31.74 1.47e+00 4.63e-01 4.66e+02 angle pdb=" C ARG C 353 " pdb=" N SER C 354 " pdb=" CA SER C 354 " ideal model delta sigma weight residual 121.70 156.57 -34.87 1.80e+00 3.09e-01 3.75e+02 ... (remaining 57375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 14152 17.64 - 35.28: 520 35.28 - 52.92: 204 52.92 - 70.56: 80 70.56 - 88.20: 20 Dihedral angle restraints: 14976 sinusoidal: 8416 harmonic: 6560 Sorted by residual: dihedral pdb=" CB CYS A 248 " pdb=" SG CYS A 248 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual -86.00 -34.82 -51.18 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS C 248 " pdb=" SG CYS C 248 " pdb=" SG CYS C 448 " pdb=" CB CYS C 448 " ideal model delta sinusoidal sigma weight residual -86.00 -34.87 -51.13 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS B 248 " pdb=" SG CYS B 248 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual -86.00 -34.87 -51.13 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 14973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1202 0.065 - 0.131: 813 0.131 - 0.196: 308 0.196 - 0.262: 127 0.262 - 0.327: 46 Chirality restraints: 2496 Sorted by residual: chirality pdb=" CA ASP A 379 " pdb=" N ASP A 379 " pdb=" C ASP A 379 " pdb=" CB ASP A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASP D 379 " pdb=" N ASP D 379 " pdb=" C ASP D 379 " pdb=" CB ASP D 379 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ASP B 379 " pdb=" N ASP B 379 " pdb=" C ASP B 379 " pdb=" CB ASP B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2493 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 401 " 0.084 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" N THR D 402 " -0.267 2.00e-02 2.50e+03 pdb=" CA THR D 402 " 0.071 2.00e-02 2.50e+03 pdb=" H THR D 402 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 401 " -0.084 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" N THR A 402 " 0.267 2.00e-02 2.50e+03 pdb=" CA THR A 402 " -0.071 2.00e-02 2.50e+03 pdb=" H THR A 402 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 401 " 0.084 2.00e-02 2.50e+03 1.55e-01 2.40e+02 pdb=" N THR B 402 " -0.267 2.00e-02 2.50e+03 pdb=" CA THR B 402 " 0.071 2.00e-02 2.50e+03 pdb=" H THR B 402 " 0.113 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 367 1.87 - 2.55: 29483 2.55 - 3.23: 101736 3.23 - 3.92: 132518 3.92 - 4.60: 206314 Nonbonded interactions: 470418 Sorted by model distance: nonbonded pdb=" H THR C 402 " pdb=" H GLU C 403 " model vdw 1.187 2.100 nonbonded pdb=" H THR D 402 " pdb=" H GLU D 403 " model vdw 1.188 2.100 nonbonded pdb=" H THR A 402 " pdb=" H GLU A 403 " model vdw 1.188 2.100 nonbonded pdb=" H THR B 402 " pdb=" H GLU B 403 " model vdw 1.188 2.100 nonbonded pdb=" H SER A 354 " pdb=" HA SER A 354 " model vdw 1.606 1.816 ... (remaining 470413 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.022 0.177 16024 Z= 1.184 Angle : 2.063 34.868 21708 Z= 1.384 Chirality : 0.105 0.327 2496 Planarity : 0.012 0.140 2772 Dihedral : 11.590 88.198 6168 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.91 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 1992 helix: -0.20 (0.15), residues: 936 sheet: 0.55 (0.32), residues: 204 loop : 1.07 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 417 TYR 0.075 0.010 TYR C 165 PHE 0.051 0.008 PHE C 104 TRP 0.020 0.006 TRP B 180 HIS 0.010 0.002 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.02207 (16020) covalent geometry : angle 2.05999 (21700) SS BOND : bond 0.17708 ( 4) SS BOND : angle 6.45089 ( 8) hydrogen bonds : bond 0.18847 ( 868) hydrogen bonds : angle 7.48776 ( 2520) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.848 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 ILE cc_start: 0.8723 (mt) cc_final: 0.8481 (mp) REVERT: A 496 CYS cc_start: 0.7809 (m) cc_final: 0.7538 (m) REVERT: B 219 THR cc_start: 0.8863 (p) cc_final: 0.8624 (p) REVERT: B 333 GLU cc_start: 0.8314 (tp30) cc_final: 0.7912 (tp30) REVERT: C 192 LYS cc_start: 0.7644 (mttp) cc_final: 0.7360 (tppt) REVERT: C 210 ILE cc_start: 0.7685 (mt) cc_final: 0.7426 (tt) REVERT: C 265 ILE cc_start: 0.8873 (mt) cc_final: 0.8649 (mt) REVERT: C 288 VAL cc_start: 0.8939 (t) cc_final: 0.8619 (m) REVERT: C 333 GLU cc_start: 0.8169 (tp30) cc_final: 0.7749 (tp30) REVERT: D 36 THR cc_start: 0.8359 (m) cc_final: 0.8139 (m) REVERT: D 219 THR cc_start: 0.8701 (p) cc_final: 0.8447 (p) REVERT: D 246 ILE cc_start: 0.8611 (mt) cc_final: 0.8386 (mp) REVERT: D 496 CYS cc_start: 0.7529 (m) cc_final: 0.7287 (m) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.3500 time to fit residues: 220.7758 Evaluate side-chains 251 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 169 GLN B 367 GLN D 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.150390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130481 restraints weight = 71314.