Starting phenix.real_space_refine on Sun Nov 17 04:05:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip5_35632/11_2024/8ip5_35632.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip5_35632/11_2024/8ip5_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip5_35632/11_2024/8ip5_35632.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip5_35632/11_2024/8ip5_35632.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip5_35632/11_2024/8ip5_35632.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip5_35632/11_2024/8ip5_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-5513/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: 13.84, per 1000 atoms: 1.07 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: 3.25 Conformation dependent library (CDL) restraints added in 3.8 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: 0.97 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: 3.93 Time building geometry restraints manager: 3.68 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 38.840 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.380 ------------------------------------------------------------------------------- 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= 0.138 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 *********************** 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 : 1.482 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: 1.5566 time to fit residues: 457.0985 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 : 1.563 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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= 0.415 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 *********************** 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 : 1.669 Fit side-chains REVERT: A 286 ILE cc_start: 0.8640 (mt) cc_final: 0.8323 (mp) REVERT: A 297 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: A 344 MET cc_start: 0.8879 (mtt) cc_final: 0.8590 (mtt) REVERT: A 368 GLU cc_start: 0.7923 (mp0) cc_final: 0.7639 (mp0) REVERT: A 398 ARG cc_start: 0.7841 (mtm110) cc_final: 0.7640 (mtp180) REVERT: B 286 ILE cc_start: 0.8559 (mt) cc_final: 0.8230 (mp) REVERT: C 368 GLU cc_start: 0.7871 (mp0) cc_final: 0.7529 (mp0) REVERT: D 109 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8360 (tm-30) REVERT: D 286 ILE cc_start: 0.8645 (mt) cc_final: 0.8304 (mp) REVERT: D 390 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7176 (mpt90) REVERT: D 391 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6406 (ttp-170) REVERT: E 124 MET cc_start: 0.8873 (tpt) cc_final: 0.8606 (tpp) REVERT: E 190 GLU cc_start: 0.8365 (tt0) cc_final: 0.8032 (tt0) outliers start: 17 outliers final: 0 residues processed: 168 average time/residue: 1.6928 time to fit residues: 305.0641 Evaluate side-chains 146 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain D residue 390 ARG 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 80 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1845 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= 0.169 Angle : 0.481 9.854 17785 Z= 0.247 Chirality : 0.039 0.219 2060 Planarity : 0.003 0.029 2250 Dihedral : 3.854 14.752 1740 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.85 % Allowed : 9.15 % 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 : 0.41 (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 A 154 ARG 0.008 0.001 ARG C 155 *********************** 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 183 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.726 Fit side-chains REVERT: A 137 MET cc_start: 0.9047 (mpp) cc_final: 0.8638 (mtt) REVERT: A 138 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8056 (mm-30) REVERT: A 286 ILE cc_start: 0.8676 (mt) cc_final: 0.8358 (mp) REVERT: A 297 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: A 344 MET cc_start: 0.8878 (mtt) cc_final: 0.8591 (mtt) REVERT: A 368 GLU cc_start: 0.7859 (mp0) cc_final: 0.7554 (mp0) REVERT: B 286 ILE cc_start: 0.8601 (mt) cc_final: 0.8273 (mp) REVERT: C 138 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 368 GLU cc_start: 0.7822 (mp0) cc_final: 0.7515 (mp0) REVERT: D 109 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8316 (tm-30) REVERT: D 286 ILE cc_start: 0.8651 (mt) cc_final: 0.8322 (mp) REVERT: D 337 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7805 (ttm-80) REVERT: D 391 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6383 (ttp-170) REVERT: E 138 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8085 (mm-30) REVERT: E 368 GLU cc_start: 0.7819 (mp0) cc_final: 0.7568 (mp0) outliers start: 12 outliers final: 1 residues processed: 176 average time/residue: 1.5926 time to fit residues: 301.7580 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 : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 314 ARG 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 143 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 146 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1901 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= 0.188 Angle : 0.496 9.326 17785 Z= 0.249 Chirality : 0.039 0.210 2060 Planarity : 0.003 0.028 2250 Dihedral : 3.813 14.297 1740 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.85 % Allowed : 10.21 % 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: 3.65 (0.21), residues: 1595 helix: 3.13 (0.15), residues: 1050 sheet: 2.22 (0.37), residues: 145 loop : 0.47 (0.35), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.001 0.000 HIS D 371 PHE 0.016 0.001 PHE A 352 TYR 0.019 0.002 TYR B 299 ARG 0.007 0.001 ARG C 155 *********************** 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 184 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 1.629 Fit side-chains REVERT: A 137 MET cc_start: 0.9039 (mpp) cc_final: 0.8688 (mtt) REVERT: A 138 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8073 (mm-30) REVERT: A 286 ILE cc_start: 0.8700 (mt) cc_final: 0.8382 (mp) REVERT: A 297 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: A 344 MET cc_start: 0.8919 (mtt) cc_final: 0.8645 (mtt) REVERT: A 368 GLU cc_start: 0.7862 (mp0) cc_final: 0.7527 (mp0) REVERT: B 138 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8141 (mm-30) REVERT: B 286 ILE cc_start: 0.8620 (mt) cc_final: 0.8299 (mp) REVERT: C 138 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8017 (mm-30) REVERT: C 368 GLU cc_start: 0.7816 (mp0) cc_final: 0.7481 (mp0) REVERT: D 109 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8322 (tm-30) REVERT: D 286 ILE cc_start: 0.8682 (mt) cc_final: 0.8343 (mp) REVERT: D 337 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7796 (ttm-80) REVERT: D 390 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7066 (mpt90) REVERT: D 391 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6379 (ttp-170) REVERT: E 138 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8096 (mm-30) REVERT: E 297 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: E 368 GLU cc_start: 0.7841 (mp0) cc_final: 0.7553 (mp0) outliers start: 12 outliers final: 3 residues processed: 176 average time/residue: 1.5383 time to fit residues: 292.0191 Evaluate side-chains 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 337 ARG Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 390 ARG 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 128 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 13155 Z= 0.256 Angle : 0.519 9.898 17785 Z= 0.261 Chirality : 0.040 0.223 2060 Planarity : 0.003 0.028 2250 Dihedral : 3.923 14.539 1740 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.70 % Allowed : 10.85 % Favored : 88.45 % 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: 3.65 (0.21), residues: 1595 helix: 3.17 (0.15), residues: 1040 sheet: 2.25 (0.37), residues: 145 loop : 0.39 (0.34), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 162 HIS 0.002 0.000 HIS D 371 PHE 0.018 0.002 PHE A 86 TYR 0.021 0.002 TYR B 299 ARG 0.006 0.001 ARG D 398 *********************** 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 174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 1.652 Fit side-chains REVERT: A 137 MET cc_start: 0.9050 (mpp) cc_final: 0.8685 (mtt) REVERT: A 138 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8050 (mm-30) REVERT: A 190 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7850 (tp30) REVERT: A 286 ILE cc_start: 0.8693 (mt) cc_final: 0.8371 (mp) REVERT: A 297 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: A 344 MET cc_start: 0.8930 (mtt) cc_final: 0.8644 (mtt) REVERT: A 368 GLU cc_start: 0.7916 (mp0) cc_final: 0.7587 (mp0) REVERT: B 286 ILE cc_start: 0.8611 (mt) cc_final: 0.8290 (mp) REVERT: C 138 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8041 (mm-30) REVERT: C 368 GLU cc_start: 0.7914 (mp0) cc_final: 0.7558 (mp0) REVERT: D 109 GLN cc_start: 0.8642 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 286 ILE cc_start: 0.8693 (mt) cc_final: 0.8353 (mp) REVERT: D 372 ARG cc_start: 0.8253 (mpp80) cc_final: 0.7920 (ptt90) REVERT: D 390 