Starting phenix.real_space_refine on Sat Aug 23 14:50:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip5_35632/08_2025/8ip5_35632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip5_35632/08_2025/8ip5_35632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ip5_35632/08_2025/8ip5_35632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip5_35632/08_2025/8ip5_35632.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip5_35632/08_2025/8ip5_35632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip5_35632/08_2025/8ip5_35632.cif" } resolution = 2.5 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= 0.027 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 2370 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: 12928 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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: 2613 Chain: "B" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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: 2613 Chain: "C" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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: 2613 Chain: "D" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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: 2613 Chain: "E" Number of atoms: 2584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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, 2576 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 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: 2613 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: "C" 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: 5.27, per 1000 atoms: 0.41 Number of scatterers: 12928 At special positions: 0 Unit cell: (108.81, 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 2370 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: 1.03 Conformation dependent library (CDL) restraints added in 824.7 milliseconds Enol-peptide restraints added in 953.7 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, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.642A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 173 removed outlier: 4.238A pdb=" N LEU A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 219 removed outlier: 3.645A 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: 3.865A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.552A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.866A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.123A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 359 removed outlier: 3.850A pdb=" N PHE A 359 " --> pdb=" O MET A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 401 removed outlier: 4.548A pdb=" N TRP A 375 " --> pdb=" O HIS A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.642A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 removed outlier: 4.239A pdb=" N LEU B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 183 through 219 removed outlier: 3.646A 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: 3.865A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.551A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.866A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 4.122A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 359 removed outlier: 3.851A pdb=" N PHE B 359 " --> pdb=" O MET B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 401 removed outlier: 4.550A pdb=" N TRP B 375 " --> pdb=" O HIS B 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.642A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 173 removed outlier: 4.239A pdb=" N LEU C 167 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 183 through 219 removed outlier: 3.645A 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: 3.865A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.552A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.866A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 4.122A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 359 removed outlier: 3.851A pdb=" N PHE C 359 " --> pdb=" O MET C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 401 removed outlier: 4.549A pdb=" N TRP C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.642A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 removed outlier: 4.238A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 183 through 219 removed outlier: 3.646A 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: 