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.135846 restraints weight = 33666.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.139257 restraints weight = 20022.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.141461 restraints weight = 13731.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142931 restraints weight = 10340.116| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16024 Z= 0.221 Angle : 0.953 22.880 21708 Z= 0.528 Chirality : 0.045 0.174 2496 Planarity : 0.005 0.047 2772 Dihedral : 9.288 73.904 2364 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.91 % Allowed : 7.13 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 1992 helix: 0.56 (0.15), residues: 980 sheet: -0.15 (0.30), residues: 236 loop : -0.04 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 360 TYR 0.024 0.002 TYR C 165 PHE 0.014 0.002 PHE A 330 TRP 0.007 0.001 TRP B 180 HIS 0.009 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00464 (16020) covalent geometry : angle 0.95273 (21700) SS BOND : bond 0.00743 ( 4) SS BOND : angle 2.18265 ( 8) hydrogen bonds : bond 0.07841 ( 868) hydrogen bonds : angle 6.09648 ( 2520) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.903 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASP cc_start: 0.7051 (t0) cc_final: 0.6812 (t0) REVERT: A 315 THR cc_start: 0.9091 (p) cc_final: 0.8890 (t) REVERT: B 147 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6958 (mm-30) REVERT: B 157 MET cc_start: 0.7374 (mmm) cc_final: 0.6978 (mmt) REVERT: B 295 ASN cc_start: 0.8142 (m-40) cc_final: 0.7921 (m-40) REVERT: B 323 GLU cc_start: 0.8031 (tt0) cc_final: 0.7602 (tt0) REVERT: C 109 MET cc_start: 0.7981 (ttm) cc_final: 0.7631 (ttm) REVERT: C 188 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7457 (t0) outliers start: 33 outliers final: 21 residues processed: 293 average time/residue: 0.2763 time to fit residues: 124.7361 Evaluate side-chains 227 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 43 MET Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 326 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 169 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 192 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS B 169 GLN C 169 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.148278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128656 restraints weight = 71781.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.133996 restraints weight = 34136.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137388 restraints weight = 20363.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.139603 restraints weight = 13991.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.141103 restraints weight = 10490.095| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16024 Z= 0.168 Angle : 0.849 21.717 21708 Z= 0.463 Chirality : 0.042 0.168 2496 Planarity : 0.005 0.045 2772 Dihedral : 8.947 78.103 2364 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.28 % Allowed : 10.15 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 1992 helix: 0.84 (0.15), residues: 988 sheet: -0.49 (0.27), residues: 288 loop : -0.22 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 385 TYR 0.017 0.001 TYR A 165 PHE 0.016 0.002 PHE D 330 TRP 0.006 0.001 TRP C 290 HIS 0.009 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00345 (16020) covalent geometry : angle 0.84590 (21700) SS BOND : bond 0.00566 ( 4) SS BOND : angle 3.62397 ( 8) hydrogen bonds : bond 0.06267 ( 868) hydrogen bonds : angle 5.72703 ( 2520) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 0.821 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.8885 (mtm) cc_final: 0.8656 (mtp) REVERT: A 106 MET cc_start: 0.7079 (ttp) cc_final: 0.6360 (ttp) REVERT: A 264 LYS cc_start: 0.7467 (mttp) cc_final: 0.7211 (tptm) REVERT: B 157 MET cc_start: 