Starting phenix.real_space_refine on Sat Aug 23 15:04:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip4_35631/08_2025/8ip4_35631.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip4_35631/08_2025/8ip4_35631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ip4_35631/08_2025/8ip4_35631.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip4_35631/08_2025/8ip4_35631.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip4_35631/08_2025/8ip4_35631.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip4_35631/08_2025/8ip4_35631.cif" } resolution = 2.7 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 2 5.21 5 S 65 5.16 5 Cl 1 4.86 5 C 8315 2.51 5 N 2175 2.21 5 O 2375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12933 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "B" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "C" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "D" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "E" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.94, per 1000 atoms: 0.38 Number of scatterers: 12933 At special positions: 0 Unit cell: (110.67, 108.81, 140.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 65 16.00 Mg 2 11.99 O 2375 8.00 N 2175 7.00 C 8315 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: 0.85 Conformation dependent library (CDL) restraints added in 932.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 72.2% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.851A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 360 removed outlier: 3.788A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 401 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Proline residue: B 209 - end of helix Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.850A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 4.165A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 360 removed outlier: 3.789A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 401 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.530A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 removed outlier: 4.721A pdb=" N TRP C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.851A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 360 removed outlier: 3.789A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 401 Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP D 162 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 209 - end of helix Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.850A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 360 removed outlier: 3.788A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 401 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP E 162 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.532A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.850A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 360 removed outlier: 3.789A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 401 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.082A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 4.083A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 4.083A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 4.082A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 4.083A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2965 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: 1.86 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4230 1.34 - 1.46: 2363 1.46 - 1.58: 6447 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13160 Sorted by residual: bond pdb=" C LEU B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.331 1.346 -0.015 1.21e-02 6.83e+03 1.49e+00 bond pdb=" C LEU D 182 " pdb=" N PRO D 183 " ideal model delta sigma weight residual 1.331 1.346 -0.014 1.21e-02 6.83e+03 1.38e+00 bond pdb=" C LEU E 182 " pdb=" N PRO E 183 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.21e-02 6.83e+03 1.29e+00 bond pdb=" C LEU A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 1.331 1.345 -0.013 1.21e-02 6.83e+03 1.23e+00 bond pdb=" C LEU C 182 " pdb=" N PRO C 183 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.21e-02 6.83e+03 1.16e+00 ... (remaining 13155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 17314 1.04 - 2.08: 342 2.08 - 3.12: 83 3.12 - 4.16: 26 4.16 - 5.20: 25 Bond angle restraints: 17790 Sorted by residual: angle pdb=" C LEU D 351 " pdb=" N PHE D 352 " pdb=" CA PHE D 352 " ideal model delta sigma weight residual 121.66 118.21 3.45 1.76e+00 3.23e-01 3.85e+00 angle pdb=" C LEU E 351 " pdb=" N PHE E 352 " pdb=" CA PHE E 352 " ideal model delta sigma weight residual 121.66 118.22 3.44 