Starting phenix.real_space_refine on Thu May 15 06:24:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ip5_35632/05_2025/8ip5_35632.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ip5_35632/05_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_35632/05_2025/8ip5_35632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ip5_35632/05_2025/8ip5_35632.map" model { file = "/net/cci-nas-00/data/ceres_data/8ip5_35632/05_2025/8ip5_35632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ip5_35632/05_2025/8ip5_35632.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: {'GLN:plan1': 2, 'GLU:plan': 3, '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: 13.33, per 1000 atoms: 1.03 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: 2.92 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 1.04 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: 3.95 Time building geometry restraints manager: 3.48 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: 3.510 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: 0.000 Extract box with map and model: 1.540 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.510 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.140 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (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 TRP 0.005 0.001 TRP C 196 HIS 0.002 0.000 HIS B 122 PHE 0.014 0.001 PHE A 352 TYR 0.012 0.001 TYR A 299 ARG 0.002 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.08422 ( 1005) hydrogen bonds : angle 4.33404 ( 2935) covalent geometry : bond 0.00211 (13155) covalent geometry : angle 0.43424 (17785) *********************** 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 : 1.397 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: 1.4359 time to fit residues: 422.6853 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 : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN C 121 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.100327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.071724 restraints weight = 52798.001| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.06 r_work: 0.2720 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13155 Z= 0.272 Angle : 0.614 9.580 17785 Z= 0.306 Chirality : 0.044 0.229 2060 Planarity : 0.004 0.038 2250 Dihedral : 4.046 15.753 1740 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.20 % Allowed : 8.80 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.40 (0.21), residues: 1595 helix: 2.85 (0.15), residues: 1080 sheet: 2.14 (0.37), residues: 145 loop : 0.43 (0.37), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 162 HIS 0.002 0.001 HIS C 331 PHE 0.026 0.002 PHE A 86 TYR 0.025 0.002 TYR D 299 ARG 0.011 0.001 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 1005) hydrogen bonds : angle 4.06491 ( 2935) covalent geometry : bond 0.00637 (13155) covalent geometry : angle 0.61376 (17785) *********************** 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 180 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 1.495 Fit side-chains REVERT: A 286 ILE cc_start: 0.8592 (mt) cc_final: 0.8200 (mp) REVERT: A 344 MET cc_start: 0.9063 (mtt) cc_final: 0.8819 (mtt) REVERT: A 368 GLU cc_start: 0.7971 (mp0) cc_final: 0.7601 (mp0) REVERT: A 390 ARG cc_start: 0.8095 (mtt180) cc_final: 0.7434 (mpt180) REVERT: B 286 ILE cc_start: 0.8493 (mt) cc_final: 0.8089 (mp) REVERT: C 368 GLU cc_start: 0.7916 (mp0) cc_final: 0.7481 (mp0) REVERT: D 109 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8581 (tm-30) REVERT: D 286 ILE cc_start: 0.8584 (mt) cc_final: 0.8158 (mp) REVERT: D 391 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6850 (ttp-170) REVERT: E 124 MET cc_start: 0.9005 (tpt) cc_final: 0.8671 (tpp) REVERT: E 190 GLU cc_start: 0.8822 (tt0) cc_final: 0.8454 (tt0) outliers start: 17 outliers final: 0 residues processed: 168 average time/residue: 1.4429 time to fit residues: 261.1352 Evaluate side-chains 143 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 391 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3461 r_free = 0.3461 target = 0.107047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.080206 restraints weight = 42433.118| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.57 r_work: 0.2840 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1834 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= 0.124 Angle : 0.481 9.580 17785 Z= 0.247 Chirality : 