Starting phenix.real_space_refine on Tue Jul 29 16:25:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zye_11560/07_2025/6zye_11560.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zye_11560/07_2025/6zye_11560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zye_11560/07_2025/6zye_11560.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zye_11560/07_2025/6zye_11560.map" model { file = "/net/cci-nas-00/data/ceres_data/6zye_11560/07_2025/6zye_11560.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zye_11560/07_2025/6zye_11560.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 7392 2.51 5 N 1995 2.21 5 O 2156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11592 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1656 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.18, per 1000 atoms: 0.36 Number of scatterers: 11592 At special positions: 0 Unit cell: (97.842, 98.9055, 108.477, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 49 16.00 O 2156 8.00 N 1995 7.00 C 7392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2912 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 22 sheets defined 54.4% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'E' and resid -35 through -16 Processing helix chain 'E' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET E 158 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 176 Processing helix chain 'E' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE E 224 " --> pdb=" O PHE E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 232 Processing helix chain 'E' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA E 248 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 298 through 320 Processing helix chain 'C' and resid -34 through -16 Processing helix chain 'C' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 176 Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE C 224 " --> pdb=" O PHE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 232 Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA C 248 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 298 through 320 Processing helix chain 'A' and resid -34 through -16 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 160 " --> pdb=" O VAL A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 176 Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.661A pdb=" N ILE A 224 " --> pdb=" O PHE A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.525A pdb=" N ALA A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 298 through 320 Processing helix chain 'B' and resid -34 through -16 Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 176 Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE B 224 " --> pdb=" O PHE B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA B 248 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 264 Processing helix chain 'B' and resid 298 through 320 Processing helix chain 'D' and resid -34 through -16 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY D 157 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET D 158 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 160 " --> pdb=" O VAL D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 176 Processing helix chain 'D' and resid 219 through 224 removed outlier: 3.661A pdb=" N ILE D 224 " --> pdb=" O PHE D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 232 Processing helix chain 'D' and resid 244 through 249 removed outlier: 3.525A pdb=" N ALA D 248 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 264 Processing helix chain 'D' and resid 298 through 320 Processing helix chain 'F' and resid -34 through -16 Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY F 157 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET F 158 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY F 160 " --> pdb=" O VAL F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 176 Processing helix chain 'F' and resid 219 through 224 removed outlier: 3.663A pdb=" N ILE F 224 " --> pdb=" O PHE F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.524A pdb=" N ALA F 248 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 264 Processing helix chain 'F' and resid 298 through 320 Processing helix chain 'G' and resid -34 through -16 Processing helix chain 'G' and resid 150 through 160 removed outlier: 3.839A pdb=" N GLY G 157 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET G 158 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY G 160 " --> pdb=" O VAL G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 176 Processing helix chain 'G' and resid 219 through 224 removed outlier: 3.662A pdb=" N ILE G 224 " --> pdb=" O PHE G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 232 Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.525A pdb=" N ALA G 248 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA G 249 " --> pdb=" O GLU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 264 Processing helix chain 'G' and resid 298 through 320 Processing sheet with id=AA1, first strand: chain 'E' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS E 205 