3.865A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.552A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.866A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.122A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 359 removed outlier: 3.851A pdb=" N PHE D 359 " --> pdb=" O MET D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 401 removed outlier: 4.548A pdb=" N TRP D 375 " --> pdb=" O HIS D 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.642A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 173 removed outlier: 4.238A pdb=" N LEU E 167 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 219 removed outlier: 3.645A 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: 3.865A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.552A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.867A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.123A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 359 removed outlier: 3.851A pdb=" N PHE E 359 " --> pdb=" O MET E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 401 removed outlier: 4.549A pdb=" N TRP E 375 " --> pdb=" O HIS E 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.137A 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: 4.137A 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: 4.138A 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: 4.138A 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: 4.138A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2935 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: 1.46 Time building geometry restraints manager: 1.38 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: 4235 1.34 - 1.46: 2050 1.46 - 1.57: 6750 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13155 Sorted by residual: bond pdb=" N GLY C 353 " pdb=" CA GLY C 353 " ideal model delta sigma weight residual 1.453 1.444 0.009 1.24e-02 6.50e+03 5.37e-01 bond pdb=" CA VAL B 82 " pdb=" CB VAL B 82 " ideal model delta sigma weight residual 1.540 1.521 0.019 2.70e-02 1.37e+03 5.17e-01 bond pdb=" CB MET B 344 " pdb=" CG MET B 344 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.16e-01 bond pdb=" CB MET C 344 " pdb=" CG MET C 344 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 5.09e-01 bond pdb=" CB MET D 344 " pdb=" CG MET D 344 " ideal model delta sigma weight residual 1.520 1.499 0.021 3.00e-02 1.11e+03 5.09e-01 ... (remaining 13150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 17221 1.00 - 1.99: 446 1.99 - 2.99: 69 2.99 - 3.98: 34 3.98 - 4.98: 15 Bond angle restraints: 17785 Sorted by residual: angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 111.28 109.20 2.08 1.09e+00 8.42e-01 3.63e+00 angle pdb=" N LEU E 354 " pdb=" CA LEU E 354 " pdb=" C LEU E 354 " ideal model delta sigma weight residual 111.28 109.21 2.07 1.09e+00 8.42e-01 3.59e+00 angle pdb=" N LEU D 354 " pdb=" CA LEU D 354 " pdb=" C LEU D 354 " ideal model delta sigma weight residual 111.28 109.25 2.03 1.09e+00 8.42e-01 3.48e+00 angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.28 109.25 2.03 1.09e+00 8.42e-01 3.46e+00 angle pdb=" N LEU C 354 " pdb=" CA LEU C 354 " pdb=" C LEU C 354 " ideal model delta sigma weight residual 111.28 109.26 2.02 1.09e+00 8.42e-01 3.45e+00 ... (remaining 17780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 7325 17.43 - 34.86: 580 34.86 - 52.30: 70 52.30 - 69.73: 10 69.73 - 87.16: 10 Dihedral angle restraints: 7995 sinusoidal: 3295 harmonic: 4700 Sorted by residual: dihedral pdb=" CB GLU E 147 " pdb=" CG GLU E 147 " pdb=" CD GLU E 147 " pdb=" OE1 GLU E 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.16 -87.16 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU B 147 " pdb=" CG GLU B 147 " pdb=" CD GLU B 147 " pdb=" OE1 GLU B 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.14 -87.14 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " pdb=" CD GLU C 147 " pdb=" OE1 GLU C 147 " ideal model delta sinusoidal sigma weight residual 0.00 87.07 -87.07 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 7992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1289 0.025 - 0.050: 446 0.050 - 0.074: 218 0.074 - 0.099: 54 0.099 - 0.124: 53 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA LEU B 167 " pdb=" N LEU B 167 " pdb=" C LEU B 167 " pdb=" CB LEU B 167 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.84e-01 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 2.39 0.12 2.00e-01 2.50e+01 3.79e-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 2.39 0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 2057 