1.76e+00 3.23e-01 3.83e+00 angle pdb=" C LEU C 351 " pdb=" N PHE C 352 " pdb=" CA PHE C 352 " ideal model delta sigma weight residual 121.66 118.22 3.44 1.76e+00 3.23e-01 3.82e+00 angle pdb=" C LEU B 351 " pdb=" N PHE B 352 " pdb=" CA PHE B 352 " ideal model delta sigma weight residual 121.66 118.24 3.42 1.76e+00 3.23e-01 3.77e+00 angle pdb=" C LEU A 351 " pdb=" N PHE A 352 " pdb=" CA PHE A 352 " ideal model delta sigma weight residual 121.66 118.25 3.41 1.76e+00 3.23e-01 3.76e+00 ... (remaining 17785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.30: 6947 13.30 - 26.60: 688 26.60 - 39.90: 310 39.90 - 53.20: 45 53.20 - 66.50: 10 Dihedral angle restraints: 8000 sinusoidal: 3300 harmonic: 4700 Sorted by residual: dihedral pdb=" CG LYS D 104 " pdb=" CD LYS D 104 " pdb=" CE LYS D 104 " pdb=" NZ LYS D 104 " ideal model delta sinusoidal sigma weight residual 60.00 117.72 -57.72 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG LYS C 104 " pdb=" CD LYS C 104 " pdb=" CE LYS C 104 " pdb=" NZ LYS C 104 " ideal model delta sinusoidal sigma weight residual 60.00 117.69 -57.69 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG LYS E 104 " pdb=" CD LYS E 104 " pdb=" CE LYS E 104 " pdb=" NZ LYS E 104 " ideal model delta sinusoidal sigma weight residual 60.00 117.68 -57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 7997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1521 0.030 - 0.060: 329 0.060 - 0.091: 134 0.091 - 0.121: 62 0.121 - 0.151: 14 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA LEU E 167 " pdb=" N LEU E 167 " pdb=" C LEU E 167 " pdb=" CB LEU E 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA LEU C 167 " pdb=" N LEU C 167 " pdb=" C LEU C 167 " pdb=" CB LEU C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA LEU D 167 " pdb=" N LEU D 167 " pdb=" C LEU D 167 " pdb=" CB LEU D 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 2057 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 145 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO D 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO C 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 145 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 146 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4028 2.84 - 3.35: 12930 3.35 - 3.87: 21750 3.87 - 4.38: 25115 4.38 - 4.90: 43911 Nonbonded interactions: 107734 Sorted by model distance: nonbonded pdb=" OG1 THR D 179 " pdb=" OE1 GLU D 190 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR C 179 " pdb=" OE1 GLU C 190 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR B 179 " pdb=" OE1 GLU B 190 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR A 179 " pdb=" OE1 GLU A 190 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR E 179 " pdb=" OE1 GLU E 190 " model vdw 2.320 3.040 ... (remaining 107729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'B' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'C' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'D' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'E' and (resid 82 through 128 or resid 130 through 401)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.970 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.002 0.022 13160 Z= 0.110 Angle : 0.442 5.196 17790 Z= 0.237 Chirality : 0.036 0.151 2060 Planarity : 0.004 0.050 2250 Dihedral : 12.813 66.498 4940 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.99 (0.21), residues: 1595 helix: 3.48 (0.15), residues: 1085 sheet: 1.45 (0.39), residues: 145 loop : 0.39 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.008 0.001 TYR C 299 PHE 0.014 0.001 PHE D 352 TRP 0.011 0.001 TRP C 162 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00203 (13160) covalent geometry : angle 0.44157 (17790) hydrogen bonds : bond 0.08125 ( 1010) hydrogen bonds : angle 4.08005 ( 2965) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.8540 (mt0) cc_final: 0.8333 (pm20) REVERT: A 223 HIS cc_start: 0.8476 (m170) cc_final: 0.8144 (m-70) REVERT: A 383 MET cc_start: 0.7776 (mmp) cc_final: 0.7520 (mpp) REVERT: A 390 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7196 (mpt180) REVERT: A 391 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.7044 (ttt180) REVERT: B 121 GLN cc_start: 0.8605 (mt0) cc_final: 0.8352 (pm20) REVERT: B 158 ASN cc_start: 0.9048 (m-40) cc_final: 0.8617 (t0) REVERT: B 222 LYS cc_start: 0.8631 (pptt) cc_final: 0.8334 (pptt) REVERT: B 383 MET cc_start: 0.7732 (mmp) cc_final: 0.7448 (mmt) REVERT: B 390 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7004 (mpt180) REVERT: B 391 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6742 (ttt180) REVERT: C 390 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7049 (mpt180) REVERT: C 391 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6795 (tmt170) REVERT: D 121 GLN cc_start: 0.8661 (mt0) cc_final: 0.8443 (pm20) REVERT: D 154 TYR cc_start: 0.8649 (p90) cc_final: 0.8384 (p90) REVERT: D 253 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7883 (mm-30) REVERT: D 261 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7601 (mp0) REVERT: D 292 MET cc_start: 0.8802 (tpp) cc_final: 0.8482 (tpp) REVERT: D 383 MET cc_start: 0.7792 (mmp) cc_final: 0.7556 (mpp) REVERT: D 390 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7232 (mpt180) REVERT: D 391 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6672 (ttt180) REVERT: E 292 MET cc_start: 0.8771 (tpp) cc_final: 0.8309 (tpp) REVERT: E 383 MET cc_start: 0.7991 (mmp) cc_final: 0.7748 (mpp) REVERT: E 390 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7197 (mpt180) REVERT: E 391 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6965 (ttt180) outliers start: 0 outliers final: 1 residues processed: 290 average time/residue: 0.6047 time to fit residues: 187.5932 Evaluate side-chains 172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN D 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.101425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075184 restraints weight = 46033.770| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.83 r_work: 0.2810 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13160 Z= 0.168 Angle : 0.534 9.708 17790 Z= 0.272 Chirality : 0.041 0.231 2060 Planarity : 0.005 0.050 2250 Dihedral : 3.647 13.655 1742 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.18 % Allowed : 8.49 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.21), residues: 1595 helix: 3.20 (0.15), residues: 1090 sheet: 1.47 (0.39), residues: 145 loop : 0.74 (0.38), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 301 TYR 0.024 0.002 TYR E 154 PHE 0.016 0.002 PHE A 352 TRP 0.007 0.001 TRP B 162 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00385 (13160) covalent geometry : angle 0.53385 (17790) hydrogen bonds : bond 0.04465 ( 1010) hydrogen bonds : angle 3.77615 ( 2965) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7161 (mpt180) REVERT: A 391 ARG cc_start: 0.7641 (ttm-80) cc_final: 0.7171 (ttt180) REVERT: B 222 LYS cc_start: 0.8566 (pptt) cc_final: 0.8270 (pptt) REVERT: B 383 MET cc_start: 0.7776 (mmp) cc_final: 0.7484 (mmt) REVERT: B 390 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7045 (mpt180) REVERT: B 391 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6778 (tmt170) REVERT: C 292 MET cc_start: 0.8843 (tpp) cc_final: 0.8374 (tpp) REVERT: C 344 MET cc_start: 0.8789 (mtt) cc_final: 0.8529 (mtt) REVERT: C 390 ARG cc_start: 0.7753 (mtt180) cc_final: 0.7041 (mpt180) REVERT: C 391 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6803 (tmt170) REVERT: D 253 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8221 (mm-30) REVERT: D 261 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7729 (mp0) REVERT: D 383 MET cc_start: 0.7755 (mmp) cc_final: 0.7476 (mpp) REVERT: D 390 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7227 (mpt180) REVERT: D 391 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.6725 (ttt180) REVERT: E 293 GLU cc_start: 0.8152 (tt0) cc_final: 0.7627 (tm-30) REVERT: E 383 MET cc_start: 0.7986 (mmp) cc_final: 0.7764 (mpp) REVERT: E 390 ARG cc_start: 0.7859 (mtt180) cc_final: 0.7249 (mpt180) REVERT: E 391 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7066 (ttt180) outliers start: 31 outliers final: 11 residues processed: 192 average time/residue: 0.4713 time to fit residues: 98.8928 Evaluate side-chains 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 148 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.068910 restraints weight = 63358.700| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 4.31 r_work: 0.2715 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13160 Z= 0.217 Angle : 0.552 9.354 17790 Z= 0.281 Chirality : 0.042 0.245 2060 Planarity : 0.005 0.051 2250 Dihedral : 3.823 14.577 1742 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.46 % Allowed : 9.68 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.21), residues: 1595 helix: 2.93 (0.15), residues: 1105 sheet: 1.53 (0.39), residues: 145 loop : 0.53 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 155 TYR 0.022 0.003 TYR B 154 PHE 0.017 0.002 PHE B 352 TRP 0.008 0.001 TRP C 375 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00503 (13160) covalent geometry : angle 0.55157 (17790) hydrogen bonds : bond 0.04720 ( 