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.7107 (mpt90) REVERT: D 391 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6395 (ttp-170) REVERT: E 138 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8114 (mm-30) REVERT: E 297 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: E 368 GLU cc_start: 0.7872 (mp0) cc_final: 0.7552 (mp0) outliers start: 10 outliers final: 1 residues processed: 169 average time/residue: 1.5429 time to fit residues: 280.8471 Evaluate side-chains 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain D residue 390 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 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2092 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= 0.241 Angle : 0.514 9.795 17785 Z= 0.257 Chirality : 0.039 0.231 2060 Planarity : 0.003 0.029 2250 Dihedral : 3.915 14.718 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 : 0.70 % Allowed : 11.34 % 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: 3.48 (0.21), residues: 1595 helix: 2.97 (0.15), residues: 1070 sheet: 2.27 (0.38), residues: 145 loop : 0.30 (0.36), residues: 380 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 0.002 PHE A 86 TYR 0.022 0.002 TYR B 299 ARG 0.007 0.001 ARG D 398 *********************** 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 170 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.497 Fit side-chains REVERT: A 137 MET cc_start: 0.9050 (mpp) cc_final: 0.8716 (mtt) REVERT: A 138 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 190 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: A 286 ILE cc_start: 0.8723 (mt) cc_final: 0.8406 (mp) REVERT: A 297 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7730 (tt0) REVERT: A 344 MET cc_start: 0.8935 (mtt) cc_final: 0.8648 (mtt) REVERT: A 368 GLU cc_start: 0.7911 (mp0) cc_final: 0.7587 (mp0) REVERT: B 286 ILE cc_start: 0.8616 (mt) cc_final: 0.8297 (mp) REVERT: C 138 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8025 (mm-30) REVERT: C 368 GLU cc_start: 0.7913 (mp0) cc_final: 0.7538 (mp0) REVERT: D 109 GLN cc_start: 0.8648 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 286 ILE cc_start: 0.8690 (mt) cc_final: 0.8342 (mp) REVERT: D 372 ARG cc_start: 0.8259 (mpp80) cc_final: 0.7929 (ptt90) REVERT: D 390 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.7119 (mpt90) REVERT: D 391 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6402 (ttp-170) REVERT: E 138 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8070 (mm-30) REVERT: E 297 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7752 (tt0) outliers start: 10 outliers final: 1 residues processed: 166 average time/residue: 1.5589 time to fit residues: 278.6030 Evaluate side-chains 160 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain D residue 390 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 149 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2112 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= 0.236 Angle : 0.506 8.827 17785 Z= 0.256 Chirality : 0.039 0.233 2060 Planarity : 0.003 0.030 2250 Dihedral : 3.930 15.124 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.70 % Allowed : 11.34 % 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: 3.48 (0.21), residues: 1595 helix: 2.97 (0.15), residues: 1070 sheet: 2.27 (0.38), residues: 145 loop : 0.29 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.001 0.000 HIS B 371 PHE 0.016 0.002 PHE A 86 TYR 0.020 0.002 TYR B 299 ARG 0.007 0.001 ARG D 398 *********************** 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 168 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.588 Fit side-chains REVERT: A 137 MET cc_start: 0.9050 (mpp) cc_final: 0.8696 (mtt) REVERT: A 138 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 190 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: A 286 ILE cc_start: 0.8720 (mt) cc_final: 0.8402 (mp) REVERT: A 297 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: A 344 MET cc_start: 0.8937 (mtt) cc_final: 0.8652 (mtt) REVERT: A 368 GLU cc_start: 0.7924 (mp0) cc_final: 0.7588 (mp0) REVERT: B 286 ILE cc_start: 0.8637 (mt) cc_final: 0.8316 (mp) REVERT: C 138 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 368 GLU cc_start: 0.7921 (mp0) cc_final: 0.7536 (mp0) REVERT: D 109 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8327 (tm-30) REVERT: D 286 ILE cc_start: 0.8677 (mt) cc_final: 0.8326 (mp) REVERT: D 372 ARG cc_start: 0.8235 (mpp80) cc_final: 0.7922 (ptt90) REVERT: D 390 