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 226 through 227 removed outlier: 6.613A pdb=" N LYS D 205 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 239 " --> pdb=" O VAL E 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG E 235 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR E 239 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER E 285 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 280 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET E 289 " --> pdb=" O PHE E 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE E 278 " --> pdb=" O MET E 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 328 through 332 removed outlier: 8.444A pdb=" N GLN D 329 " --> pdb=" O SER E 328 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR E 330 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU D 331 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TYR E 332 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLN G 329 " --> pdb=" O SER C 328 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N THR C 330 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU G 331 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR C 332 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 184 through 186 removed outlier: 6.612A pdb=" N LYS C 205 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 227 removed outlier: 6.613A pdb=" N LYS G 205 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 239 " --> pdb=" O VAL C 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG C 235 " --> pdb=" O THR C 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 239 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 285 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN C 280 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N MET C 289 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE C 278 " --> pdb=" O MET C 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS A 205 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 239 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG A 235 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 239 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 280 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET A 289 " --> pdb=" O PHE A 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 278 " --> pdb=" O MET A 289 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS B 205 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 239 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG B 235 " --> pdb=" O THR B 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 239 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 285 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN B 280 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET B 289 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 278 " --> pdb=" O MET B 289 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 239 " --> pdb=" O VAL D 290 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG D 235 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 239 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 280 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET D 289 " --> pdb=" O PHE D 278 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N PHE D 278 " --> pdb=" O MET D 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 184 through 186 removed outlier: 6.613A pdb=" N LYS F 205 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 239 " --> pdb=" O VAL F 290 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 235 through 243 removed outlier: 3.686A pdb=" N ARG F 235 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 239 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER F 285 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN F 280 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET F 289 " --> pdb=" O PHE F 278 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE F 278 " --> pdb=" O MET F 289 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR G 239 " --> pdb=" O VAL G 290 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 235 through 243 removed outlier: 3.685A pdb=" N ARG G 235 " --> pdb=" O THR G 294 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR G 239 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER G 285 " --> pdb=" O ALA G 282 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN G 280 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N MET G 289 " --> pdb=" O PHE G 278 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE G 278 " --> pdb=" O MET G 289 " (cutoff:3.500A) 695 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.63 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3843 1.34 - 1.46: 3054 1.46 - 1.58: 4835 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11823 Sorted by residual: bond pdb=" CG LEU D 214 " pdb=" CD2 LEU D 214 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.61e+00 bond pdb=" CG LEU F 214 " pdb=" CD2 LEU F 214 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.54e+00 bond pdb=" CG LEU C 214 " pdb=" CD2 LEU C 214 