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 182 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.12e+00 pdb=" N PRO A 183 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 183 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 183 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 182 " -0.017 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO C 183 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 183 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 183 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 182 " -0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO D 183 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 183 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 183 " -0.015 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2121 2.77 - 3.30: 12626 3.30 - 3.83: 22547 3.83 - 4.37: 25128 4.37 - 4.90: 45168 Nonbonded interactions: 107590 Sorted by model distance: nonbonded pdb=" OG1 THR B 179 " pdb=" OE1 GLU B 190 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR E 179 " pdb=" OE1 GLU E 190 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR A 179 " pdb=" OE1 GLU A 190 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR C 179 " pdb=" OE1 GLU C 190 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR D 179 " pdb=" OE1 GLU D 190 " model vdw 2.236 3.040 ... (remaining 107585 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 13155 Z= 0.112 Angle : 0.434 4.981 17785 Z= 0.241 Chirality : 0.036 0.124 2060 Planarity : 0.003 0.026 2250 Dihedral : 12.761 87.159 4935 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.88 (0.21), residues: 1595 helix: 3.36 (0.15), residues: 1070 sheet: 2.09 (0.37), residues: 145 loop : 0.28 (0.35), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.012 0.001 TYR A 299 PHE 0.014 0.001 PHE A 352 TRP 0.005 0.001 TRP C 196 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00211 (13155) covalent geometry : angle 0.43424 (17785) hydrogen bonds : bond 0.08422 ( 1005) hydrogen bonds : angle 4.33404 ( 2935) *********************** 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 274 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.488 Fit side-chains REVERT: A 138 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8052 (mm-30) REVERT: A 286 ILE cc_start: 0.8478 (mt) cc_final: 0.8115 (mp) REVERT: A 344 MET cc_start: 0.8824 (mtt) cc_final: 0.8570 (mtt) REVERT: A 390 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7371 (mpt180) REVERT: B 286 ILE cc_start: 0.8474 (mt) cc_final: 0.8115 (mp) REVERT: C 103 LYS cc_start: 0.8760 (mttm) cc_final: 0.8526 (mmmm) REVERT: C 138 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8010 (mm-30) REVERT: C 368 GLU cc_start: 0.7688 (mp0) cc_final: 0.7470 (mp0) REVERT: D 109 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 138 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8047 (mm-30) REVERT: D 286 ILE cc_start: 0.8508 (mt) cc_final: 0.8154 (mp) REVERT: E 138 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8026 (mm-30) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.6085 time to fit residues: 178.4407 Evaluate side-chains 182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 94 GLN C 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.075819 restraints weight = 47652.881| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.77 r_work: 0.2810 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13155 Z= 0.156 Angle : 0.536 9.413 17785 Z= 0.268 Chirality : 0.040 0.220 2060 Planarity : 0.004 0.040 2250 Dihedral : 3.785 14.185 1740 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.13 % Allowed : 8.66 % Favored : 90.21 % 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: 3.67 (0.21), residues: 1595 helix: 3.10 (0.15), residues: 1080 sheet: 2.05 (0.36), residues: 145 loop : 0.48 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 398 TYR 0.018 0.002 TYR D 299 PHE 0.019 0.002 PHE A 86 TRP 0.007 0.001 TRP C 162 HIS 0.001 0.000 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00355 (13155) covalent geometry : angle 0.53638 (17785) hydrogen bonds : bond 0.04794 ( 1005) hydrogen bonds : angle 3.83030 ( 2935) *********************** 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 197 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.337 Fit side-chains REVERT: A 138 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 286 ILE cc_start: 0.8559 (mt) cc_final: 0.8163 (mp) REVERT: A 297 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8159 (tt0) REVERT: A 344 MET cc_start: 0.9033 (mtt) cc_final: 0.8789 (mtt) REVERT: A 368 GLU cc_start: 0.7875 (mp0) cc_final: 0.7527 (mp0) REVERT: A 390 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7407 (mpt180) REVERT: A 398 ARG cc_start: 0.8023 (mtm110) cc_final: 0.7579 (mtm110) REVERT: B 286 ILE cc_start: 0.8496 (mt) cc_final: 0.8092 (mp) REVERT: C 138 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8496 (mm-30) REVERT: C 368 GLU cc_start: 0.7791 (mp0) cc_final: 0.7392 (mp0) REVERT: D 109 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8536 (tm-30) REVERT: D 138 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8586 (mm-30) REVERT: D 286 ILE cc_start: 0.8603 (mt) cc_final: 0.8171 (mp) REVERT: D 337 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8188 (ttt-90) REVERT: D 372 ARG cc_start: 0.8387 (mpp80) cc_final: 0.7086 (mtp180) REVERT: E 124 MET cc_start: 0.8851 (tpt) cc_final: 0.8593 (tpp) REVERT: E 138 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8532 (mm-30) outliers start: 16 outliers final: 2 residues processed: 185 average time/residue: 0.5423 time to fit residues: 108.2506 Evaluate side-chains 169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 337 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.103194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.076506 restraints weight = 33548.285| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.20 r_work: 0.2821 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2812 r_free = 0.2812 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13155 Z= 0.302 Angle : 0.605 9.264 17785 Z= 0.306 Chirality : 0.044 0.223 2060 Planarity : 0.004 0.027 2250 Dihedral : 4.154 15.391 1740 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.70 % Allowed : 9.23 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.50 (0.21), residues: 1595 helix: 3.05 (0.15), residues: 1020 sheet: 2.19 (0.37), residues: 145 loop : 0.54 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 136 TYR 0.027 0.003 TYR E 299 PHE 0.027 0.002 PHE A 86 TRP 0.010 0.001 TRP C 162 HIS 0.002 0.001 HIS C 331 Details of bonding type rmsd covalent geometry : bond 0.00713 (13155) covalent geometry : angle 0.60548 (17785) hydrogen bonds : bond 0.05589 ( 1005) hydrogen bonds : angle 4.10071 ( 2935) *********************** 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 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.344 Fit side-chains REVERT: A 286 ILE cc_start: 0.8610 (mt) cc_final: 0.8238 (mp) REVERT: A 344 MET cc_start: 0.9019 (mtt) cc_final: 0.8766 (mtt) REVERT: A 368 GLU cc_start: 0.8029 (mp0) cc_final: 0.7631 (mp0) REVERT: A 390 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7352 (mpt180) REVERT: B 286 ILE cc_start: 0.8517 (mt) cc_final: 0.8138 (mp) REVERT: C 368 GLU cc_start: 0.8000 (mp0) cc_final: 0.7545 (mp0) REVERT: D 109 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8565 (tm-30) REVERT: D 286 ILE cc_start: 0.8574 (mt) cc_final: 0.8174 (mp) REVERT: D 372 ARG cc_start: 0.8386 (mpp80) cc_final: 0.8078 (ptt90) REVERT: D 391 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6776 (ttp-170) REVERT: E 124 MET cc_start: 0.8949 (tpt) cc_final: 0.8631 (tpp) REVERT: E 190 GLU cc_start: 0.8774 (tt0) cc_final: 0.8406 (tt0) outliers start: 10 outliers final: 2 residues processed: 163 average time/residue: 0.6133 time to fit residues: 107.5243 Evaluate side-chains 151 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain D residue 391 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 139 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.106930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.079009 restraints weight = 65540.487| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 4.26 r_work: 0.2830 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13155 Z= 0.119 Angle : 0.470 6.887 17785 Z= 0.245 Chirality : 0.039 0.220 2060 Planarity : 0.003 0.029 2250 Dihedral : 3.901 15.144 1740 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.85 % Allowed : 9.93 % Favored : 89.23 % 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: 3.76 (0.21), residues: 1595 helix: 3.28 (0.15), residues: 1020 sheet: 2.18 (0.38), residues: 145 loop : 0.57 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 314 TYR 0.019 0.002 TYR B 299 PHE 0.015 0.001 PHE A 352 TRP 0.007 0.001 TRP A 162 HIS 0.001 0.000 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00248 (13155) covalent geometry : angle 0.47039 (17785) hydrogen