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7116 (mpt90) REVERT: D 391 ARG cc_start: 0.7030 (OUTLIER) cc_final: 0.6396 (ttp-170) REVERT: E 138 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8065 (mm-30) REVERT: E 297 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7744 (tt0) outliers start: 10 outliers final: 1 residues processed: 163 average time/residue: 1.5648 time to fit residues: 274.6977 Evaluate side-chains 165 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain D residue 390 ARG 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 95 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 76 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2095 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= 0.203 Angle : 0.506 9.843 17785 Z= 0.253 Chirality : 0.039 0.235 2060 Planarity : 0.003 0.031 2250 Dihedral : 3.901 14.920 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.56 % Allowed : 11.83 % 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: 3.51 (0.21), residues: 1595 helix: 3.00 (0.15), residues: 1070 sheet: 2.19 (0.38), residues: 145 loop : 0.30 (0.36), residues: 380 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 0.016 0.001 PHE A 352 TYR 0.021 0.002 TYR B 299 ARG 0.007 0.001 ARG E 398 *********************** 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 174 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 1.618 Fit side-chains REVERT: A 137 MET cc_start: 0.9040 (mpp) cc_final: 0.8659 (mtt) REVERT: A 138 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 190 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: A 286 ILE cc_start: 0.8721 (mt) cc_final: 0.8402 (mp) REVERT: A 297 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: A 344 MET cc_start: 0.8944 (mtt) cc_final: 0.8663 (mtt) REVERT: A 368 GLU cc_start: 0.7903 (mp0) cc_final: 0.7558 (mp0) REVERT: B 138 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 286 ILE cc_start: 0.8639 (mt) cc_final: 0.8319 (mp) REVERT: C 138 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8033 (mm-30) REVERT: C 368 GLU cc_start: 0.7911 (mp0) cc_final: 0.7526 (mp0) REVERT: D 109 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8320 (tm-30) REVERT: D 286 ILE cc_start: 0.8679 (mt) cc_final: 0.8327 (mp) REVERT: D 372 ARG cc_start: 0.8216 (mpp80) cc_final: 0.7914 (ptt90) REVERT: D 390 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7122 (mpt90) REVERT: D 391 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6386 (ttp-170) REVERT: E 138 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8105 (mm-30) REVERT: E 297 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7630 (tt0) REVERT: E 368 GLU cc_start: 0.7910 (mp0) cc_final: 0.7632 (mp0) outliers start: 8 outliers final: 1 residues processed: 171 average time/residue: 1.4899 time to fit residues: 275.0375 Evaluate side-chains 166 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain D residue 390 ARG 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 140 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 134 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 129 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2027 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= 0.153 Angle : 0.473 9.170 17785 Z= 0.240 Chirality : 0.038 0.238 2060 Planarity : 0.003 0.033 2250 Dihedral : 3.821 20.283 1740 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.63 % Allowed : 11.62 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.70 (0.21), residues: 1595 helix: 3.18 (0.15), residues: 1050 sheet: 2.14 (0.38), residues: 145 loop : 0.51 (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 0.015 0.001 PHE A 352 TYR 0.021 0.002 TYR B 299 ARG 0.008 0.001 ARG D 398 *********************** 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 183 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 1.642 Fit side-chains REVERT: A 137 MET cc_start: 0.9045 (mpp) cc_final: 0.8603 (mtt) REVERT: A 138 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8127 (mm-30) REVERT: A 190 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7893 (tp30) REVERT: A 286 ILE cc_start: 0.8721 (mt) cc_final: 0.8399 (mp) REVERT: A 297 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: A 344 MET cc_start: 0.8957 (mtt) cc_final: 0.8701 (mtt) REVERT: A 368 GLU cc_start: 0.7860 (mp0) cc_final: 0.7481 (mp0) REVERT: B 138 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 286 ILE cc_start: 0.8651 (mt) cc_final: 0.8329 (mp) REVERT: C 138 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8024 (mm-30) REVERT: C 368 GLU cc_start: 0.7868 (mp0) cc_final: 0.7497 (mp0) REVERT: D 109 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8349 (tm-30) REVERT: D 286 ILE cc_start: 0.8695 (mt) cc_final: 0.8340 (mp) REVERT: D 372 ARG cc_start: 0.8187 (mpp80) cc_final: 0.7850 (ptt90) REVERT: D 390 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7122 (mpt90) REVERT: D 391 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6385 (ttp-170) REVERT: E 138 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8067 (mm-30) REVERT: E 297 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: E 368 GLU cc_start: 0.7881 (mp0) cc_final: 0.7631 (mp0) REVERT: E 398 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7795 (mtm110) outliers start: 9 outliers final: 0 residues processed: 179 average time/residue: 1.4472 time to fit residues: 280.2555 Evaluate side-chains 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain D residue 390 ARG 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 151 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2059 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= 0.180 Angle : 0.508 10.090 17785 Z= 0.250 Chirality : 0.039 0.233 2060 Planarity : 0.003 0.034 2250 Dihedral : 3.822 16.516 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.35 % Allowed : 11.97 % Favored : 87.68 % 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: 3.09 (0.15), residues: 1070 sheet: 2.17 (0.38), residues: 145 loop : 0.37 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 196 HIS 0.001 0.000 HIS B 371 PHE 0.016 0.001 PHE A 352 TYR 0.023 0.002 TYR B 299 ARG 0.008 0.001 ARG D 398 ********************** 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 175 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 1.622 Fit side-chains REVERT: A 137 MET cc_start: 0.9063 (mpp) cc_final: 0.8619 (mtt) REVERT: A 138 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 190 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: A 286 ILE cc_start: 0.8719 (mt) cc_final: 0.8395 (mp) REVERT: A 297 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 344 MET cc_start: 0.8968 (mtt) cc_final: 0.8691 (mtt) REVERT: A 368 GLU cc_start: 0.7880 (mp0) cc_final: 0.7503 (mp0) REVERT: B 138 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8025 (mm-30) REVERT: B 286 ILE cc_start: 0.8649 (mt) cc_final: 0.8327 (mp) REVERT: C 138 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8034 (mm-30) REVERT: C 368 GLU cc_start: 0.7883 (mp0) cc_final: 0.7509 (mp0) REVERT: D 109 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8367 (tm-30) REVERT: D 286 ILE cc_start: 0.8698 (mt) cc_final: 0.8343 (mp) REVERT: D 372 ARG cc_start: 0.8181 (mpp80) cc_final: 0.7269 (mtp180) REVERT: D 390 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7118 (mpt90) REVERT: D 391 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6367 (ttp-170) REVERT: D 398 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7686 (mtp85) REVERT: E 138 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8079 (mm-30) REVERT: E 297 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: E 368 GLU cc_start: 0.7890 (mp0) cc_final: 0.7607 (mp0) outliers start: 5 outliers final: 0 residues processed: 173 average time/residue: 1.4739 time to fit residues: 275.5112 Evaluate side-chains 171 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 166 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain D residue 390 ARG 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 135 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.106824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.079100 restraints weight = 55431.691| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.98 r_work: 0.2817 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2072 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= 0.202 Angle : 0.500 9.588 17785 Z= 0.252 Chirality : 0.039 0.235 2060 Planarity : 0.003 0.032 2250 Dihedral : 3.863 17.577 1740 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.42 % Allowed : 11.69 % Favored : 87.89 % 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: 3.59 (0.21), residues: 1595 helix: 3.07 (0.15), residues: 1070 sheet: 2.17 (0.38), residues: 145 loop : 0.35 (0.36), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 196 HIS 0.001 0.000 HIS B 371 PHE 0.015 0.001 PHE A 86 TYR 0.024 0.002 TYR B 299 ARG 0.008 0.001 ARG E 398 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5196.15 seconds wall clock time: 93 minutes 42.57 seconds (5622.57 seconds total)