0.7572 (mmm) cc_final: 0.7162 (mmt) REVERT: B 219 THR cc_start: 0.8771 (p) cc_final: 0.8524 (p) REVERT: B 295 ASN cc_start: 0.8304 (m-40) cc_final: 0.8066 (m-40) REVERT: B 323 GLU cc_start: 0.8005 (tt0) cc_final: 0.7784 (tt0) REVERT: C 109 MET cc_start: 0.8019 (ttm) cc_final: 0.7467 (ttm) REVERT: D 43 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8235 (mtm) REVERT: D 157 MET cc_start: 0.7155 (mmm) cc_final: 0.6340 (mmm) outliers start: 22 outliers final: 13 residues processed: 228 average time/residue: 0.2606 time to fit residues: 92.8595 Evaluate side-chains 200 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 138 optimal weight: 0.0670 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.145648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125990 restraints weight = 71172.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131244 restraints weight = 34247.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134605 restraints weight = 20579.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136770 restraints weight = 14188.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138272 restraints weight = 10719.290| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16024 Z= 0.161 Angle : 0.800 21.319 21708 Z= 0.435 Chirality : 0.041 0.221 2496 Planarity : 0.004 0.046 2772 Dihedral : 8.665 78.606 2364 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.12 % Favored : 95.78 % Rotamer: Outliers : 1.51 % Allowed : 10.15 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 1992 helix: 1.08 (0.16), residues: 988 sheet: -0.83 (0.26), residues: 288 loop : -0.32 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 385 TYR 0.011 0.001 TYR A 165 PHE 0.015 0.001 PHE B 330 TRP 0.004 0.001 TRP A 290 HIS 0.010 0.001 HIS B 343 Details of bonding type rmsd covalent geometry : bond 0.00340 (16020) covalent geometry : angle 0.79771 (21700) SS BOND : bond 0.01751 ( 4) SS BOND : angle 3.11443 ( 8) hydrogen bonds : bond 0.05388 ( 868) hydrogen bonds : angle 5.47229 ( 2520) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 0.755 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8333 (mt) cc_final: 0.8126 (mp) REVERT: A 264 LYS cc_start: 0.7468 (mttp) cc_final: 0.7201 (tptm) REVERT: B 157 MET cc_start: 0.7777 (mmm) cc_final: 0.7405 (mmt) REVERT: B 295 ASN cc_start: 0.8394 (m-40) cc_final: 0.8105 (m-40) REVERT: D 157 MET cc_start: 0.7376 (mmm) cc_final: 0.6717 (mmm) outliers start: 26 outliers final: 16 residues processed: 227 average time/residue: 0.2528 time to fit residues: 90.2281 Evaluate side-chains 204 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.138849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119731 restraints weight = 71864.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124683 restraints weight = 34769.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.127871 restraints weight = 21025.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129939 restraints weight = 14613.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131319 restraints weight = 11127.488| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16024 Z= 0.218 Angle : 0.814 21.666 21708 Z= 0.444 Chirality : 0.041 0.263 2496 Planarity : 0.004 0.046 2772 Dihedral : 8.710 83.014 2364 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.33 % Rotamer: Outliers : 1.33 % Allowed : 10.50 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.18), residues: 1992 helix: 0.97 (0.16), residues: 992 sheet: -0.93 (0.27), residues: 284 loop : -0.52 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 385 TYR 0.015 0.002 TYR C 165 PHE 0.017 0.002 PHE B 330 TRP 0.005 0.002 TRP D 290 HIS 0.010 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00483 (16020) covalent geometry : angle 0.80899 (21700) SS BOND : bond 0.02500 ( 4) SS BOND : angle 4.68607 ( 8) hydrogen bonds : bond 0.05401 ( 868) hydrogen bonds : angle 5.43972 ( 2520) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.787 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: B 157 MET cc_start: 0.7882 (mmm) cc_final: 0.7556 (mmt) REVERT: B 295 ASN cc_start: 0.8527 (m-40) cc_final: 0.8236 (m-40) REVERT: D 157 MET cc_start: 0.7442 (mmm) cc_final: 0.6888 (mmm) REVERT: D 182 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8117 (ttpp) REVERT: D 389 LEU cc_start: 0.7827 (tp) cc_final: 0.7580 (tp) outliers start: 23 outliers final: 13 residues processed: 209 average time/residue: 0.2605 time to fit residues: 85.6884 Evaluate side-chains 193 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 182 LYS Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 296 GLU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 108 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.141118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.122272 restraints weight = 71008.