bonds : bond 0.04700 ( 1005) hydrogen bonds : angle 3.81416 ( 2935) *********************** 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 180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.405 Fit side-chains REVERT: A 137 MET cc_start: 0.9330 (mpp) cc_final: 0.9058 (mtt) REVERT: A 138 GLU cc_start: 0.9015 (mm-30) cc_final: 0.8596 (mm-30) REVERT: A 286 ILE cc_start: 0.8674 (mt) cc_final: 0.8291 (mp) REVERT: A 344 MET cc_start: 0.9112 (mtt) cc_final: 0.8873 (mtt) REVERT: A 368 GLU cc_start: 0.7986 (mp0) cc_final: 0.7580 (mp0) REVERT: A 390 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7472 (mpt180) REVERT: B 286 ILE cc_start: 0.8592 (mt) cc_final: 0.8197 (mp) REVERT: C 103 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8636 (mttt) REVERT: C 138 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8578 (mm-30) REVERT: C 368 GLU cc_start: 0.7965 (mp0) cc_final: 0.7509 (mp0) REVERT: D 109 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8546 (tm-30) REVERT: D 286 ILE cc_start: 0.8630 (mt) cc_final: 0.8228 (mp) REVERT: D 337 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8237 (ttt-90) REVERT: D 372 ARG cc_start: 0.8334 (mpp80) cc_final: 0.8034 (ptt90) REVERT: D 391 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6840 (ttp-170) REVERT: E 137 MET cc_start: 0.9306 (mtm) cc_final: 0.8349 (mtm) REVERT: E 138 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8553 (mm-30) REVERT: E 297 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: E 368 GLU cc_start: 0.7889 (mp0) cc_final: 0.7522 (mp0) outliers start: 12 outliers final: 2 residues processed: 174 average time/residue: 0.6573 time to fit residues: 123.2909 Evaluate side-chains 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 47 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.104203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.076460 restraints weight = 50441.208| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.82 r_work: 0.2777 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13155 Z= 0.228 Angle : 0.563 9.591 17785 Z= 0.280 Chirality : 0.041 0.216 2060 Planarity : 0.004 0.029 2250 Dihedral : 4.069 15.142 1740 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.99 % Allowed : 10.70 % Favored : 88.31 % 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: 3.52 (0.21), residues: 1595 helix: 3.05 (0.15), residues: 1040 sheet: 2.24 (0.38), residues: 145 loop : 0.41 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 398 TYR 0.023 0.002 TYR D 299 PHE 0.021 0.002 PHE A 86 TRP 0.007 0.001 TRP C 162 HIS 0.002 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00533 (13155) covalent geometry : angle 0.56305 (17785) hydrogen bonds : bond 0.05237 ( 1005) hydrogen bonds : angle 3.97234 ( 2935) *********************** 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 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.533 Fit side-chains REVERT: A 137 MET cc_start: 0.9334 (mpp) cc_final: 0.9014 (mtt) REVERT: A 138 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8523 (mm-30) REVERT: A 286 ILE cc_start: 0.8643 (mt) cc_final: 0.8258 (mp) REVERT: A 344 MET cc_start: 0.9112 (mtt) cc_final: 0.8878 (mtt) REVERT: A 368 GLU cc_start: 0.8037 (mp0) cc_final: 0.7614 (mp0) REVERT: A 390 ARG cc_start: 0.8102 (mtt180) cc_final: 0.7438 (mpt180) REVERT: B 286 ILE cc_start: 0.8546 (mt) cc_final: 0.8165 (mp) REVERT: C 368 GLU cc_start: 0.8002 (mp0) cc_final: 0.7508 (mp0) REVERT: D 109 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8609 (tm-30) REVERT: D 286 ILE cc_start: 0.8625 (mt) cc_final: 0.8213 (mp) REVERT: D 372 ARG cc_start: 0.8343 (mpp80) cc_final: 0.8096 (ptt90) REVERT: D 391 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6884 (ttp-170) REVERT: E 124 MET cc_start: 0.8959 (tpt) cc_final: 0.8652 (tpp) REVERT: E 297 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8247 (tt0) outliers start: 14 outliers final: 1 residues processed: 162 average time/residue: 0.6810 time to fit residues: 118.7427 Evaluate side-chains 152 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 101 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.105307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.077548 restraints weight = 53975.617| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.93 r_work: 0.2778 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13155 Z= 0.156 Angle : 0.498 8.300 17785 Z= 0.255 Chirality : 0.039 0.227 2060 Planarity : 0.003 0.030 2250 Dihedral : 3.976 15.374 