Starting phenix.real_space_refine on Thu Sep 26 10:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/09_2024/8ip4_35631.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/09_2024/8ip4_35631.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/09_2024/8ip4_35631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/09_2024/8ip4_35631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/09_2024/8ip4_35631.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/09_2024/8ip4_35631.cif" } resolution = 2.7 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 2 5.21 5 S 65 5.16 5 Cl 1 4.86 5 C 8315 2.51 5 N 2175 2.21 5 O 2375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12933 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "B" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "C" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "D" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "E" Number of atoms: 2585 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 320, 2577 Classifications: {'peptide': 320} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 311} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 2614 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CL': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.86, per 1000 atoms: 1.07 Number of scatterers: 12933 At special positions: 0 Unit cell: (110.67, 108.81, 140.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 65 16.00 Mg 2 11.99 O 2375 8.00 N 2175 7.00 C 8315 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.80 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, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG A 187 " --> pdb=" O PRO A 183 " (cutoff:3.500A) Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 275 removed outlier: 3.851A pdb=" N ASP A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 360 removed outlier: 3.788A pdb=" N MET A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 401 Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG B 119 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Proline residue: B 209 - end of helix Processing helix chain 'B' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 275 removed outlier: 3.850A pdb=" N ASP B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 283 removed outlier: 4.165A pdb=" N LYS B 281 " --> pdb=" O GLN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 360 removed outlier: 3.789A pdb=" N MET B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 401 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.530A pdb=" N ARG C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 removed outlier: 4.721A pdb=" N TRP C 162 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU C 261 " --> pdb=" O GLU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.851A pdb=" N ASP C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 360 removed outlier: 3.789A pdb=" N MET C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 401 Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP D 162 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Proline residue: D 168 - end of helix Processing helix chain 'D' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 209 - end of helix Processing helix chain 'D' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.533A pdb=" N LEU D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.850A pdb=" N ASP D 275 " --> pdb=" O SER D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS D 281 " --> pdb=" O GLN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 360 removed outlier: 3.788A pdb=" N MET D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 401 Processing helix chain 'E' and resid 104 through 112 Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.531A pdb=" N ARG E 119 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 removed outlier: 4.720A pdb=" N TRP E 162 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Proline residue: E 168 - end of helix Processing helix chain 'E' and resid 183 through 219 removed outlier: 3.611A pdb=" N ARG E 187 " --> pdb=" O PRO E 183 " (cutoff:3.500A) Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 227 through 261 removed outlier: 3.917A pdb=" N GLU E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 269 removed outlier: 3.532A pdb=" N LEU E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS E 269 " --> pdb=" O LEU E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 275 removed outlier: 3.850A pdb=" N ASP E 275 " --> pdb=" O SER E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 283 removed outlier: 4.164A pdb=" N LYS E 281 " --> pdb=" O