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" CG LEU B 214 " pdb=" CD2 LEU B 214 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.50e+00 bond pdb=" CB VAL D 196 " pdb=" CG2 VAL D 196 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 ... (remaining 11818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 14709 1.68 - 3.37: 1171 3.37 - 5.05: 151 5.05 - 6.74: 48 6.74 - 8.42: 14 Bond angle restraints: 16093 Sorted by residual: angle pdb=" N LYS G 161 " pdb=" CA LYS G 161 " pdb=" C LYS G 161 " ideal model delta sigma weight residual 111.28 118.59 -7.31 1.09e+00 8.42e-01 4.50e+01 angle pdb=" N LYS C 161 " pdb=" CA LYS C 161 " pdb=" C LYS C 161 " ideal model delta sigma weight residual 111.28 118.56 -7.28 1.09e+00 8.42e-01 4.47e+01 angle pdb=" N LYS F 161 " pdb=" CA LYS F 161 " pdb=" C LYS F 161 " ideal model delta sigma weight residual 111.28 118.56 -7.28 1.09e+00 8.42e-01 4.46e+01 angle pdb=" N LYS E 161 " pdb=" CA LYS E 161 " pdb=" C LYS E 161 " ideal model delta sigma weight residual 111.28 118.55 -7.27 1.09e+00 8.42e-01 4.45e+01 angle pdb=" N LYS A 161 " pdb=" CA LYS A 161 " pdb=" C LYS A 161 " ideal model delta sigma weight residual 111.28 118.54 -7.26 1.09e+00 8.42e-01 4.44e+01 ... (remaining 16088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 6405 17.39 - 34.78: 476 34.78 - 52.16: 56 52.16 - 69.55: 14 69.55 - 86.94: 7 Dihedral angle restraints: 6958 sinusoidal: 2457 harmonic: 4501 Sorted by residual: dihedral pdb=" CA PHE D 326 " pdb=" C PHE D 326 " pdb=" N PRO D 327 " pdb=" CA PRO D 327 " ideal model delta harmonic sigma weight residual 180.00 160.48 19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE B 326 " pdb=" C PHE B 326 " pdb=" N PRO B 327 " pdb=" CA PRO B 327 " ideal model delta harmonic sigma weight residual 180.00 160.49 19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA PHE G 326 " pdb=" C PHE G 326 " pdb=" N PRO G 327 " pdb=" CA PRO G 327 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1071 0.049 - 0.097: 541 0.097 - 0.146: 181 0.146 - 0.194: 55 0.194 - 0.243: 7 Chirality restraints: 1855 Sorted by residual: chirality pdb=" CA LYS G 161 " pdb=" N LYS G 161 " pdb=" C LYS G 161 " pdb=" CB LYS G 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA LYS A 161 " pdb=" N LYS A 161 " pdb=" C LYS A 161 " pdb=" CB LYS A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS F 161 " pdb=" N LYS F 161 " pdb=" C LYS F 161 " pdb=" CB LYS F 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1852 not shown) Planarity restraints: 2079 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 160 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C GLY A 160 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY A 160 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 161 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 160 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.74e+00 pdb=" C GLY B 160 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY B 160 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 161 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 160 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C GLY D 160 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY D 160 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS D 161 " -0.015 2.00e-02 2.50e+03 ... (remaining 2076 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2766 2.77 - 3.30: 12298 3.30 - 3.84: 18947 3.84 - 4.37: 22630 4.37 - 4.90: 38197 Nonbonded interactions: 94838 Sorted by model distance: nonbonded pdb=" OD2 ASP A 162 " pdb=" O SER B 222 " model vdw 2.241 3.040 nonbonded pdb=" O ILE B 268 " pdb=" NZ LYS B 295 " model vdw 2.290 3.120 nonbonded pdb=" O ILE C 268 " pdb=" NZ LYS C 295 " model vdw 2.290 3.120 nonbonded pdb=" O ARG C 202 " pdb=" ND2 ASN C 218 " model vdw 2.290 3.120 nonbonded pdb=" O ARG F 202 " pdb=" ND2 ASN F 218 " model vdw 2.290 3.120 ... (remaining 94833 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 26.430 Find NCS groups from input model: 0.250 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.016 0.082 11823 Z= 0.694 Angle : 1.047 8.425 16093 Z= 0.605 Chirality : 0.064 0.243 1855 Planarity : 0.006 0.040 2079 Dihedral : 13.053 86.940 4046 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.22), residues: 1288 helix: -1.24 (0.21), residues: 490 sheet: -4.36 (0.29), residues: 161 loop : -2.20 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 184 HIS 0.006 0.002 HIS D 265 PHE 0.022 0.003 PHE G 281 TYR 0.020 0.003 TYR C 277 ARG 0.007 0.001 ARG G 236 Details of bonding type rmsd hydrogen bonds : bond 0.18411 ( 639) hydrogen bonds : angle 8.26066 ( 1980) covalent geometry : bond 0.01571 (11823) covalent geometry : angle 1.04673 (16093) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.285 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: E 189 ASP cc_start: 0.7123 (m-30) cc_final: 0.6844 (m-30) REVERT: E 215 TYR cc_start: 0.8494 (m-80) cc_final: 0.8175 (m-80) REVERT: E 312 LYS cc_start: 0.8415 (mttt) cc_final: 0.7859 (mttm) REVERT: C 164 LEU cc_start: 0.7669 (mt) cc_final: 0.7399 (mm) REVERT: C 165 SER cc_start: 0.8766 (m) cc_final: 