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127234 restraints weight = 34008.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130417 restraints weight = 20419.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132503 restraints weight = 14097.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133929 restraints weight = 10649.829| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16024 Z= 0.152 Angle : 0.791 21.436 21708 Z= 0.431 Chirality : 0.041 0.342 2496 Planarity : 0.004 0.045 2772 Dihedral : 8.561 83.522 2364 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 1.16 % Allowed : 11.25 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.19), residues: 1992 helix: 1.14 (0.16), residues: 992 sheet: -1.13 (0.27), residues: 288 loop : -0.53 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 360 TYR 0.009 0.001 TYR A 165 PHE 0.014 0.001 PHE C 250 TRP 0.004 0.001 TRP D 290 HIS 0.008 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00324 (16020) covalent geometry : angle 0.78604 (21700) SS BOND : bond 0.01816 ( 4) SS BOND : angle 4.86415 ( 8) hydrogen bonds : bond 0.04992 ( 868) hydrogen bonds : angle 5.31296 ( 2520) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.868 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7304 (mmm) cc_final: 0.6943 (mmm) REVERT: B 157 MET cc_start: 0.7898 (mmm) cc_final: 0.7618 (mmt) REVERT: B 295 ASN cc_start: 0.8548 (m-40) cc_final: 0.8239 (m-40) REVERT: D 157 MET cc_start: 0.7397 (mmm) cc_final: 0.6913 (mmm) REVERT: D 389 LEU cc_start: 0.7780 (tp) cc_final: 0.7522 (tp) outliers start: 20 outliers final: 13 residues processed: 206 average time/residue: 0.2489 time to fit residues: 81.8069 Evaluate side-chains 189 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 448 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 135 optimal weight: 0.7980 chunk 185 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.142509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.122858 restraints weight = 71972.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128088 restraints weight = 34588.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.131427 restraints weight = 20801.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133573 restraints weight = 14369.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135049 restraints weight = 10897.640| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16024 Z= 0.142 Angle : 0.770 21.405 21708 Z= 0.417 Chirality : 0.040 0.232 2496 Planarity : 0.004 0.047 2772 Dihedral : 8.409 83.658 2364 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 1.28 % Allowed : 11.31 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.19), residues: 1992 helix: 1.26 (0.16), residues: 992 sheet: -1.13 (0.27), residues: 284 loop : -0.54 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 360 TYR 0.009 0.001 TYR B 258 PHE 0.014 0.001 PHE C 139 TRP 0.003 0.001 TRP D 290 HIS 0.008 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00305 (16020) covalent geometry : angle 0.76523 (21700) SS BOND : bond 0.00959 ( 4) SS BOND : angle 4.69822 ( 8) hydrogen bonds : bond 0.04687 ( 868) hydrogen bonds : angle 5.22927 ( 2520) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.810 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7269 (mmm) cc_final: 0.6951 (mmm) REVERT: B 157 MET cc_start: 0.7959 (mmm) cc_final: 0.7678 (mmt) REVERT: B 295 ASN cc_start: 0.8580 (m-40) cc_final: 0.8252 (m-40) REVERT: C 192 LYS cc_start: 0.7787 (mttp) cc_final: 0.7528 (mtmm) REVERT: D 43 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7985 (mtm) REVERT: D 157 MET cc_start: 0.7437 (mmm) cc_final: 0.6751 (mmm) REVERT: D 389 LEU cc_start: 0.7766 (tp) cc_final: 0.7524 (tp) outliers start: 22 outliers final: 14 residues processed: 206 average time/residue: 0.2385 time to fit residues: 78.3742 Evaluate side-chains 196 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 16 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN C 173 ASN D 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118170 restraints weight = 72250.