GLN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 360 removed outlier: 3.789A pdb=" N MET E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 401 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 103 removed outlier: 4.082A pdb=" N LYS A 141 " --> pdb=" O LEU A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 103 removed outlier: 4.083A pdb=" N LYS B 141 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 103 removed outlier: 4.083A pdb=" N LYS C 141 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 97 through 103 removed outlier: 4.082A pdb=" N LYS D 141 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 97 through 103 removed outlier: 4.083A pdb=" N LYS E 141 " --> pdb=" O LEU E 152 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2965 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.16 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4230 1.34 - 1.46: 2363 1.46 - 1.58: 6447 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 13160 Sorted by residual: bond pdb=" C LEU B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.331 1.346 -0.015 1.21e-02 6.83e+03 1.49e+00 bond pdb=" C LEU D 182 " pdb=" N PRO D 183 " ideal model delta sigma weight residual 1.331 1.346 -0.014 1.21e-02 6.83e+03 1.38e+00 bond pdb=" C LEU E 182 " pdb=" N PRO E 183 " ideal model delta sigma weight residual 1.331 1.345 -0.014 1.21e-02 6.83e+03 1.29e+00 bond pdb=" C LEU A 182 " pdb=" N PRO A 183 " ideal model delta sigma weight residual 1.331 1.345 -0.013 1.21e-02 6.83e+03 1.23e+00 bond pdb=" C LEU C 182 " pdb=" N PRO C 183 " ideal model delta sigma weight residual 1.331 1.344 -0.013 1.21e-02 6.83e+03 1.16e+00 ... (remaining 13155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 17314 1.04 - 2.08: 342 2.08 - 3.12: 83 3.12 - 4.16: 26 4.16 - 5.20: 25 Bond angle restraints: 17790 Sorted by residual: angle pdb=" C LEU D 351 " pdb=" N PHE D 352 " pdb=" CA PHE D 352 " ideal model delta sigma weight residual 121.66 118.21 3.45 1.76e+00 3.23e-01 3.85e+00 angle pdb=" C LEU E 351 " pdb=" N PHE E 352 " pdb=" CA PHE E 352 " ideal model delta sigma weight residual 121.66 118.22 3.44 1.76e+00 3.23e-01 3.83e+00 angle pdb=" C LEU C 351 " pdb=" N PHE C 352 " pdb=" CA PHE C 352 " ideal model delta sigma weight residual 121.66 118.22 3.44 1.76e+00 3.23e-01 3.82e+00 angle pdb=" C LEU B 351 " pdb=" N PHE B 352 " pdb=" CA PHE B 352 " ideal model delta sigma weight residual 121.66 118.24 3.42 1.76e+00 3.23e-01 3.77e+00 angle pdb=" C LEU A 351 " pdb=" N PHE A 352 " pdb=" CA PHE A 352 " ideal model delta sigma weight residual 121.66 118.25 3.41 1.76e+00 3.23e-01 3.76e+00 ... (remaining 17785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.30: 6947 13.30 - 26.60: 688 26.60 - 39.90: 310 39.90 - 53.20: 45 53.20 - 66.50: 10 Dihedral angle restraints: 8000 sinusoidal: 3300 harmonic: 4700 Sorted by residual: dihedral pdb=" CG LYS D 104 " pdb=" CD LYS D 104 " pdb=" CE LYS D 104 " pdb=" NZ LYS D 104 " ideal model delta sinusoidal sigma weight residual 60.00 117.72 -57.72 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG LYS C 104 " pdb=" CD LYS C 104 " pdb=" CE LYS C 104 " pdb=" NZ LYS C 104 " ideal model delta sinusoidal sigma weight residual 60.00 117.69 -57.69 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG LYS E 104 " pdb=" CD LYS E 104 " pdb=" CE LYS E 104 " pdb=" NZ LYS E 104 " ideal model delta sinusoidal sigma weight residual 60.00 117.68 -57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 7997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1521 0.030 - 0.060: 329 0.060 - 0.091: 134 0.091 - 0.121: 62 0.121 - 0.151: 14 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA LEU E 167 " pdb=" N LEU E 167 " pdb=" C LEU E 167 " pdb=" CB LEU E 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA LEU C 167 " pdb=" N LEU C 167 " pdb=" C LEU C 167 " pdb=" CB LEU C 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA LEU D 167 " pdb=" N LEU D 167 " pdb=" C LEU D 167 " pdb=" CB LEU D 167 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 2057 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 145 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO D 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 145 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO C 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 145 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 146 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4028 2.84 - 3.35: 12930 3.35 - 3.87: 21750 3.87 - 4.38: 25115 4.38 - 4.90: 43911 Nonbonded interactions: 107734 Sorted by model distance: nonbonded pdb=" OG1 THR D 179 " pdb=" OE1 GLU D 190 