0.039 0.216 2060 Planarity : 0.003 0.029 2250 Dihedral : 3.854 14.701 1740 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.77 % Allowed : 9.23 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.21), residues: 1595 helix: 3.09 (0.15), residues: 1050 sheet: 2.13 (0.37), residues: 145 loop : 0.40 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 162 HIS 0.001 0.000 HIS D 371 PHE 0.015 0.001 PHE A 352 TYR 0.016 0.002 TYR B 299 ARG 0.008 0.001 ARG C 155 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 1005) hydrogen bonds : angle 3.79574 ( 2935) covalent geometry : bond 0.00263 (13155) covalent geometry : angle 0.48050 (17785) *********************** 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 182 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.426 Fit side-chains REVERT: A 137 MET cc_start: 0.9350 (mpp) cc_final: 0.8970 (mtt) REVERT: A 138 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 286 ILE cc_start: 0.8632 (mt) cc_final: 0.8250 (mp) REVERT: A 344 MET cc_start: 0.9052 (mtt) cc_final: 0.8808 (mtt) REVERT: A 368 GLU cc_start: 0.7906 (mp0) cc_final: 0.7526 (mp0) REVERT: A 390 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7427 (mpt180) REVERT: B 286 ILE cc_start: 0.8550 (mt) cc_final: 0.8156 (mp) REVERT: C 138 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8499 (mm-30) REVERT: C 368 GLU cc_start: 0.7877 (mp0) cc_final: 0.7464 (mp0) REVERT: D 109 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8541 (tm-30) REVERT: D 286 ILE cc_start: 0.8616 (mt) cc_final: 0.8210 (mp) REVERT: D 337 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8209 (ttm-80) REVERT: D 391 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6797 (ttp-170) REVERT: E 138 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8490 (mm-30) REVERT: E 368 GLU cc_start: 0.7817 (mp0) cc_final: 0.7502 (mp0) REVERT: E 391 ARG cc_start: 0.7283 (ttt180) cc_final: 0.6986 (mmm160) outliers start: 11 outliers final: 2 residues processed: 175 average time/residue: 1.4400 time to fit residues: 271.9788 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 : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain D residue 337 ARG 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 69 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 125 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3483 r_free = 0.3483 target = 0.108558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.081144 restraints weight = 51661.084| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.90 r_work: 0.2867 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13155 Z= 0.110 Angle : 0.476 9.800 17785 Z= 0.240 Chirality : 0.038 0.213 2060 Planarity : 0.003 0.029 2250 Dihedral : 3.723 14.064 1740 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.70 % Allowed : 10.35 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.21), residues: 1595 helix: 3.21 (0.15), residues: 1050 sheet: 2.19 (0.36), residues: 145 loop : 0.47 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 162 HIS 0.001 0.000 HIS D 371 PHE 0.015 0.001 PHE A 352 TYR 0.018 0.002 TYR B 299 ARG 0.006 0.001 ARG C 155 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 1005) hydrogen bonds : angle 3.69007 ( 2935) covalent geometry : bond 0.00224 (13155) covalent geometry : angle 0.47557 (17785) *********************** 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 192 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 1.610 Fit side-chains REVERT: A 137 MET cc_start: 0.9321 (mpp) cc_final: 0.8955 (mtt) REVERT: A 138 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8568 (mm-30) REVERT: A 286 ILE cc_start: 0.8617 (mt) cc_final: 0.8230 (mp) REVERT: A 344 MET cc_start: 0.9097 (mtt) cc_final: 0.8863 (mtt) REVERT: A 368 GLU cc_start: 0.7893 (mp0) cc_final: 0.7522 (mp0) REVERT: A 390 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7424 (mpt180) REVERT: B 138 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8477 (mm-30) REVERT: B 286 ILE cc_start: 0.8577 (mt) cc_final: 0.8186 (mp) REVERT: C 138 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8513 (mm-30) REVERT: C 368 GLU cc_start: 0.7840 (mp0) cc_final: 0.7409 (mp0) REVERT: D 109 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8557 (tm-30) REVERT: D 286 ILE cc_start: 0.8650 (mt) cc_final: 0.8235 (mp) REVERT: D 337 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (ttm-80) REVERT: D 391 