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123305 restraints weight = 35502.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126607 restraints weight = 21690.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128700 restraints weight = 15176.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.130175 restraints weight = 11671.295| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16024 Z= 0.234 Angle : 0.810 21.321 21708 Z= 0.444 Chirality : 0.042 0.226 2496 Planarity : 0.004 0.044 2772 Dihedral : 8.652 86.910 2364 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 1.68 % Allowed : 11.43 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.19), residues: 1992 helix: 1.09 (0.16), residues: 992 sheet: -1.18 (0.27), residues: 284 loop : -0.73 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 360 TYR 0.011 0.002 TYR D 165 PHE 0.019 0.002 PHE B 250 TRP 0.008 0.002 TRP A 290 HIS 0.010 0.001 HIS D 343 Details of bonding type rmsd covalent geometry : bond 0.00521 (16020) covalent geometry : angle 0.80533 (21700) SS BOND : bond 0.00940 ( 4) SS BOND : angle 4.39749 ( 8) hydrogen bonds : bond 0.05073 ( 868) hydrogen bonds : angle 5.32342 ( 2520) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.879 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7271 (mmm) cc_final: 0.7030 (mmm) REVERT: A 259 MET cc_start: 0.8868 (tpt) cc_final: 0.8493 (tpt) REVERT: B 157 MET cc_start: 0.8143 (mmm) cc_final: 0.7859 (mmt) REVERT: B 295 ASN cc_start: 0.8653 (m-40) cc_final: 0.8343 (m-40) REVERT: C 192 LYS cc_start: 0.7821 (mttp) cc_final: 0.7561 (mtmm) REVERT: D 43 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: D 157 MET cc_start: 0.7480 (mmm) cc_final: 0.7080 (mmm) outliers start: 29 outliers final: 23 residues processed: 203 average time/residue: 0.2447 time to fit residues: 78.6325 Evaluate side-chains 201 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 177 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 248 CYS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 138 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 181 optimal weight: 0.0060 chunk 123 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.0770 chunk 160 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 163 optimal weight: 0.5980 chunk 125 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.141399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.121764 restraints weight = 71385.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126956 restraints weight = 34430.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130274 restraints weight = 20732.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132411 restraints weight = 14344.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133853 restraints weight = 10893.172| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16024 Z= 0.125 Angle : 0.770 21.446 21708 Z= 0.417 Chirality : 0.040 0.159 2496 Planarity : 0.004 0.044 2772 Dihedral : 8.598 89.177 2364 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.68 % Rotamer: Outliers : 1.33 % Allowed : 12.06 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.19), residues: 1992 helix: 1.21 (0.16), residues: 996 sheet: -1.17 (0.28), residues: 284 loop : -0.53 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 336 TYR 0.008 0.001 TYR B 258 PHE 0.012 0.001 PHE B 250 TRP 0.004 0.001 TRP C 180 HIS 0.007 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00262 (16020) covalent geometry : angle 0.76446 (21700) SS BOND : bond 0.00522 ( 4) SS BOND : angle 5.03049 ( 8) hydrogen bonds : bond 0.04597 ( 868) hydrogen bonds : angle 5.17098 ( 2520) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.838 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: 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: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7213 (mmm) cc_final: 0.6966 (mmm) REVERT: B 101 ASP cc_start: 0.7908 (p0) cc_final: 0.7424 (p0) REVERT: B 157 MET cc_start: 0.8194 (mmm) cc_final: 0.7889 (mmt) REVERT: B 295 ASN cc_start: 0.8619 (m-40) cc_final: 0.8295 (m-40) REVERT: C 192 LYS cc_start: 0.7833 (mttp) cc_final: 0.7571 (mtmm) REVERT: D 43 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: D 157 MET cc_start: 0.7459 (mmm) cc_final: 0.7026 (mmm) outliers start: 23 outliers final: 16 residues processed: 198 average time/residue: 0.2367 time to fit residues: 74.5440 Evaluate side-chains 196 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 176 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.120990 restraints weight = 71366.