0.8432 (p) REVERT: C 215 TYR cc_start: 0.8449 (m-80) cc_final: 0.8157 (m-10) REVERT: C 312 LYS cc_start: 0.8310 (mttt) cc_final: 0.7793 (mttp) REVERT: A 312 LYS cc_start: 0.8316 (mttt) cc_final: 0.7635 (mttm) REVERT: B 158 MET cc_start: 0.5287 (mtm) cc_final: 0.4790 (ttm) REVERT: B 185 ILE cc_start: 0.8606 (mt) cc_final: 0.8023 (mt) REVERT: B 312 LYS cc_start: 0.8431 (mttt) cc_final: 0.8009 (mttp) REVERT: D 179 PHE cc_start: 0.8182 (p90) cc_final: 0.7701 (p90) REVERT: D 312 LYS cc_start: 0.8357 (mttt) cc_final: 0.7712 (mttm) REVERT: F 260 GLU cc_start: 0.6706 (tp30) cc_final: 0.6463 (tp30) REVERT: F 291 TYR cc_start: 0.8027 (t80) cc_final: 0.7798 (t80) REVERT: F 312 LYS cc_start: 0.8257 (mttt) cc_final: 0.7637 (mttm) REVERT: G 312 LYS cc_start: 0.8322 (mttt) cc_final: 0.7589 (mttm) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 0.3244 time to fit residues: 156.4641 Evaluate side-chains 206 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 40.0000 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 40.0000 chunk 139 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 228 ASN E 264 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 320 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN D 320 HIS G 264 ASN G 280 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.099178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078615 restraints weight = 33614.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080287 restraints weight = 21019.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081386 restraints weight = 15320.128| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11823 Z= 0.198 Angle : 0.675 6.858 16093 Z= 0.352 Chirality : 0.048 0.154 1855 Planarity : 0.004 0.035 2079 Dihedral : 5.315 18.466 1666 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1288 helix: 1.21 (0.23), residues: 504 sheet: -3.15 (0.33), residues: 189 loop : -1.82 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 201 HIS 0.001 0.001 HIS A 265 PHE 0.017 0.002 PHE A 168 TYR 0.017 0.002 TYR B 291 ARG 0.007 0.001 ARG C 212 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 639) hydrogen bonds : angle 5.19062 ( 1980) covalent geometry : bond 0.00426 (11823) covalent geometry : angle 0.67548 (16093) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.342 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: E 205 LYS cc_start: 0.8963 (tmmt) cc_final: 0.8744 (ttpt) REVERT: E 215 TYR cc_start: 0.8444 (m-80) cc_final: 0.8045 (m-80) REVERT: E 228 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8480 (m110) REVERT: E 272 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7769 (mm-40) REVERT: E 312 LYS cc_start: 0.9030 (mttt) cc_final: 0.8664 (mttm) REVERT: C 189 ASP cc_start: 0.7282 (m-30) cc_final: 0.6857 (m-30) REVERT: C 215 TYR cc_start: 0.8361 (m-80) cc_final: 0.8093 (m-80) REVERT: C 312 LYS cc_start: 0.8849 (mttt) cc_final: 0.8454 (mttp) REVERT: B 215 TYR cc_start: 0.8620 (m-80) cc_final: 0.8195 (m-10) REVERT: B 312 LYS cc_start: 0.8958 (mttt) cc_final: 0.8681 (mttm) REVERT: D 179 PHE cc_start: 0.8587 (p90) cc_final: 0.8204 (p90) REVERT: D 312 LYS cc_start: 0.8910 (mttt) cc_final: 0.8643 (mttm) REVERT: F 172 MET cc_start: 0.7134 (tpt) cc_final: 0.6743 (tpt) REVERT: F 179 PHE cc_start: 0.8746 (p90) cc_final: 0.8019 (p90) REVERT: F 201 TRP cc_start: 0.5759 (m100) cc_final: 0.5484 (m-10) REVERT: F 308 ASP cc_start: 0.8357 (p0) cc_final: 0.8141 (p0) REVERT: F 312 LYS cc_start: 0.8960 (mttt) cc_final: 0.8393 (mttm) REVERT: G 201 TRP cc_start: 0.6128 (m100) cc_final: 0.5748 (m-10) REVERT: G 279 ASN cc_start: 0.8706 (p0) cc_final: 0.8474 (p0) REVERT: G 312 LYS cc_start: 0.9017 (mttt) cc_final: 0.8571 (mttm) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.3158 time to fit residues: 134.1915 Evaluate side-chains 203 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 202 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 4 optimal weight: 9.9990 chunk 146 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 133 optimal weight: 40.0000 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 228 ASN E 320 HIS C 280 GLN C 320 HIS A 318 GLN B 280 GLN D 228 ASN D 280 GLN F 264 ASN F 280 GLN F 320 HIS G 228 ASN G 280 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.074368 restraints weight = 33789.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075994 restraints weight = 20845.