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6791 (ttp-170) REVERT: E 124 MET cc_start: 0.8786 (tpt) cc_final: 0.8541 (tpp) REVERT: E 138 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8560 (mm-30) REVERT: E 297 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: E 368 GLU cc_start: 0.7913 (mp0) cc_final: 0.7589 (mp0) REVERT: E 391 ARG cc_start: 0.7266 (ttt180) cc_final: 0.6993 (mmm160) outliers start: 10 outliers final: 3 residues processed: 187 average time/residue: 1.3882 time to fit residues: 280.7462 Evaluate side-chains 177 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain C residue 314 ARG 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 54 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.104740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.077153 restraints weight = 48167.590| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.76 r_work: 0.2795 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13155 Z= 0.209 Angle : 0.546 9.649 17785 Z= 0.273 Chirality : 0.041 0.225 2060 Planarity : 0.003 0.028 2250 Dihedral : 3.970 14.381 1740 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.77 % Allowed : 10.99 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.21), residues: 1595 helix: 3.14 (0.15), residues: 1040 sheet: 2.23 (0.38), residues: 145 loop : 0.41 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.002 0.001 HIS D 371 PHE 0.021 0.002 PHE A 86 TYR 0.023 0.002 TYR B 299 ARG 0.006 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 1005) hydrogen bonds : angle 3.90760 ( 2935) covalent geometry : bond 0.00485 (13155) covalent geometry : angle 0.54610 (17785) *********************** 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 169 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.415 Fit side-chains REVERT: A 138 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8493 (mm-30) REVERT: A 190 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: A 286 ILE cc_start: 0.8605 (mt) cc_final: 0.8221 (mp) REVERT: A 344 MET cc_start: 0.9107 (mtt) cc_final: 0.8869 (mtt) REVERT: A 368 GLU cc_start: 0.7958 (mp0) cc_final: 0.7539 (mp0) REVERT: A 390 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7405 (mpt180) REVERT: B 286 ILE cc_start: 0.8534 (mt) cc_final: 0.8145 (mp) REVERT: C 138 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8516 (mm-30) REVERT: C 368 GLU cc_start: 0.7953 (mp0) cc_final: 0.7477 (mp0) REVERT: D 109 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8570 (tm-30) REVERT: D 286 ILE cc_start: 0.8615 (mt) cc_final: 0.8198 (mp) REVERT: D 372 ARG cc_start: 0.8338 (mpp80) cc_final: 0.8060 (ptt90) REVERT: D 391 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6832 (ttp-170) REVERT: E 124 MET cc_start: 0.8915 (tpt) cc_final: 0.8592 (tpp) REVERT: E 138 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8510 (mm-30) REVERT: E 297 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8224 (tt0) outliers start: 11 outliers final: 2 residues processed: 163 average time/residue: 1.4618 time to fit residues: 256.6876 Evaluate side-chains 159 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain C residue 314 ARG 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 63 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.106728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.078984 restraints weight = 52936.075| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.93 r_work: 0.2831 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13155 Z= 0.131 Angle : 0.482 9.608 17785 Z= 0.245 Chirality : 0.039 0.228 2060 Planarity : 0.003 0.030 2250 Dihedral : 3.847 14.933 1740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.21), residues: 1595 helix: 3.11 (0.15), residues: 1050 sheet: 2.22 (0.37), residues: 145 loop : 0.48 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 196 HIS 0.001 0.000 HIS C 371 PHE 0.017 0.001 PHE D 359 TYR 0.020 0.002 TYR B 299 ARG 0.007 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.04697 ( 1005) hydrogen bonds : angle 3.79045 ( 2935) covalent geometry : bond 0.00287 (13155) covalent geometry : angle 0.48210 (17785) *********************** 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 174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 167 time to evaluate : 1.509 Fit side-chains REVERT: A 137 MET cc_start: 0.9311 (mpp) cc_final: 0.9076 (mtt) REVERT: A 138 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8532 (mm-30) REVERT: A 190 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: A 286 ILE cc_start: 0.8643 (mt) cc_final: 0.8255 (mp) REVERT: A 344 MET cc_start: 0.9114 (mtt) cc_final: 0.8888 (mtt) REVERT: A 368 GLU cc_start: 0.7951 (mp0) cc_final: 0.7541 (mp0) REVERT: A 390 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7418 (mpt180) REVERT: B 286 ILE cc_start: 0.8550 (mt) cc_final: 0.8151 (mp) REVERT: C 138 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8499 (mm-30) REVERT: C 368 GLU cc_start: 0.7936 (mp0) cc_final: 0.7461 (mp0) REVERT: D 109 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8551 (tm-30) REVERT: D 286 ILE cc_start: 0.8644 (mt) cc_final: 0.8218 (mp) REVERT: D 372 ARG cc_start: 0.8283 (mpp80) cc_final: 0.8033 (ptt90) REVERT: D 391 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6817 (ttp-170) REVERT: E 137 MET cc_start: 0.9281 (mtm) cc_final: 0.8279 (mtm) REVERT: E 138 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8523 (mm-30) REVERT: E 297 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: E 368 GLU cc_start: 0.7929 (mp0) cc_final: 0.7580 (mp0) outliers start: 7 outliers final: 2 residues processed: 171 average time/residue: 1.4666 time to fit residues: 273.4363 Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain C residue 314 ARG 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 64 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.103696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075402 restraints weight = 61028.899| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.15 r_work: 0.2733 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 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 = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13155 Z= 0.265 Angle : 0.579 9.976 17785 Z= 0.289 Chirality : 0.042 0.232 2060 Planarity : 0.004 0.030 2250 Dihedral : 4.109 15.393 1740 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.70 % Allowed : 11.48 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.21), residues: 1595 helix: 3.00 (0.15), residues: 1040 sheet: 2.25 (0.38), residues: 145 loop : 0.39 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 162 HIS 0.002 0.001 HIS C 331 PHE 0.023 0.002 PHE A 86 TYR 0.026 0.002 TYR B 299 ARG 0.008 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.05377 ( 1005) hydrogen bonds : angle 4.02079 ( 2935) covalent geometry : bond 0.00624 (13155) covalent geometry : angle 0.57890 (17785) *********************** 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 163 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 153 time to evaluate : 1.557 Fit side-chains REVERT: A 190 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: A 286 ILE cc_start: 0.8646 (mt) cc_final: 0.8250 (mp) REVERT: A 344 MET cc_start: 0.9117 (mtt) cc_final: 0.8878 (mtt) REVERT: A 368 GLU cc_start: 0.8053 (mp0) cc_final: 0.7601 (mp0) REVERT: A 390 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7440 (mpt180) REVERT: B 286 ILE cc_start: 0.8541 (mt) cc_final: 0.8151 (mp) REVERT: C 368 GLU cc_start: 0.8073 (mp0) cc_final: 0.7563 (mp0) REVERT: D 109 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8619 (tm-30) REVERT: D 286 ILE cc_start: 0.8628 (mt) cc_final: 0.8203 (mp) REVERT: D 372 ARG cc_start: 0.8336 (mpp80) cc_final: 0.8082 (ptt90) REVERT: D 391 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6896 (ttp-170) REVERT: E 124 MET cc_start: 0.9005 (tpt) cc_final: 0.8695 (tpp) REVERT: E 190 GLU cc_start: 0.8859 (tt0) cc_final: 0.8497 (tt0) outliers start: 10 outliers final: 3 residues processed: 158 average time/residue: 1.4398 time to fit residues: 245.6892 Evaluate side-chains 155 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain D residue 391 ARG 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 86 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 0.0770 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.107418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079586 restraints weight = 57937.529| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 4.07 r_work: 0.2837 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.067 | | 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: 0.8190 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13155 Z= 0.113 Angle : 0.479 10.169 17785 Z= 0.242 Chirality : 0.038 0.236 2060 Planarity : 0.003 0.031 2250 Dihedral : 3.865 15.617 1740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.49 % Allowed : 12.04 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.21), residues: 1595 helix: 3.23 (0.15), residues: 1040 sheet: 2.16 (0.38), residues: 145 loop : 0.43 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 196 HIS 0.002 0.000 HIS B 122 PHE 0.016 0.001 PHE A 352 TYR 0.019 0.002 TYR B 299 ARG 0.007 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1005) hydrogen bonds : angle 3.76791 ( 2935) covalent geometry : bond 0.00235 (13155) covalent geometry : angle 0.47855 (17785) *********************** 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 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 1.409 Fit side-chains REVERT: A 137 MET cc_start: 0.9317 (mpp) cc_final: 0.9054 (mtt) REVERT: A 138 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8564 (mm-30) REVERT: A 190 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: A 286 ILE cc_start: 0.8644 (mt) cc_final: 0.8247 (mp) REVERT: A 344 MET cc_start: 0.9110 (mtt) cc_final: 0.8890 (mtt) REVERT: A 368 GLU cc_start: 0.7963 (mp0) cc_final: 0.7578 (mp0) REVERT: A 390 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7425 (mpt180) REVERT: B 286 ILE cc_start: 0.8584 (mt) cc_final: 0.8189 (mp) REVERT: C 138 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8522 (mm-30) REVERT: C 368 GLU cc_start: 0.7987 (mp0) cc_final: 0.7507 (mp0) REVERT: D 109 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8563 (tm-30) REVERT: D 286 ILE cc_start: 0.8664 (mt) cc_final: 0.8240 (mp) REVERT: D 372 ARG cc_start: 0.8295 (mpp80) cc_final: 0.7088 (mmm160) REVERT: D 391 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6802 (ttp-170) REVERT: E 137 MET cc_start: 0.9269 (mtm) cc_final: 0.8273 (mtm) REVERT: E 138 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8528 (mm-30) outliers start: 7 outliers final: 1 residues processed: 172 average time/residue: 1.3513 time to fit residues: 251.7259 Evaluate side-chains 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain D residue 391 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 131 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.106543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.078641 restraints weight = 59319.316| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.10 r_work: 0.2822 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 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 = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2080 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= 0.132 Angle : 0.508 9.901 17785 Z= 0.251 Chirality : 0.039 0.237 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.853 14.729 1740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.42 % Allowed : 12.32 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.75 (0.21), residues: 1595 helix: 3.25 (0.15), residues: 1040 sheet: 2.14 (0.38), residues: 145 loop : 0.50 (0.35), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.001 0.000 HIS C 371 PHE 0.015 0.001 PHE E 352 TYR 0.021 0.002 TYR B 299 ARG 0.008 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.04674 ( 1005) hydrogen bonds : angle 3.76737 ( 2935) covalent geometry : bond 0.00288 (13155) covalent geometry : angle 0.50775 (17785) *********************** 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 173 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 167 time to evaluate : 1.421 Fit side-chains REVERT: A 137 MET cc_start: 0.9308 (mpp) cc_final: 0.9023 (mtt) REVERT: A 138 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8568 (mm-30) REVERT: A 190 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: A 286 ILE cc_start: 0.8646 (mt) cc_final: 0.8247 (mp) REVERT: A 344 MET cc_start: 0.9135 (mtt) cc_final: 0.8913 (mtt) REVERT: A 368 GLU cc_start: 0.7974 (mp0) cc_final: 0.7505 (mp0) REVERT: A 390 ARG cc_start: 0.8072 (mtt180) cc_final: 0.7414 (mpt180) REVERT: B 286 ILE cc_start: 0.8566 (mt) cc_final: 0.8171 (mp) REVERT: C 138 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8557 (mm-30) REVERT: C 368 GLU cc_start: 0.7991 (mp0) cc_final: 0.7489 (mp0) REVERT: D 109 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8587 (tm-30) REVERT: D 286 ILE cc_start: 0.8663 (mt) cc_final: 0.8239 (mp) REVERT: D 372 ARG cc_start: 0.8321 (mpp80) cc_final: 0.7134 (mmm160) REVERT: D 391 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6836 (ttp-170) REVERT: E 137 MET cc_start: 0.9287 (mtm) cc_final: 0.8313 (mtm) REVERT: E 138 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8553 (mm-30) REVERT: E 368 GLU cc_start: 0.7891 (mp0) cc_final: 0.7521 (mp0) outliers start: 6 outliers final: 1 residues processed: 169 average time/residue: 1.3962 time to fit residues: 254.9966 Evaluate side-chains 167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain D residue 391 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.105435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.078279 restraints weight = 42653.189| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.57 r_work: 0.2774 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 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 = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2139 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= 0.165 Angle : 0.520 9.814 17785 Z= 0.260 Chirality : 0.040 0.244 2060 Planarity : 0.003 0.032 2250 Dihedral : 3.924 15.004 1740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.21 % Allowed : 12.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.21), residues: 1595 helix: 3.20 (0.15), residues: 1040 sheet: 2.15 (0.38), residues: 145 loop : 0.47 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 196 HIS 0.002 0.000 HIS C 371 PHE 0.017 0.002 PHE A 86 TYR 0.024 0.002 TYR B 299 ARG 0.008 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 1005) hydrogen bonds : angle 3.83190 ( 2935) covalent geometry : bond 0.00375 (13155) covalent geometry : angle 0.52015 (17785) ********************** 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 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.413 Fit side-chains REVERT: A 137 MET cc_start: 0.9315 (mpp) cc_final: 0.9003 (mtt) REVERT: A 138 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8528 (mm-30) REVERT: A 190 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: A 286 ILE cc_start: 0.8627 (mt) cc_final: 0.8233 (mp) REVERT: A 344 MET cc_start: 0.9102 (mtt) cc_final: 0.8870 (mtt) REVERT: A 368 GLU cc_start: 0.7988 (mp0) cc_final: 0.7524 (mp0) REVERT: A 390 ARG cc_start: 0.8059 (mtt180) cc_final: 0.7405 (mpt180) REVERT: B 286 ILE cc_start: 0.8555 (mt) cc_final: 0.8170 (mp) REVERT: C 138 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8461 (mm-30) REVERT: C 368 GLU cc_start: 0.8008 (mp0) cc_final: 0.7495 (mp0) REVERT: D 109 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8570 (tm-30) REVERT: D 286 ILE cc_start: 0.8622 (mt) cc_final: 0.8201 (mp) REVERT: D 372 ARG cc_start: 0.8306 (mpp80) cc_final: 0.7145 (mmm160) REVERT: D 391 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6811 (ttp-170) REVERT: E 137 MET cc_start: 0.9305 (mtm) cc_final: 0.8356 (mtm) REVERT: E 138 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8493 (mm-30) outliers start: 3 outliers final: 1 residues processed: 163 average time/residue: 1.4194 time to fit residues: 250.6080 Evaluate side-chains 164 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain D residue 391 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 78 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 135 optimal weight: 0.2980 chunk 93 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.106984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.078798 restraints weight = 71623.881| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 4.39 r_work: 0.2810 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 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 = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2076 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= 0.122 Angle : 0.489 10.252 17785 Z= 0.246 Chirality : 0.039 0.226 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.846 14.819 1740 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.21 % Allowed : 12.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.21), residues: 1595 helix: 3.27 (0.15), residues: 1040 sheet: 2.16 (0.38), residues: 145 loop : 0.49 (0.35), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 196 HIS 0.001 0.000 HIS C 371 PHE 0.017 0.001 PHE A 352 TYR 0.022 0.002 TYR B 299 ARG 0.008 0.001 ARG D 398 Details of bonding type rmsd hydrogen bonds : bond 0.04622 ( 1005) hydrogen bonds : angle 3.75707 ( 2935) covalent geometry : bond 0.00260 (13155) covalent geometry : angle 0.48924 (17785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10598.75 seconds wall clock time: 183 minutes 19.74 seconds (10999.74 seconds total)