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR C 179 " pdb=" OE1 GLU C 190 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR B 179 " pdb=" OE1 GLU B 190 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR A 179 " pdb=" OE1 GLU A 190 " model vdw 2.320 3.040 nonbonded pdb=" OG1 THR E 179 " pdb=" OE1 GLU E 190 " model vdw 2.320 3.040 ... (remaining 107729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'B' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'C' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'D' and (resid 82 through 128 or resid 130 through 401)) selection = (chain 'E' and (resid 82 through 128 or resid 130 through 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.970 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13160 Z= 0.129 Angle : 0.442 5.196 17790 Z= 0.237 Chirality : 0.036 0.151 2060 Planarity : 0.004 0.050 2250 Dihedral : 12.813 66.498 4940 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.99 (0.21), residues: 1595 helix: 3.48 (0.15), residues: 1085 sheet: 1.45 (0.39), residues: 145 loop : 0.39 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 162 HIS 0.003 0.001 HIS A 122 PHE 0.014 0.001 PHE D 352 TYR 0.008 0.001 TYR C 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 290 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLN cc_start: 0.8540 (mt0) cc_final: 0.8333 (pm20) REVERT: A 223 HIS cc_start: 0.8476 (m170) cc_final: 0.8144 (m-70) REVERT: A 383 MET cc_start: 0.7776 (mmp) cc_final: 0.7520 (mpp) REVERT: A 390 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7196 (mpt180) REVERT: A 391 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.7044 (ttt180) REVERT: B 121 GLN cc_start: 0.8605 (mt0) cc_final: 0.8352 (pm20) REVERT: B 158 ASN cc_start: 0.9048 (m-40) cc_final: 0.8617 (t0) REVERT: B 222 LYS cc_start: 0.8631 (pptt) cc_final: 0.8334 (pptt) REVERT: B 383 MET cc_start: 0.7732 (mmp) cc_final: 0.7448 (mmt) REVERT: B 390 ARG cc_start: 0.7511 (mtt180) cc_final: 0.7004 (mpt180) REVERT: B 391 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6742 (ttt180) REVERT: C 390 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7049 (mpt180) REVERT: C 391 ARG cc_start: 0.7249 (ttm-80) cc_final: 0.6795 (tmt170) REVERT: D 121 GLN cc_start: 0.8661 (mt0) cc_final: 0.8443 (pm20) REVERT: D 154 TYR cc_start: 0.8649 (p90) cc_final: 0.8384 (p90) REVERT: D 253 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7883 (mm-30) REVERT: D 261 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7601 (mp0) REVERT: D 292 MET cc_start: 0.8802 (tpp) cc_final: 0.8482 (tpp) REVERT: D 383 MET cc_start: 0.7792 (mmp) cc_final: 0.7556 (mpp) REVERT: D 390 ARG cc_start: 0.7567 (mtt180) cc_final: 0.7232 (mpt180) REVERT: D 391 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6672 (ttt180) REVERT: E 292 MET cc_start: 0.8771 (tpp) cc_final: 0.8309 (tpp) REVERT: E 383 MET cc_start: 0.7991 (mmp) cc_final: 0.7748 (mpp) REVERT: E 390 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7197 (mpt180) REVERT: E 391 ARG cc_start: 0.7342 (ttm-80) cc_final: 0.6965 (ttt180) outliers start: 0 outliers final: 1 residues processed: 290 average time/residue: 1.4729 time to fit residues: 457.7855 Evaluate side-chains 172 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 351 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN D 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13160 Z= 0.402 Angle : 0.601 9.602 17790 Z= 0.305 Chirality : 0.043 0.232 2060 Planarity : 0.005 0.051 2250 Dihedral : 3.824 14.667 1742 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.11 % Allowed : 9.26 % Favored : 88.63 % 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: 3.60 (0.21), residues: 1595 helix: 3.06 (0.15), residues: 1085 sheet: 1.43 (0.38), residues: 145 loop : 0.67 (0.38), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 196 HIS 0.004 0.001 HIS A 122 PHE 0.019 0.002 PHE A 86 TYR 0.026 0.003 TYR E 154 ARG 0.008 0.001 ARG A 301 *********************** 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 192 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.423 Fit side-chains REVERT: A 390 ARG cc_start: 0.7657 (mtt180) cc_final: 0.7290 (mpt180) REVERT: A 391 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.7069 (ttt180) REVERT: B 222 LYS cc_start: 0.8771 (pptt) cc_final: 0.8453 (pptt) REVERT: B 292 MET cc_start: 0.8859 (tpp) cc_final: 0.8353 (tpp) REVERT: B 390 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7119 (mpt180) REVERT: B 391 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.6853 (tmt170) REVERT: C 390 ARG cc_start: 0.7627 (mtt180) cc_final: 0.7058 (mpt180) REVERT: C 391 ARG cc_start: 