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076782 restraints weight = 15183.806| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11823 Z= 0.261 Angle : 0.733 8.513 16093 Z= 0.381 Chirality : 0.048 0.156 1855 Planarity : 0.005 0.053 2079 Dihedral : 5.503 19.385 1666 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.27 % Allowed : 3.59 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.23), residues: 1288 helix: 0.97 (0.23), residues: 497 sheet: -2.40 (0.29), residues: 259 loop : -1.68 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 201 HIS 0.002 0.001 HIS A 265 PHE 0.014 0.002 PHE A 281 TYR 0.016 0.002 TYR B 291 ARG 0.006 0.001 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 639) hydrogen bonds : angle 5.26215 ( 1980) covalent geometry : bond 0.00579 (11823) covalent geometry : angle 0.73309 (16093) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 264 time to evaluate : 1.309 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: E 167 PHE cc_start: 0.7577 (t80) cc_final: 0.7354 (t80) REVERT: E 198 GLU cc_start: 0.7587 (pp20) cc_final: 0.6798 (pp20) REVERT: E 201 TRP cc_start: 0.6121 (m100) cc_final: 0.5555 (m-10) REVERT: E 219 SER cc_start: 0.9099 (p) cc_final: 0.8772 (m) REVERT: E 312 LYS cc_start: 0.9023 (mttt) cc_final: 0.8633 (mttm) REVERT: C 215 TYR cc_start: 0.8599 (m-80) cc_final: 0.8177 (m-80) REVERT: C 260 GLU cc_start: 0.7608 (tp30) cc_final: 0.7217 (tp30) REVERT: C 261 MET cc_start: 0.8358 (tmm) cc_final: 0.8112 (tmm) REVERT: C 312 LYS cc_start: 0.8792 (mttt) cc_final: 0.8538 (mmtt) REVERT: B 312 LYS cc_start: 0.8995 (mttt) cc_final: 0.8711 (mmtt) REVERT: B 323 ASP cc_start: 0.7805 (t0) cc_final: 0.7459 (t0) REVERT: D 312 LYS cc_start: 0.9067 (mttt) cc_final: 0.8777 (mttm) REVERT: F 201 TRP cc_start: 0.6188 (m100) cc_final: 0.5896 (m-10) REVERT: F 228 ASN cc_start: 0.8560 (m-40) cc_final: 0.8238 (m-40) REVERT: F 261 MET cc_start: 0.8470 (tmm) cc_final: 0.8257 (tmm) REVERT: F 312 LYS cc_start: 0.9019 (mttt) cc_final: 0.8688 (mmtt) REVERT: G 168 PHE cc_start: 0.8239 (m-80) cc_final: 0.7807 (m-10) REVERT: G 260 GLU cc_start: 0.7352 (tp30) cc_final: 0.6983 (tp30) REVERT: G 306 GLN cc_start: 0.8549 (tt0) cc_final: 0.8144 (tt0) REVERT: G 312 LYS cc_start: 0.9006 (mttt) cc_final: 0.8588 (mttm) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.2728 time to fit residues: 98.8465 Evaluate side-chains 204 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 30.0000 chunk 114 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 40.0000 chunk 147 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 318 GLN D 228 ASN D 280 GLN F 280 GLN G 280 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.075993 restraints weight = 33037.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.077596 restraints weight = 20230.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.078625 restraints weight = 14523.483| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11823 Z= 0.169 Angle : 0.628 7.221 16093 Z= 0.324 Chirality : 0.045 0.146 1855 Planarity : 0.004 0.031 2079 Dihedral : 5.078 19.653 1666 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.23), residues: 1288 helix: 1.68 (0.24), residues: 469 sheet: -1.81 (0.27), residues: 343 loop : -1.29 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 302 HIS 0.002 0.001 HIS D 320 PHE 0.014 0.002 PHE D 167 TYR 0.016 0.002 TYR D 245 ARG 0.005 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 639) hydrogen bonds : angle 4.86052 ( 1980) covalent geometry : bond 0.00377 (11823) covalent geometry : angle 0.62815 (16093) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.6151 (mpp) cc_final: 0.5253 (ttm) REVERT: E 179 PHE cc_start: 0.8542 (p90) cc_final: 0.7968 (p90) REVERT: E 198 GLU cc_start: 0.7598 (pp20) cc_final: 0.6770 (pp20) REVERT: E 215 TYR cc_start: 0.8521 (m-80) cc_final: 0.7995 (m-80) REVERT: E 219 SER cc_start: 0.9085 (p) cc_final: 0.8708 (m) REVERT: E 312 LYS cc_start: 0.9051 (mttt) cc_final: 0.8683 (mttm) REVERT: A 198 GLU cc_start: 0.7555 (pp20) cc_final: 0.7306 (tm-30) REVERT: A 261 MET cc_start: 0.8630 (tmm) cc_final: 0.8352 (tmm) REVERT: B 312 LYS cc_start: 0.9055 (mttt) cc_final: 0.8830 (mmtt) REVERT: D 212 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7702 (mtt180) REVERT: D 261 MET cc_start: 0.8503 (tmm) cc_final: 0.8247 (tmm) REVERT: D 312 LYS cc_start: 0.9030 (mttt) cc_final: 0.8808 (mttm) REVERT: F 261 MET cc_start: 0.8513 (tmm) cc_final: 0.8248 (tmm) REVERT: F 264 ASN cc_start: 0.8281 (m110) cc_final: 0.8074 (m-40) REVERT: F 312 LYS cc_start: 0.9056 (mttt) cc_final: 0.8633 (mmtt) REVERT: G 306 GLN cc_start: 0.8576 (tt0) cc_final: 0.8153 (tt0) REVERT: G 312 LYS cc_start: 0.9074 (mttt) cc_final: 0.8712 (mttm) outliers start: 1 outliers final: 1 residues processed: 254 average time/residue: 0.3144 time to fit residues: 113.7071 Evaluate side-chains 211 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 134 optimal weight: 40.0000 chunk 26 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 228 ASN D 280 GLN G 280 GLN G 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076819 restraints weight = 32895.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078445 restraints weight = 19950.