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126139 restraints weight = 34590.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129441 restraints weight = 20891.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131587 restraints weight = 14476.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.133029 restraints weight = 10977.043| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16024 Z= 0.150 Angle : 0.775 21.476 21708 Z= 0.419 Chirality : 0.040 0.198 2496 Planarity : 0.004 0.044 2772 Dihedral : 8.641 86.600 2364 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 1.04 % Allowed : 12.59 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1992 helix: 1.27 (0.16), residues: 996 sheet: -1.16 (0.28), residues: 284 loop : -0.50 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.010 0.001 TYR B 258 PHE 0.014 0.001 PHE D 250 TRP 0.004 0.001 TRP C 180 HIS 0.008 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00327 (16020) covalent geometry : angle 0.77052 (21700) SS BOND : bond 0.00785 ( 4) SS BOND : angle 4.34872 ( 8) hydrogen bonds : bond 0.04483 ( 868) hydrogen bonds : angle 5.13332 ( 2520) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 1.198 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7215 (mmm) cc_final: 0.6973 (mmm) REVERT: B 101 ASP cc_start: 0.7907 (p0) cc_final: 0.7438 (p0) REVERT: B 157 MET cc_start: 0.8116 (mmm) cc_final: 0.7846 (mmt) REVERT: B 295 ASN cc_start: 0.8662 (m-40) cc_final: 0.8342 (m-40) REVERT: C 1 MET cc_start: 0.6167 (tpp) cc_final: 0.5457 (tpp) REVERT: C 192 LYS cc_start: 0.7848 (mttp) cc_final: 0.7597 (mtmm) REVERT: D 43 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8219 (mtm) REVERT: D 157 MET cc_start: 0.7435 (mmm) cc_final: 0.6816 (mmm) REVERT: D 259 MET cc_start: 0.8834 (tpt) cc_final: 0.8517 (tpt) outliers start: 18 outliers final: 14 residues processed: 195 average time/residue: 0.2405 time to fit residues: 74.4499 Evaluate side-chains 189 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 380 ASP Chi-restraints excluded: chain B residue 496 CYS Chi-restraints excluded: chain C residue 106 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 43 MET Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 5 optimal weight: 0.0670 chunk 11 optimal weight: 0.0000 chunk 85 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 152 optimal weight: 0.8980 chunk 143 optimal weight: 0.0000 chunk 136 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 0.2326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123734 restraints weight = 71002.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128913 restraints weight = 34217.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132214 restraints weight = 20500.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134343 restraints weight = 14128.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135812 restraints weight = 10663.505| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16024 Z= 0.115 Angle : 0.752 21.286 21708 Z= 0.405 Chirality : 0.040 0.186 2496 Planarity : 0.004 0.042 2772 Dihedral : 8.459 85.318 2364 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.87 % Allowed : 12.82 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.19), residues: 1992 helix: 1.42 (0.16), residues: 996 sheet: -1.10 (0.28), residues: 284 loop : -0.39 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 353 TYR 0.006 0.001 TYR C 258 PHE 0.011 0.001 PHE D 250 TRP 0.006 0.001 TRP D 290 HIS 0.006 0.001 HIS A 343 Details of bonding type rmsd covalent geometry : bond 0.00245 (16020) covalent geometry : angle 0.74762 (21700) SS BOND : bond 0.01118 ( 4) SS BOND : angle 4.47887 ( 8) hydrogen bonds : bond 0.04171 ( 868) hydrogen bonds : angle 5.03522 ( 2520) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4627.82 seconds wall clock time: 80 minutes 6.74 seconds (4806.74 seconds total)