0.7341 (ttm-80) cc_final: 0.6857 (tmt170) REVERT: D 253 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8036 (mm-30) REVERT: D 261 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7580 (mp0) REVERT: D 383 MET cc_start: 0.7902 (mmp) cc_final: 0.7679 (mpp) REVERT: D 390 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7248 (mpt180) REVERT: D 391 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.6765 (ttt180) REVERT: E 383 MET cc_start: 0.8053 (mmp) cc_final: 0.7789 (mpp) REVERT: E 390 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7284 (mpt180) REVERT: E 391 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.6962 (ttt180) outliers start: 30 outliers final: 9 residues processed: 184 average time/residue: 1.1099 time to fit residues: 224.4675 Evaluate side-chains 154 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13160 Z= 0.194 Angle : 0.509 9.522 17790 Z= 0.258 Chirality : 0.040 0.245 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.710 13.647 1740 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.18 % Allowed : 9.68 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.21), residues: 1595 helix: 3.04 (0.15), residues: 1085 sheet: 1.47 (0.39), residues: 145 loop : 0.70 (0.38), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 162 HIS 0.004 0.001 HIS A 122 PHE 0.016 0.001 PHE E 352 TYR 0.023 0.002 TYR E 154 ARG 0.007 0.001 ARG A 301 *********************** 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 196 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7659 (mtt180) cc_final: 0.7250 (mpt180) REVERT: A 391 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7023 (ttt180) REVERT: B 390 ARG cc_start: 0.7570 (mtt180) cc_final: 0.7063 (mpt180) REVERT: B 391 ARG cc_start: 0.7289 (ttm-80) cc_final: 0.6842 (tmt170) REVERT: C 292 MET cc_start: 0.8834 (tpp) cc_final: 0.8253 (tpp) REVERT: C 390 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7059 (mpt180) REVERT: C 391 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6899 (tmt170) REVERT: D 253 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8006 (mm-30) REVERT: D 261 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7600 (mp0) REVERT: D 390 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7223 (mpt180) REVERT: D 391 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.6757 (ttt180) REVERT: E 390 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7268 (mpt180) REVERT: E 391 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7017 (ttt180) outliers start: 31 outliers final: 12 residues processed: 182 average time/residue: 1.1690 time to fit residues: 234.1122 Evaluate side-chains 166 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 146 optimal weight: 0.0000 chunk 154 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13160 Z= 0.280 Angle : 0.527 9.028 17790 Z= 0.269 Chirality : 0.041 0.248 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.744 14.450 1740 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.89 % Allowed : 10.67 % Favored : 87.44 % 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: 3.52 (0.21), residues: 1595 helix: 2.93 (0.15), residues: 1105 sheet: 1.56 (0.39), residues: 145 loop : 0.64 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.016 0.002 PHE B 352 TYR 0.032 0.002 TYR E 154 ARG 0.006 0.001 ARG A 301 *********************** 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 190 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.592 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7705 (mtt180) cc_final: 0.7339 (mpt180) REVERT: A 391 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.6974 (ttt180) REVERT: B 390 ARG cc_start: 0.7542 (mtt180) cc_final: 0.7034 (mpt180) REVERT: B 391 ARG cc_start: 0.7302 (ttm-80) cc_final: 0.6874 (tmt170) REVERT: C 390 ARG cc_start: 0.7607 (mtt180) cc_final: 0.7047 (mpt180) REVERT: C 391 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.6916 (tmt170) REVERT: D 137 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8839 (mtp) REVERT: D 253 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8050 (mm-30) REVERT: D 261 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7589 (mp0) REVERT: D 292 MET cc_start: 0.8899 (tpp) cc_final: 0.8556 (tpp) REVERT: D 390 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7226 (mpt180) REVERT: D 391 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.6760 (ttt180) REVERT: E 390 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7269 (mpt180) REVERT: E 391 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7017 (ttt180) outliers start: 27 outliers final: 17 residues processed: 181 