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.079473 restraints weight = 14304.819| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11823 Z= 0.154 Angle : 0.610 8.089 16093 Z= 0.313 Chirality : 0.044 0.142 1855 Planarity : 0.003 0.027 2079 Dihedral : 4.992 20.061 1666 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.23), residues: 1288 helix: 2.02 (0.24), residues: 462 sheet: -1.62 (0.27), residues: 343 loop : -1.10 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 201 HIS 0.001 0.001 HIS C 320 PHE 0.014 0.001 PHE F 326 TYR 0.031 0.002 TYR A 245 ARG 0.005 0.001 ARG E 236 Details of bonding type rmsd hydrogen bonds : bond 0.03427 ( 639) hydrogen bonds : angle 4.66873 ( 1980) covalent geometry : bond 0.00347 (11823) covalent geometry : angle 0.60962 (16093) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 198 GLU cc_start: 0.7739 (pp20) cc_final: 0.7028 (pp20) REVERT: E 219 SER cc_start: 0.9002 (p) cc_final: 0.8642 (m) REVERT: E 240 THR cc_start: 0.8537 (p) cc_final: 0.8250 (p) REVERT: E 312 LYS cc_start: 0.9003 (mttt) cc_final: 0.8633 (mttm) REVERT: C 261 MET cc_start: 0.8531 (tmm) cc_final: 0.8307 (tmm) REVERT: C 306 GLN cc_start: 0.8410 (tt0) cc_final: 0.8209 (tt0) REVERT: A 198 GLU cc_start: 0.7657 (pp20) cc_final: 0.7250 (pp20) REVERT: A 261 MET cc_start: 0.8496 (tmm) cc_final: 0.8200 (tmm) REVERT: B 158 MET cc_start: 0.5692 (mpp) cc_final: 0.4564 (ttp) REVERT: B 312 LYS cc_start: 0.9003 (mttt) cc_final: 0.8774 (mmtt) REVERT: D 158 MET cc_start: 0.5592 (mpp) cc_final: 0.5154 (ttp) REVERT: D 312 LYS cc_start: 0.8968 (mttt) cc_final: 0.8729 (mttm) REVERT: F 261 MET cc_start: 0.8421 (tmm) cc_final: 0.8193 (tmm) REVERT: F 312 LYS cc_start: 0.9079 (mttt) cc_final: 0.8617 (mmtt) REVERT: G 240 THR cc_start: 0.8679 (p) cc_final: 0.8437 (p) REVERT: G 306 GLN cc_start: 0.8513 (tt0) cc_final: 0.8112 (tt0) REVERT: G 312 LYS cc_start: 0.9091 (mttt) cc_final: 0.8664 (mmtt) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.2394 time to fit residues: 86.6817 Evaluate side-chains 212 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 70 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 71 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN F 280 GLN G 280 GLN ** G 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076751 restraints weight = 32953.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078391 restraints weight = 19775.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.079481 restraints weight = 14176.150| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11823 Z= 0.169 Angle : 0.617 6.505 16093 Z= 0.321 Chirality : 0.044 0.147 1855 Planarity : 0.003 0.027 2079 Dihedral : 4.926 19.373 1666 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1288 helix: 1.92 (0.24), residues: 469 sheet: -1.75 (0.31), residues: 273 loop : -1.14 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 299 HIS 0.002 0.001 HIS D 320 PHE 0.012 0.002 PHE G 209 TYR 0.025 0.002 TYR D 245 ARG 0.005 0.001 ARG E 177 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 639) hydrogen bonds : angle 4.67376 ( 1980) covalent geometry : bond 0.00383 (11823) covalent geometry : angle 0.61741 (16093) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.6609 (ptm) cc_final: 0.6322 (ptp) REVERT: E 219 SER cc_start: 0.8969 (p) cc_final: 0.8598 (m) REVERT: E 240 THR cc_start: 0.8515 (p) cc_final: 0.8220 (p) REVERT: E 312 LYS cc_start: 0.9046 (mttt) cc_final: 0.8702 (mttm) REVERT: C 158 MET cc_start: 0.5677 (mpp) cc_final: 0.4704 (ptp) REVERT: C 260 GLU cc_start: 0.8400 (pp20) cc_final: 0.8101 (pp20) REVERT: A 158 MET cc_start: 0.5591 (mtm) cc_final: 0.4881 (ttm) REVERT: A 198 GLU cc_start: 0.7720 (pp20) cc_final: 0.7198 (pp20) REVERT: A 211 ASN cc_start: 0.8832 (m-40) cc_final: 0.8592 (t0) REVERT: B 158 MET cc_start: 0.5523 (mpp) cc_final: 0.5107 (ptp) REVERT: B 219 SER cc_start: 0.9228 (p) cc_final: 0.8848 (m) REVERT: D 158 MET cc_start: 0.5803 (mpp) cc_final: 0.5156 (ttp) REVERT: D 312 LYS cc_start: 0.9066 (mttt) cc_final: 0.8729 (mtmt) REVERT: F 303 LEU cc_start: 0.9112 (mp) cc_final: 0.8774 (mp) REVERT: F 312 LYS cc_start: 0.9073 (mttt) cc_final: 0.8854 (mmtt) REVERT: G 312 LYS cc_start: 0.9151 (mttt) cc_final: 0.8734 (mmtt) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.2413 time to fit residues: 84.9168 Evaluate side-chains 213 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 287 ASN D 280 GLN D 307 GLN G 280 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076478 restraints weight = 33345.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.078105 restraints weight = 20002.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079004 restraints weight = 14303.731| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.6725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11823 Z= 0.164 Angle : 0.617 6.927 16093 Z= 0.319 Chirality : 0.044 0.157 1855 Planarity : 0.003 0.027 2079 Dihedral : 4.875 19.205 1666 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.09 % Allowed : 1.17 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1288 helix: 2.00 (0.24), residues: 469 sheet: -1.42 (0.27), residues: 343 loop : -1.12 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 299 HIS 0.003 0.001 HIS G 265 PHE 0.011 0.001 PHE F 209 TYR 0.026 0.002 TYR A 245 ARG 0.005 0.001 ARG E 212 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 639) hydrogen bonds : angle 4.61299 ( 1980) covalent geometry : bond 0.00374 (11823) covalent geometry : angle 0.61669 (16093) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 254 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.6308 (ptm) cc_final: 0.5571 (ttp) REVERT: E 219 SER cc_start: 0.9131 (p) cc_final: 0.8680 (m) REVERT: E 240 THR