1740 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.70 % Allowed : 11.20 % Favored : 88.10 % 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: 2.92 (0.15), residues: 1070 sheet: 2.21 (0.38), residues: 145 loop : 0.27 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 398 TYR 0.019 0.002 TYR B 299 PHE 0.017 0.002 PHE A 86 TRP 0.007 0.001 TRP C 196 HIS 0.001 0.000 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00353 (13155) covalent geometry : angle 0.49774 (17785) hydrogen bonds : bond 0.04918 ( 1005) hydrogen bonds : angle 3.88279 ( 2935) *********************** 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 167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.314 Fit side-chains REVERT: A 137 MET cc_start: 0.9316 (mpp) cc_final: 0.9038 (mtt) REVERT: A 138 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8555 (mm-30) REVERT: A 286 ILE cc_start: 0.8643 (mt) cc_final: 0.8250 (mp) REVERT: A 344 MET cc_start: 0.9119 (mtt) cc_final: 0.8874 (mtt) REVERT: A 368 GLU cc_start: 0.7993 (mp0) cc_final: 0.7565 (mp0) REVERT: A 390 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7443 (mpt180) REVERT: B 286 ILE cc_start: 0.8556 (mt) cc_final: 0.8175 (mp) REVERT: C 138 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 368 GLU cc_start: 0.8025 (mp0) cc_final: 0.7531 (mp0) REVERT: D 109 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8580 (tm-30) REVERT: D 286 ILE cc_start: 0.8646 (mt) cc_final: 0.8228 (mp) REVERT: D 372 ARG cc_start: 0.8313 (mpp80) cc_final: 0.8035 (ptt90) REVERT: D 391 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6838 (ttp-170) REVERT: E 297 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8216 (tt0) outliers start: 10 outliers final: 0 residues processed: 160 average time/residue: 0.6371 time to fit residues: 109.8247 Evaluate side-chains 157 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 152 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.106300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078756 restraints weight = 52638.179| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.89 r_work: 0.2824 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2820 r_free = 0.2820 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13155 Z= 0.134 Angle : 0.489 9.538 17785 Z= 0.248 Chirality : 0.039 0.225 2060 Planarity : 0.003 0.031 2250 Dihedral : 3.908 15.267 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.49 % Allowed : 11.55 % Favored : 87.96 % 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: 3.51 (0.21), residues: 1595 helix: 3.00 (0.15), residues: 1070 sheet: 2.18 (0.38), residues: 145 loop : 0.34 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 398 TYR 0.018 0.002 TYR B 299 PHE 0.018 0.001 PHE A 352 TRP 0.007 0.001 TRP C 196 HIS 0.001 0.000 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00293 (13155) covalent geometry : angle 0.48890 (17785) hydrogen bonds : bond 0.04736 ( 1005) hydrogen bonds : angle 3.80570 ( 2935) *********************** 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 172 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.463 Fit side-chains REVERT: A 137 MET cc_start: 0.9338 (mpp) cc_final: 0.9003 (mtt) REVERT: A 138 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8587 (mm-30) REVERT: A 286 ILE cc_start: 0.8649 (mt) cc_final: 0.8259 (mp) REVERT: A 344 MET cc_start: 0.9143 (mtt) cc_final: 0.8903 (mtt) REVERT: A 368 GLU cc_start: 0.7992 (mp0) cc_final: 0.7576 (mp0) REVERT: A 390 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7484 (mpt180) REVERT: B 286 ILE cc_start: 0.8598 (mt) cc_final: 0.8218 (mp) REVERT: C 138 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8527 (mm-30) REVERT: C 368 GLU cc_start: 0.8013 (mp0) cc_final: 0.7505 (mp0) REVERT: D 109 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8549 (tm-30) REVERT: D 286 ILE cc_start: 0.8647 (mt) cc_final: 0.8231 (mp) REVERT: D 372 ARG cc_start: 0.8371 (mpp80) cc_final: 0.8071 (ptt90) REVERT: D 391 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6839 (ttp-170) REVERT: E 137 MET cc_start: 0.9301 (mtm) cc_final: 0.8334 (mtm) REVERT: E 138 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 297 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8114 (tt0) outliers start: 7 outliers final: 2 residues processed: 168 average time/residue: 0.5859 time to fit residues: 106.4136 Evaluate side-chains 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.079620 restraints weight = 