1010) hydrogen bonds : angle 3.96911 ( 2965) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 222 LYS cc_start: 0.8793 (ptpp) cc_final: 0.8491 (pmmt) REVERT: A 390 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7244 (mpt180) REVERT: A 391 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7144 (ttt180) REVERT: B 292 MET cc_start: 0.8932 (tpp) cc_final: 0.8334 (tpp) REVERT: B 390 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7039 (mpt180) REVERT: B 391 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.6801 (tmt170) REVERT: C 390 ARG cc_start: 0.7707 (mtt180) cc_final: 0.6968 (mpt180) REVERT: C 391 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.6841 (tmt170) REVERT: D 253 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8276 (mm-30) REVERT: D 261 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7741 (mp0) REVERT: D 390 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7208 (mpt180) REVERT: D 391 ARG cc_start: 0.7601 (ttm-80) cc_final: 0.6750 (ttt180) REVERT: E 383 MET cc_start: 0.7950 (mmp) cc_final: 0.7718 (mpp) REVERT: E 390 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7245 (mpt180) REVERT: E 391 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7064 (ttt180) outliers start: 35 outliers final: 16 residues processed: 182 average time/residue: 0.4864 time to fit residues: 97.3430 Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 146 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN E 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.096947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.071181 restraints weight = 48605.855| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.88 r_work: 0.2775 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13160 Z= 0.146 Angle : 0.511 9.703 17790 Z= 0.259 Chirality : 0.040 0.247 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.715 14.079 1740 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.96 % Allowed : 10.74 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.21), residues: 1595 helix: 2.98 (0.15), residues: 1105 sheet: 1.60 (0.40), residues: 145 loop : 0.54 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 301 TYR 0.034 0.002 TYR E 154 PHE 0.016 0.001 PHE B 352 TRP 0.008 0.001 TRP D 162 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00328 (13160) covalent geometry : angle 0.51117 (17790) hydrogen bonds : bond 0.04424 ( 1010) hydrogen bonds : angle 3.86222 ( 2965) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7233 (mpt180) REVERT: A 391 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.7103 (ttt180) REVERT: B 390 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7011 (mpt180) REVERT: B 391 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6827 (tmt170) REVERT: C 390 ARG cc_start: 0.7697 (mtt180) cc_final: 0.6965 (mpt180) REVERT: C 391 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.6875 (tmt170) REVERT: D 137 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8997 (mtp) REVERT: D 253 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8249 (mm-30) REVERT: D 261 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7711 (mp0) REVERT: D 292 MET cc_start: 0.9002 (tpp) cc_final: 0.8566 (tpp) REVERT: D 297 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: D 390 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7207 (mpt180) REVERT: D 391 ARG cc_start: 0.7595 (ttm-80) cc_final: 0.6746 (ttt180) REVERT: E 155 ARG cc_start: 0.8811 (mmt90) cc_final: 0.8606 (mmt90) REVERT: E 390 ARG cc_start: 0.7863 (mtt180) cc_final: 0.7227 (mpt180) REVERT: E 391 ARG cc_start: 0.7548 (ttm-80) cc_final: 0.7044 (ttt180) outliers start: 28 outliers final: 13 residues processed: 178 average time/residue: 0.4545 time to fit residues: 88.7685 Evaluate side-chains 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.094608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068386 restraints weight = 56668.726| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.09 r_work: 0.2707 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13160 Z= 0.250 Angle : 0.575 9.356 17790 Z= 0.290 Chirality : 0.043 0.253 2060 Planarity : 0.005 0.051 2250 Dihedral : 3.863 15.441 1740 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.04 % Allowed : 11.37 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.21), residues: 1595 helix: 2.81 (0.15), residues: 1105 sheet: 1.54 (0.39), residues: 145 loop : 0.55 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 155 TYR 0.031 0.003 TYR E 154 PHE 0.017 0.002 PHE B 352 TRP 0.010 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00580 (13160) covalent geometry : angle 0.57497 (17790) hydrogen bonds : bond 0.04842 ( 1010) hydrogen bonds : angle 4.06362 ( 2965) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.9155 (ptm) REVERT: A 390 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7305 (mpt180) REVERT: A 391 ARG cc_start: 0.7643 (ttm-80) cc_final: 0.7144 (ttt180) REVERT: B 292 MET cc_start: 0.8954 (tpp) cc_final: 0.8365 (tpp) REVERT: B 390 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7035 (mpt180) REVERT: B 391 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.6875 (tmt170) REVERT: C 390 ARG cc_start: 0.7701 (mtt180) cc_final: 0.6966 (mpt180) REVERT: C 391 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.6815 (tmt170) REVERT: D 253 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8307 (mm-30) REVERT: D 261 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7694 (mp0) REVERT: D 292 MET cc_start: 0.9058 (tpp) cc_final: 0.8646 (tpp) REVERT: D 390 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7221 (mpt180) REVERT: D 391 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.6784 (ttt180) REVERT: E 155 ARG cc_start: 0.8823 (mmt90) cc_final: 0.8500 (mmt90) REVERT: E 390 ARG cc_start: 0.7865 (mtt180) cc_final: 0.7254 (mpt180) REVERT: E 391 ARG cc_start: 0.7546 (ttm-80) cc_final: 0.7041 (ttt180) outliers start: 29 outliers final: 15 residues processed: 176 average time/residue: 0.4791 time to fit residues: 92.2114 Evaluate side-chains 165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 136 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.069835 restraints weight = 50106.521| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.91 r_work: 0.2791 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2796 r_free = 0.2796 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13160 Z= 0.173 Angle : 0.520 9.678 17790 Z= 0.265 Chirality : 0.041 0.253 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.777 14.900 1740 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.33 % Allowed : 12.28 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.41 (0.21), residues: 1595 helix: 2.85 (0.15), residues: 1105 sheet: 1.54 (0.39), residues: 145 loop : 0.58 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 155 TYR 0.033 0.003 TYR E 154 PHE 0.016 0.001 PHE B 352 TRP 0.009 0.001 TRP C 375 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00396 (13160) covalent geometry : angle 0.51953 (17790) hydrogen bonds : bond 0.04562 ( 1010) hydrogen bonds : angle 3.97485 ( 2965) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7249 (mpt180) REVERT: A 391 ARG cc_start: 0.7593 (ttm-80) cc_final: 0.7051 (ttt180) REVERT: B 253 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8209 (mm-30) REVERT: B 390 ARG cc_start: 0.7594 (mtt180) cc_final: 0.6945 (mpt180) REVERT: B 391 ARG cc_start: 0.7463 (ttm-80) cc_final: 0.6849 (tmt170) REVERT: C 390 ARG cc_start: 0.7621 (mtt180) cc_final: 0.6904 (mpt180) REVERT: C 391 ARG cc_start: 0.7471 (ttm-80) cc_final: 0.6747 (tmt170) REVERT: D 253 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8246 (mm-30) REVERT: D 261 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7657 (mp0) REVERT: D 292 MET cc_start: 0.8993 (tpp) cc_final: 0.8569 (tpp) REVERT: D 390 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7168 (mpt180) REVERT: D 391 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.6732 (ttt180) REVERT: E 155 ARG cc_start: 0.8799 (mmt90) cc_final: 0.8522 (mmt90) REVERT: E 390 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7202 (mpt180) REVERT: E 391 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.7007 (ttt180) outliers start: 19 outliers final: 12 residues processed: 171 average time/residue: 0.4438 time to fit residues: 83.2033 Evaluate side-chains 163 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 20 optimal weight: 0.0670 chunk 70 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.102578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.076916 restraints weight = 47878.779| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.88 r_work: 0.2817 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13160 Z= 0.116 Angle : 0.484 9.212 17790 Z= 0.246 Chirality : 0.039 0.260 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.599 13.636 1740 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.19 % Allowed : 12.63 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.21), residues: 1595 helix: 3.00 (0.15), residues: 1105 sheet: 1.64 (0.40), residues: 145 loop : 0.61 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 301 TYR 0.035 0.002 TYR B 154 PHE 0.017 0.001 PHE E 352 TRP 0.012 0.001 TRP E 389 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00246 (13160) covalent geometry : angle 0.48378 (17790) hydrogen bonds : bond 0.04229 ( 1010) hydrogen bonds : angle 3.79788 ( 2965) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7182 (mpt180) REVERT: A 391 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7060 (ttt180) REVERT: B 93 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8469 (mttm) REVERT: B 390 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6967 (mpt180) REVERT: B 391 ARG cc_start: 0.7468 (ttm-80) cc_final: 0.6867 (tmt170) REVERT: C 267 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8565 (mt-10) REVERT: C 390 ARG cc_start: 0.7625 (mtt180) cc_final: 0.6915 (mpt180) REVERT: C 391 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.6850 (tmt170) REVERT: D 253 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8191 (mm-30) REVERT: D 261 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7595 (mp0) REVERT: D 292 MET cc_start: 0.8947 (tpp) cc_final: 0.8549 (tpp) REVERT: D 390 ARG cc_start: 0.7754 (mtt180) cc_final: 0.7187 (mpt180) REVERT: D 391 ARG cc_start: 0.7611 (ttm-80) cc_final: 0.6786 (tmt170) REVERT: E 155 ARG cc_start: 0.8795 (mmt90) cc_final: 0.8556 (mmt90) REVERT: E 390 ARG cc_start: 0.7802 (mtt180) cc_final: 0.7108 (mpt180) REVERT: E 391 ARG cc_start: 0.7519 (ttm-80) cc_final: 0.7009 (ttt180) outliers start: 17 outliers final: 11 residues processed: 181 average time/residue: 0.4221 time to fit residues: 84.5618 Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.069503 restraints weight = 50894.131| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.94 r_work: 0.2757 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13160 Z= 0.202 Angle : 0.546 9.100 17790 Z= 0.275 Chirality : 0.042 0.254 2060 Planarity : 0.004 0.051 2250 Dihedral : 3.740 15.096 1740 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.12 % Allowed : 13.12 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.40 (0.21), residues: 1595 helix: 2.83 (0.15), residues: 1105 sheet: 1.56 (0.40), residues: 145 loop : 0.59 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 155 TYR 0.034 0.003 TYR B 154 PHE 0.025 0.002 PHE A 374 TRP 0.014 0.001 TRP A 389 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00468 (13160) covalent geometry : angle 0.54566 (17790) hydrogen bonds : bond 0.04656 ( 1010) hydrogen bonds : angle 3.94829 ( 2965) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7204 (mpt180) REVERT: A 391 ARG cc_start: 0.7648 (ttm-80) cc_final: 0.7092 (ttt180) REVERT: B 253 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8238 (mm-30) REVERT: B 390 ARG cc_start: 0.7633 (mtt180) cc_final: 0.6980 (mpt180) REVERT: B 391 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.6859 (tmt170) REVERT: C 390 ARG cc_start: 0.7668 (mtt180) cc_final: 0.6949 (mpt180) REVERT: C 391 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.6841 (tmt170) REVERT: D 253 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8277 (mm-30) REVERT: D 261 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7740 (mp0) REVERT: D 390 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7207 (mpt180) REVERT: D 391 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.6790 (ttt180) REVERT: E 390 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7235 (mpt180) REVERT: E 391 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7021 (ttt180) outliers start: 16 outliers final: 10 residues processed: 168 average time/residue: 0.4409 time to fit residues: 81.2686 Evaluate side-chains 159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 159 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.101247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075359 restraints weight = 43746.493| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.65 r_work: 0.2849 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13160 Z= 0.118 Angle : 0.489 9.288 17790 Z= 0.248 Chirality : 0.039 0.259 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.599 14.358 1740 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.84 % Allowed : 13.68 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.55 (0.22), residues: 1595 helix: 2.97 (0.15), residues: 1105 sheet: 1.56 (0.41), residues: 145 loop : 0.61 (0.41), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 155 TYR 0.033 0.002 TYR B 154 PHE 0.026 0.001 PHE A 374 TRP 0.015 0.001 TRP E 389 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00251 (13160) covalent geometry : angle 0.48890 (17790) hydrogen bonds : bond 0.04260 ( 1010) hydrogen bonds : angle 3.78405 ( 2965) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7809 (mtt180) cc_final: 0.7226 (mpt180) REVERT: A 391 ARG cc_start: 0.7623 (ttm-80) cc_final: 0.6826 (ttt180) REVERT: B 93 LYS cc_start: 0.8753 (mtmt) cc_final: 0.8436 (mttm) REVERT: B 253 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8150 (mm-30) REVERT: B 390 ARG cc_start: 0.7646 (mtt180) cc_final: 0.6972 (mpt180) REVERT: B 391 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.6835 (tmt170) REVERT: C 267 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8578 (mt-10) REVERT: C 390 ARG cc_start: 0.7633 (mtt180) cc_final: 0.6921 (mpt180) REVERT: C 391 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.6827 (tmt170) REVERT: D 253 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8249 (mm-30) REVERT: D 261 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7606 (mp0) REVERT: D 292 MET cc_start: 0.8945 (tpp) cc_final: 0.8559 (tpp) REVERT: D 390 ARG cc_start: 0.7768 (mtt180) cc_final: 0.7186 (mpt180) REVERT: D 391 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.6791 (tmt170) REVERT: E 390 ARG cc_start: 0.7834 (mtt180) cc_final: 0.7130 (mpt180) REVERT: E 391 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7045 (ttt180) outliers start: 12 outliers final: 10 residues processed: 173 average time/residue: 0.4747 time to fit residues: 89.8826 Evaluate side-chains 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 116 optimal weight: 0.0070 chunk 140 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.075609 restraints weight = 42434.833| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.59 r_work: 0.2855 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13160 Z= 0.119 Angle : 0.504 10.941 17790 Z= 0.254 Chirality : 0.040 0.263 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.598 14.858 1740 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.84 % Allowed : 13.96 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.21), residues: 1595 helix: 2.96 (0.15), residues: 1105 sheet: 1.56 (0.41), residues: 145 loop : 0.55 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 155 TYR 0.038 0.002 TYR E 154 PHE 0.016 0.001 PHE D 352 TRP 0.018 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00253 (13160) covalent geometry : angle 0.50366 (17790) hydrogen bonds : bond 0.04255 ( 1010) hydrogen bonds : angle 3.75783 ( 2965) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7215 (mpt180) REVERT: A 391 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7127 (ttt180) REVERT: B 253 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8140 (mm-30) REVERT: B 390 ARG cc_start: 0.7637 (mtt180) cc_final: 0.6963 (mpt180) REVERT: B 391 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.6831 (tmt170) REVERT: C 267 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8442 (mt-10) REVERT: C 390 ARG cc_start: 0.7631 (mtt180) cc_final: 0.6927 (mpt180) REVERT: C 391 ARG cc_start: 0.7529 (ttm-80) cc_final: 0.6817 (tmt170) REVERT: D 253 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8242 (mm-30) REVERT: D 261 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7643 (mp0) REVERT: D 292 MET cc_start: 0.8913 (tpp) cc_final: 0.8539 (tpp) REVERT: D 390 ARG cc_start: 0.7761 (mtt180) cc_final: 0.7179 (mpt180) REVERT: D 391 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.6782 (tmt170) REVERT: E 390 ARG cc_start: 0.7815 (mtt180) cc_final: 0.7124 (mpt180) REVERT: E 391 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7030 (ttt180) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.4643 time to fit residues: 85.8945 Evaluate side-chains 161 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.0470 chunk 116 optimal weight: 0.0060 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.075457 restraints weight = 46325.906| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.73 r_work: 0.2850 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13160 Z= 0.117 Angle : 0.493 9.324 17790 Z= 0.252 Chirality : 0.040 0.317 2060 Planarity : 0.004 0.054 2250 Dihedral : 3.561 14.582 1740 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.84 % Allowed : 14.18 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.53 (0.22), residues: 1595 helix: 2.96 (0.15), residues: 1105 sheet: 1.60 (0.41), residues: 145 loop : 0.54 (0.41), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 155 TYR 0.036 0.002 TYR E 154 PHE 0.027 0.001 PHE C 374 TRP 0.020 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00248 (13160) covalent geometry : angle 0.49348 (17790) hydrogen bonds : bond 0.04215 ( 1010) hydrogen bonds : angle 3.73567 ( 2965) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3974.09 seconds wall clock time: 68 minutes 18.16 seconds (4098.16 seconds total)