cc_start: 0.8510 (p) cc_final: 0.8283 (p) REVERT: E 312 LYS cc_start: 0.9052 (mttt) cc_final: 0.8681 (mttm) REVERT: C 158 MET cc_start: 0.5607 (mpp) cc_final: 0.5217 (ptp) REVERT: A 198 GLU cc_start: 0.7839 (pp20) cc_final: 0.7303 (pp20) REVERT: A 211 ASN cc_start: 0.8768 (m-40) cc_final: 0.8350 (t0) REVERT: B 219 SER cc_start: 0.9195 (p) cc_final: 0.8772 (m) REVERT: D 158 MET cc_start: 0.5911 (mpp) cc_final: 0.5143 (ttp) REVERT: D 219 SER cc_start: 0.8956 (p) cc_final: 0.8528 (m) REVERT: F 261 MET cc_start: 0.8455 (tmm) cc_final: 0.8231 (tmm) REVERT: F 291 TYR cc_start: 0.8131 (t80) cc_final: 0.7929 (t80) REVERT: F 312 LYS cc_start: 0.9099 (mttt) cc_final: 0.8583 (mptt) REVERT: G 312 LYS cc_start: 0.9162 (mttt) cc_final: 0.8797 (mptp) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 0.2349 time to fit residues: 84.0140 Evaluate side-chains 210 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.099753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079421 restraints weight = 32952.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.081135 restraints weight = 19469.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.082219 restraints weight = 13825.545| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11823 Z= 0.109 Angle : 0.565 6.953 16093 Z= 0.292 Chirality : 0.043 0.160 1855 Planarity : 0.003 0.025 2079 Dihedral : 4.573 18.395 1666 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1288 helix: 2.11 (0.24), residues: 469 sheet: -1.40 (0.31), residues: 273 loop : -1.06 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 302 HIS 0.002 0.000 HIS G 265 PHE 0.015 0.001 PHE E 168 TYR 0.017 0.001 TYR D 245 ARG 0.005 0.000 ARG E 236 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 639) hydrogen bonds : angle 4.40812 ( 1980) covalent geometry : bond 0.00241 (11823) covalent geometry : angle 0.56477 (16093) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.6222 (ptm) cc_final: 0.4813 (tmm) REVERT: E 219 SER cc_start: 0.8955 (p) cc_final: 0.8528 (m) REVERT: E 240 THR cc_start: 0.8526 (p) cc_final: 0.8231 (p) REVERT: E 312 LYS cc_start: 0.9109 (mttt) cc_final: 0.8709 (mttm) REVERT: C 164 LEU cc_start: 0.7906 (mm) cc_final: 0.7176 (mm) REVERT: A 158 MET cc_start: 0.5778 (mtm) cc_final: 0.4962 (ttm) REVERT: A 198 GLU cc_start: 0.7767 (pp20) cc_final: 0.7372 (tm-30) REVERT: A 211 ASN cc_start: 0.8730 (m-40) cc_final: 0.8337 (t0) REVERT: B 219 SER cc_start: 0.9167 (p) cc_final: 0.8674 (m) REVERT: D 219 SER cc_start: 0.8954 (p) cc_final: 0.8502 (m) REVERT: D 256 GLU cc_start: 0.7932 (pp20) cc_final: 0.7727 (tm-30) REVERT: D 312 LYS cc_start: 0.9020 (mttp) cc_final: 0.8707 (mtmt) REVERT: F 158 MET cc_start: 0.5103 (mpp) cc_final: 0.4866 (ptp) REVERT: F 261 MET cc_start: 0.8487 (tmm) cc_final: 0.8276 (tmm) REVERT: F 312 LYS cc_start: 0.9137 (mttt) cc_final: 0.8600 (mptt) REVERT: G 198 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7188 (tm-30) REVERT: G 312 LYS cc_start: 0.9205 (mttt) cc_final: 0.8908 (mptp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2647 time to fit residues: 100.6734 Evaluate side-chains 214 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 0.0030 chunk 134 optimal weight: 50.0000 chunk 92 optimal weight: 7.9990 chunk 133 optimal weight: 40.0000 chunk 102 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 89 optimal weight: 40.0000 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 280 GLN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.075167 restraints weight = 33887.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076852 restraints weight = 20124.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077913 restraints weight = 14421.289| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11823 Z= 0.216 Angle : 0.663 8.309 16093 Z= 0.348 Chirality : 0.046 0.174 1855 Planarity : 0.004 0.036 2079 Dihedral : 4.975 18.983 1666 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.09 % Allowed : 0.72 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1288 helix: 2.32 (0.24), residues: 455 sheet: -1.22 (0.27), residues: 343 loop : -1.24 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 299 HIS 0.003 0.001 HIS B 265 PHE 0.014 0.002 PHE A 281 TYR 0.022 0.002 TYR D 245 ARG 0.005 0.001 ARG C 235 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 639) hydrogen bonds : angle 4.79510 ( 1980) covalent geometry : bond 0.00494 (11823) covalent geometry : angle 0.66272 (16093) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.6227 (ptm) cc_final: 0.5393 (ttp) REVERT: E 168 PHE cc_start: 0.8533 (m-80) cc_final: 0.8150 (m-10) REVERT: E 205 LYS cc_start: 0.8790 (ttmt) cc_final: 0.8582 (tttp) REVERT: E 219 SER cc_start: 0.9170 (p) cc_final: 0.8723 (m) REVERT: E 312 LYS cc_start: 0.9128 (mttt) cc_final: 0.8784 (mttm) REVERT: C 168 PHE cc_start: 0.8577 (m-80) cc_final: 0.8252 (m-10) REVERT: A 158 MET cc_start: 0.5813 (mtm) cc_final: 0.5005 (ttm) REVERT: A 168 PHE cc_start: 0.8373 (m-80) cc_final: 0.8101 (m-10) REVERT: A 198 GLU cc_start: 0.7886 (pp20) cc_final: 0.7337 (pp20) REVERT: A 211 ASN cc_start: 0.8851 (m-40) cc_final: 0.8323 (t0) REVERT: B 158 MET cc_start: 0.4366 (ptp) cc_final: 0.3700 (ptp) REVERT: B 219 SER cc_start: 0.9204 (p) cc_final: 0.8754 (m) REVERT: D 168 PHE cc_start: 0.8319 (m-80) cc_final: 0.8065 (m-10) REVERT: D 219 SER cc_start: 0.8928 (p) cc_final: 0.8510 (m) REVERT: F 158 MET cc_start: 0.5287 (mpp) cc_final: 0.4728 (ptp) REVERT: F 312 LYS cc_start: 0.9115 (mttt) cc_final: 0.8674 (mptt) REVERT: G 168 PHE cc_start: 0.8360 (m-80) cc_final: 0.7965 (m-10) REVERT: G 312 LYS cc_start: 0.9150 (mttt) cc_final: 0.8906 (mptp) outliers start: 1 outliers final: 0 residues processed: 244 average time/residue: 0.2353 time to fit residues: 81.8760 Evaluate side-chains 205 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 69 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 4 optimal weight: 30.0000 chunk 111 optimal weight: 40.0000 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN D 280 GLN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.076799 restraints weight = 33041.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078417 restraints weight = 19817.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079509 restraints weight = 14327.953| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11823 Z= 0.159 Angle : 0.629 8.011 16093 Z= 0.328 Chirality : 0.045 0.167 1855 Planarity : 0.003 0.027 2079 Dihedral : 4.830 19.426 1666 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.09 % Allowed : 0.18 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.23), residues: 1288 helix: 2.12 (0.24), residues: 469 sheet: -1.17 (0.32), residues: 273 loop : -1.33 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 302 HIS 0.003 0.001 HIS G 265 PHE 0.019 0.002 PHE B 168 TYR 0.017 0.002 TYR D 245 ARG 0.004 0.001 ARG E 236 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 639) hydrogen bonds : angle 4.61936 ( 1980) covalent geometry : bond 0.00368 (11823) covalent geometry : angle 0.62941 (16093) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 158 MET cc_start: 0.6081 (ptm) cc_final: 0.4660 (tmm) REVERT: E 168 PHE cc_start: 0.8536 (m-80) cc_final: 0.8307 (m-10) REVERT: E 219 SER cc_start: 0.9022 (p) cc_final: 0.8628 (m) REVERT: E 312 LYS cc_start: 0.9094 (mttt) cc_final: 0.8748 (mttm) REVERT: C 168 PHE cc_start: 0.8508 (m-80) cc_final: 0.8250 (m-10) REVERT: C 261 MET cc_start: 0.8652 (tmm) cc_final: 0.8394 (tmm) REVERT: A 158 MET cc_start: 0.5769 (mtm) cc_final: 0.5132 (ttm) REVERT: A 198 GLU cc_start: 0.7891 (pp20) cc_final: 0.7332 (pp20) REVERT: A 211 ASN cc_start: 0.8785 (m-40) cc_final: 0.8318 (t0) REVERT: B 158 MET cc_start: 0.4406 (ptp) cc_final: 0.3686 (ptp) REVERT: B 168 PHE cc_start: 0.8590 (m-80) cc_final: 0.8189 (m-10) REVERT: B 219 SER cc_start: 0.9179 (p) cc_final: 0.8717 (m) REVERT: D 168 PHE cc_start: 0.8207 (m-80) cc_final: 0.8002 (m-10) REVERT: D 219 SER cc_start: 0.8972 (p) cc_final: 0.8587 (m) REVERT: F 158 MET cc_start: 0.5270 (mpp) cc_final: 0.4896 (ptp) REVERT: F 168 PHE cc_start: 0.8459 (m-80) cc_final: 0.8234 (m-10) REVERT: F 261 MET cc_start: 0.8513 (tmm) cc_final: 0.8279 (tmm) REVERT: F 312 LYS cc_start: 0.9121 (mttt) cc_final: 0.8665 (mptt) REVERT: G 168 PHE cc_start: 0.8299 (m-80) cc_final: 0.7979 (m-10) REVERT: G 260 GLU cc_start: 0.8542 (pp20) cc_final: 0.7941 (tp30) REVERT: G 261 MET cc_start: 0.8675 (tmm) cc_final: 0.8474 (tmm) REVERT: G 312 LYS cc_start: 0.9153 (mttt) cc_final: 0.8883 (mptp) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.2326 time to fit residues: 80.6719 Evaluate side-chains 208 residues out of total 1113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 134 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 chunk 77 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 89 optimal weight: 40.0000 chunk 94 optimal weight: 3.9990 chunk 136 optimal weight: 0.0370 chunk 153 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 211 ASN B 211 ASN D 280 GLN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.077654 restraints weight = 32934.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.079289 restraints weight = 19698.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080317 restraints weight = 14205.066| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.7262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11823 Z= 0.134 Angle : 0.608 8.947 16093 Z= 0.316 Chirality : 0.044 0.157 1855 Planarity : 0.003 0.026 2079 Dihedral : 4.711 18.996 1666 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.18 % Allowed : 0.45 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.23), residues: 1288 helix: 2.20 (0.24), residues: 469 sheet: -1.16 (0.31), residues: 273 loop : -1.30 (0.23), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 201 HIS 0.002 0.001 HIS G 265 PHE 0.015 0.001 PHE B 168 TYR 0.015 0.002 TYR D 245 ARG 0.005 0.000 ARG E 236 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 639) hydrogen bonds : angle 4.51360 ( 1980) covalent geometry : bond 0.00307 (11823) covalent geometry : angle 0.60822 (16093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.09 seconds wall clock time: 62 minutes 38.70 seconds (3758.70 seconds total)