average time/residue: 1.1495 time to fit residues: 228.4738 Evaluate side-chains 168 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.1980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13160 Z= 0.158 Angle : 0.484 9.366 17790 Z= 0.245 Chirality : 0.039 0.247 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.607 14.378 1740 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.68 % Allowed : 11.65 % Favored : 86.67 % 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: 3.60 (0.21), residues: 1595 helix: 3.00 (0.15), residues: 1105 sheet: 1.62 (0.40), residues: 145 loop : 0.59 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.004 0.001 HIS A 122 PHE 0.016 0.001 PHE B 352 TYR 0.033 0.002 TYR E 154 ARG 0.007 0.000 ARG E 155 *********************** 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 190 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.551 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7214 (mpt180) REVERT: A 391 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.7042 (ttt180) REVERT: B 390 ARG cc_start: 0.7554 (mtt180) cc_final: 0.7024 (mpt180) REVERT: B 391 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6894 (tmt170) REVERT: C 267 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8411 (mt-10) REVERT: C 390 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7026 (mpt180) REVERT: C 391 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.6859 (tmt170) REVERT: D 253 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7988 (mm-30) REVERT: D 261 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7551 (mp0) REVERT: D 292 MET cc_start: 0.8818 (tpp) cc_final: 0.8492 (tpp) REVERT: D 390 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7210 (mpt180) REVERT: D 391 ARG cc_start: 0.7417 (ttm-80) cc_final: 0.6754 (ttt180) REVERT: E 137 MET cc_start: 0.9314 (mtm) cc_final: 0.9065 (mpp) REVERT: E 390 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7145 (mpt180) REVERT: E 391 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.6992 (ttt180) outliers start: 24 outliers final: 10 residues processed: 179 average time/residue: 1.0838 time to fit residues: 214.0945 Evaluate side-chains 161 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 151 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13160 Z= 0.197 Angle : 0.505 10.056 17790 Z= 0.255 Chirality : 0.040 0.232 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.595 14.462 1740 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.61 % Allowed : 11.93 % Favored : 86.46 % 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: 3.62 (0.21), residues: 1595 helix: 3.01 (0.15), residues: 1105 sheet: 1.61 (0.40), residues: 145 loop : 0.65 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.025 0.001 PHE A 374 TYR 0.034 0.002 TYR B 154 ARG 0.006 0.000 ARG E 155 *********************** 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 181 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7222 (mpt180) REVERT: A 391 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6859 (ttt180) REVERT: B 390 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7029 (mpt180) REVERT: B 391 ARG cc_start: 0.7287 (ttm-80) cc_final: 0.6875 (tmt170) REVERT: C 267 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8437 (mt-10) REVERT: C 390 ARG cc_start: 0.7583 (mtt180) cc_final: 0.7012 (mpt180) REVERT: C 391 ARG cc_start: 0.7325 (ttm-80) cc_final: 0.6867 (tmt170) REVERT: D 137 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8894 (mtp) REVERT: D 253 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8032 (mm-30) REVERT: D 261 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7511 (mp0) REVERT: D 292 MET cc_start: 0.8840 (tpp) cc_final: 0.8498 (tpp) REVERT: D 390 ARG cc_start: 0.7574 (mtt180) cc_final: 0.7213 (mpt180) REVERT: D 391 ARG cc_start: 0.7422 (ttm-80) cc_final: 0.6756 (ttt180) REVERT: E 390 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7137 (mpt180) REVERT: E 391 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6970 (ttt180) outliers start: 23 outliers final: 13 residues processed: 171 average time/residue: 1.0863 time to fit residues: 204.7651 Evaluate side-chains 166 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13160 Z= 0.227 Angle : 0.512 9.713 17790 Z= 0.259 Chirality : 0.040 0.235 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.648 14.656 1740 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.33 % Allowed : 12.42 % Favored : 86.25 % 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: 3.55 (0.21), residues: 1595 helix: 2.95 (0.15), residues: 1105 sheet: 1.64 (0.40), residues: 145 