51925.165| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.91 r_work: 0.2824 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13155 Z= 0.120 Angle : 0.478 9.254 17785 Z= 0.242 Chirality : 0.038 0.240 2060 Planarity : 0.003 0.032 2250 Dihedral : 3.840 14.647 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.42 % Allowed : 11.48 % Favored : 88.10 % 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: 3.59 (0.21), residues: 1595 helix: 3.06 (0.15), residues: 1070 sheet: 2.17 (0.38), residues: 145 loop : 0.38 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 398 TYR 0.017 0.002 TYR B 299 PHE 0.016 0.001 PHE A 352 TRP 0.007 0.001 TRP C 196 HIS 0.001 0.000 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00254 (13155) covalent geometry : angle 0.47770 (17785) hydrogen bonds : bond 0.04605 ( 1005) hydrogen bonds : angle 3.73969 ( 2935) *********************** 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 179 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.428 Fit side-chains REVERT: A 137 MET cc_start: 0.9329 (mpp) cc_final: 0.8966 (mtt) REVERT: A 138 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8621 (mm-30) REVERT: A 190 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: A 344 MET cc_start: 0.9128 (mtt) cc_final: 0.8901 (mtt) REVERT: A 368 GLU cc_start: 0.7972 (mp0) cc_final: 0.7588 (mp0) REVERT: A 390 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7452 (mpt180) REVERT: B 138 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8543 (mm-30) REVERT: B 286 ILE cc_start: 0.8581 (mt) cc_final: 0.8186 (mp) REVERT: C 138 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8514 (mm-30) REVERT: C 368 GLU cc_start: 0.7972 (mp0) cc_final: 0.7460 (mp0) REVERT: D 109 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8573 (tm-30) REVERT: D 286 ILE cc_start: 0.8647 (mt) cc_final: 0.8226 (mp) REVERT: D 372 ARG cc_start: 0.8301 (mpp80) cc_final: 0.8018 (ptt90) REVERT: D 391 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6798 (ttp-170) REVERT: E 137 MET cc_start: 0.9281 (mtm) cc_final: 0.8299 (mtm) REVERT: E 138 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8543 (mm-30) REVERT: E 297 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: E 368 GLU cc_start: 0.7913 (mp0) cc_final: 0.7602 (mp0) outliers start: 6 outliers final: 3 residues processed: 176 average time/residue: 0.5925 time to fit residues: 112.6411 Evaluate side-chains 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.105626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.077806 restraints weight = 57163.503| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.03 r_work: 0.2799 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13155 Z= 0.157 Angle : 0.518 10.102 17785 Z= 0.258 Chirality : 0.040 0.237 2060 Planarity : 0.003 0.032 2250 Dihedral : 3.915 14.785 1740 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.42 % Allowed : 11.97 % Favored : 87.61 % 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: 2.99 (0.15), residues: 1070 sheet: 2.22 (0.38), residues: 145 loop : 0.39 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 398 TYR 0.021 0.002 TYR B 299 PHE 0.017 0.002 PHE A 352 TRP 0.007 0.001 TRP B 196 HIS 0.001 0.000 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00355 (13155) covalent geometry : angle 0.51789 (17785) hydrogen bonds : bond 0.04845 ( 1005) hydrogen bonds : angle 3.81925 ( 2935) *********************** 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 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 162 time to evaluate : 0.331 Fit side-chains REVERT: A 137 MET cc_start: 0.9354 (mpp) cc_final: 0.9025 (mtt) REVERT: A 138 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8594 (mm-30) REVERT: A 190 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8369 (tp30) REVERT: A 344 MET cc_start: 0.9147 (mtt) cc_final: 0.8908 (mtt) REVERT: A 368 GLU cc_start: 0.7992 (mp0) cc_final: 0.7526 (mp0) REVERT: A 390 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7455 (mpt180) REVERT: B 286 ILE cc_start: 0.8580 (mt) cc_final: 0.8191 (mp) REVERT: C 138 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8544 (mm-30) REVERT: C 368 GLU cc_start: 0.8021 (mp0) cc_final: 0.7516 (mp0) REVERT: D 109 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8602 (tm-30) REVERT: D 286 ILE cc_start: 0.8637 (mt) cc_final: 0.8223 (mp) REVERT: D 372 ARG cc_start: 0.8352 (mpp80) cc_final: 0.8031 (ptt90) REVERT: D 391 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6864 (ttp-170) REVERT: E 137 MET cc_start: 0.9323 (mtm) cc_final: 0.8380 (mtm) REVERT: E 138 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8542 (mm-30) REVERT: E 297 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8147 (tt0) outliers start: 6 outliers final: 1 residues processed: 165 average time/residue: 0.6413 time to fit residues: 114.1916 Evaluate side-chains 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 160 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 116 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 152 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.106276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.078768 restraints weight = 50440.085| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.86 r_work: 0.2825 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13155 Z= 0.135 Angle : 0.493 9.545 17785 Z= 0.249 Chirality : 0.039 0.235 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.887 14.969 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.35 % Allowed : 12.11 % Favored : 87.54 % 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: 3.02 (0.15), residues: 1070 sheet: 2.23 (0.38), residues: 145 loop : 0.37 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 398 TYR 0.021 0.002 TYR B 299 PHE 0.017 0.001 PHE A 352 TRP 0.007 0.001 TRP B 196 HIS 0.001 0.000 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00297 (13155) covalent geometry : angle 0.49272 (17785) hydrogen bonds : bond 0.04725 ( 1005) hydrogen bonds : angle 3.78322 ( 2935) ********************** 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 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 165 time to evaluate : 0.349 Fit side-chains REVERT: A 137 MET cc_start: 0.9328 (mpp) cc_final: 0.8971 (mtt) REVERT: A 138 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8574 (mm-30) REVERT: A 190 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8306 (tp30) REVERT: A 344 MET cc_start: 0.9129 (mtt) cc_final: 0.8895 (mtt) REVERT: A 368 GLU cc_start: 0.7984 (mp0) cc_final: 0.7558 (mp0) REVERT: A 390 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7433 (mpt180) REVERT: B 138 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8546 (mm-30) REVERT: B 286 ILE cc_start: 0.8598 (mt) cc_final: 0.8210 (mp) REVERT: C 138 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8518 (mm-30) REVERT: C 368 GLU cc_start: 0.8018 (mp0) cc_final: 0.7516 (mp0) REVERT: D 109 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8574 (tm-30) REVERT: D 286 ILE cc_start: 0.8648 (mt) cc_final: 0.8227 (mp) REVERT: D 372 ARG cc_start: 0.8315 (mpp80) cc_final: 0.8005 (ptt90) REVERT: D 391 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6837 (ttp-170) REVERT: E 137 MET cc_start: 0.9302 (mtm) cc_final: 0.8342 (mtm) REVERT: E 138 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8537 (mm-30) REVERT: E 297 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8039 (tt0) outliers start: 5 outliers final: 1 residues processed: 169 average time/residue: 0.6517 time to fit residues: 119.1901 Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 164 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain D residue 391 ARG Chi-restraints excluded: chain E residue 297 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 127 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 33 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.105487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.077747 restraints weight = 54441.267| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.97 r_work: 0.2790 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13155 Z= 0.160 Angle : 0.513 10.148 17785 Z= 0.257 Chirality : 0.040 0.242 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.926 14.825 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.28 % Allowed : 12.11 % Favored : 87.61 % 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: 3.51 (0.21), residues: 1595 helix: 2.98 (0.15), residues: 1070 sheet: 2.23 (0.38), residues: 145 loop : 0.39 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 398 TYR 0.023 0.002 TYR B 299 PHE 0.017 0.002 PHE A 86 TRP 0.007 0.001 TRP B 196 HIS 0.001 0.000 HIS C 371 Details of bonding type rmsd covalent geometry : bond 0.00364 (13155) covalent geometry : angle 0.51337 (17785) hydrogen bonds : bond 0.04861 ( 1005) hydrogen bonds : angle 3.82571 ( 2935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.10 seconds wall clock time: 80 minutes 15.65 seconds (4815.65 seconds total)