loop : 0.63 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 389 HIS 0.003 0.001 HIS A 122 PHE 0.024 0.001 PHE A 374 TYR 0.034 0.002 TYR B 154 ARG 0.006 0.000 ARG E 155 *********************** 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 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 154 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7228 (mpt180) REVERT: A 391 ARG cc_start: 0.7433 (ttm-80) cc_final: 0.6861 (ttt180) REVERT: B 222 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8657 (pmmt) REVERT: B 253 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7988 (mm-30) REVERT: B 390 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7022 (mpt180) REVERT: B 391 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.6893 (tmt170) REVERT: C 390 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7015 (mpt180) REVERT: C 391 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6873 (tmt170) REVERT: D 137 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8909 (mtp) REVERT: D 253 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8068 (mm-30) REVERT: D 261 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7512 (mp0) REVERT: D 292 MET cc_start: 0.8864 (tpp) cc_final: 0.8522 (tpp) REVERT: D 390 ARG cc_start: 0.7589 (mtt180) cc_final: 0.7167 (mpt180) REVERT: D 391 ARG cc_start: 0.7431 (ttm-80) cc_final: 0.6768 (ttt180) REVERT: E 390 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7160 (mpt180) REVERT: E 391 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.6983 (ttt180) outliers start: 19 outliers final: 12 residues processed: 166 average time/residue: 1.1050 time to fit residues: 202.0710 Evaluate side-chains 162 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU 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 95 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 46 optimal weight: 0.2980 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13160 Z= 0.264 Angle : 0.529 10.523 17790 Z= 0.267 Chirality : 0.041 0.241 2060 Planarity : 0.004 0.051 2250 Dihedral : 3.702 14.558 1740 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.40 % Allowed : 12.28 % Favored : 86.32 % 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: 3.46 (0.21), residues: 1595 helix: 2.88 (0.15), residues: 1105 sheet: 1.64 (0.40), residues: 145 loop : 0.60 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 389 HIS 0.003 0.001 HIS A 122 PHE 0.024 0.002 PHE A 374 TYR 0.032 0.002 TYR B 154 ARG 0.006 0.000 ARG E 155 *********************** 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 177 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 157 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8868 (ptm) REVERT: A 390 ARG cc_start: 0.7663 (mtt180) cc_final: 0.7270 (mpt180) REVERT: A 391 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.6860 (ttt180) REVERT: B 222 LYS cc_start: 0.9070 (ptpp) cc_final: 0.8651 (pmmt) REVERT: B 390 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7028 (mpt180) REVERT: B 391 ARG cc_start: 0.7299 (ttm-80) cc_final: 0.6884 (tmt170) REVERT: C 390 ARG cc_start: 0.7555 (mtt180) cc_final: 0.7006 (mpt180) REVERT: C 391 ARG cc_start: 0.7317 (ttm-80) cc_final: 0.6843 (tmt170) REVERT: D 137 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8970 (mtp) REVERT: D 261 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7538 (mp0) REVERT: D 390 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7175 (mpt180) REVERT: D 391 ARG cc_start: 0.7438 (ttm-80) cc_final: 0.6771 (ttt180) REVERT: E 390 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7200 (mpt180) REVERT: E 391 ARG cc_start: 0.7341 (ttm-80) cc_final: 0.6952 (ttt180) outliers start: 20 outliers final: 12 residues processed: 169 average time/residue: 1.1117 time to fit residues: 206.8254 Evaluate side-chains 164 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 134 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13160 Z= 0.188 Angle : 0.503 9.388 17790 Z= 0.256 Chirality : 0.040 0.298 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.632 14.196 1740 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.98 % Allowed : 13.12 % Favored : 85.89 % 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: 3.55 (0.21), residues: 1595 helix: 2.96 (0.15), residues: 1105 sheet: 1.63 (0.40), residues: 145 loop : 0.60 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.024 0.001 PHE A 374 TYR 0.034 0.002 TYR E 154 ARG 0.006 0.000 ARG E 155 *********************** 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 171 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.675 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7278 (mpt180) REVERT: A 391 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6855 (ttt180) REVERT: B 222 LYS cc_start: 0.9055 (ptpp) cc_final: 0.8618 (pmmt) REVERT: B 390 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7014 (mpt180) REVERT: B 391 ARG cc_start: 0.7276 (ttm-80) cc_final: 0.6888 (tmt170) REVERT: C 376 LEU cc_start: 0.8795 (tp) cc_final: 0.8592 (tm) REVERT: C 390 ARG cc_start: 0.7544 (mtt180) cc_final: 0.6990 (mpt180) REVERT: C 391 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.6897 (tmt170) REVERT: D 137 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (mtp) REVERT: D 261 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7478 (mp0) REVERT: D 292 MET cc_start: 0.8859 (tpp) cc_final: 0.8512 (tpp) REVERT: D 390 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7204 (mpt180) REVERT: D 391 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.6765 (ttt180) REVERT: E 155 ARG cc_start: 0.8673 (mmt90) cc_final: 0.8447 (mmt90) REVERT: E 390 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7158 (mpt180) REVERT: E 391 ARG cc_start: 0.7341 (ttm-80) cc_final: 0.6929 (ttt180) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 1.1269 time to fit residues: 204.6286 Evaluate side-chains 161 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7994 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13160 Z= 0.169 Angle : 0.496 10.668 17790 Z= 0.252 Chirality : 0.040 0.275 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.601 14.759 1740 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.77 % Allowed : 13.26 % Favored : 85.96 % 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: 3.53 (0.21), residues: 1595 helix: 2.95 (0.15), residues: 1105 sheet: 1.59 (0.40), residues: 145 loop : 0.58 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 389 HIS 0.003 0.001 HIS A 122 PHE 0.017 0.001 PHE D 352 TYR 0.033 0.002 TYR B 154 ARG 0.005 0.000 ARG E 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3190 Ramachandran restraints generated. 1595 Oldfield, 0 Emsley, 1595 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 160 time to evaluate : 1.565 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7661 (mtt180) cc_final: 0.7277 (mpt180) REVERT: A 391 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7041 (ttt180) REVERT: B 222 LYS cc_start: 0.9067 (ptpp) cc_final: 0.8616 (pmmt) REVERT: B 253 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7898 (mm-30) REVERT: B 390 ARG cc_start: 0.7504 (mtt180) cc_final: 0.7012 (mpt180) REVERT: B 391 ARG cc_start: 0.7271 (ttm-80) cc_final: 0.6851 (tmt170) REVERT: C 390 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6996 (mpt180) REVERT: C 391 ARG cc_start: 0.7356 (ttm-80) cc_final: 0.6895 (tmt170) REVERT: D 261 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7483 (mp0) REVERT: D 292 MET cc_start: 0.8831 (tpp) cc_final: 0.8503 (tpp) REVERT: D 390 ARG cc_start: 0.7616 (mtt180) cc_final: 0.7200 (mpt180) REVERT: D 391 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.6795 (tmt170) REVERT: E 155 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8459 (mmt90) REVERT: E 390 ARG cc_start: 0.7639 (mtt180) cc_final: 0.7144 (mpt180) REVERT: E 391 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.6937 (ttt180) outliers start: 11 outliers final: 9 residues processed: 167 average time/residue: 1.1362 time to fit residues: 208.7660 Evaluate side-chains 162 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 0.4980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.101817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.075288 restraints weight = 54969.994| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.04 r_work: 0.2785 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2856 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2856 r_free = 0.2856 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2856 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13160 Z= 0.154 Angle : 0.493 9.389 17790 Z= 0.248 Chirality : 0.040 0.254 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.542 14.147 1740 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.91 % Allowed : 13.61 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.58 (0.21), residues: 1595 helix: 3.00 (0.15), residues: 1105 sheet: 1.58 (0.40), residues: 145 loop : 0.54 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 389 HIS 0.004 0.000 HIS D 122 PHE 0.025 0.001 PHE C 374 TYR 0.032 0.002 TYR B 154 ARG 0.005 0.000 ARG E 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4448.11 seconds wall clock time: 78 minutes 27.36 seconds (4707.36 seconds total)