Starting phenix.real_space_refine on Fri Mar 15 22:13:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/03_2024/8ip4_35631.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/03_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_35631/03_2024/8ip4_35631.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/03_2024/8ip4_35631.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/03_2024/8ip4_35631.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip4_35631/03_2024/8ip4_35631.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.82, per 1000 atoms: 0.99 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 - 3.50 Amino acid : False - 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: 5.44 Conformation dependent library (CDL) restraints added in 4.6 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: 1.15 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: 4.07 Time building geometry restraints manager: 5.82 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: 98.55 - 105.64: 181 105.64 - 112.72: 7211 112.72 - 119.81: 4136 119.81 - 126.90: 6127 126.90 - 133.98: 135 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 2.440 nonbonded pdb=" OG1 THR C 179 " pdb=" OE1 GLU C 190 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR B 179 " pdb=" OE1 GLU B 190 " model vdw 2.320 2.440 nonbonded pdb=" OG1 THR A 179 " pdb=" OE1 GLU A 190 " model vdw 2.320 2.440 nonbonded pdb=" OG1 THR E 179 " pdb=" OE1 GLU E 190 " model vdw 2.320 2.440 ... (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 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: 1.150 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: 0.040 Extract box with map and model: 4.630 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 45.030 Find NCS groups from input model: 0.780 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: 0.000 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.410 ------------------------------------------------------------------------------- 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 : 1.612 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: 1.4601 time to fit residues: 454.8172 Evaluate side-chains 172 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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: 5.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 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: 5.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 194 GLN D 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 13160 Z= 0.429 Angle : 0.603 9.365 17790 Z= 0.305 Chirality : 0.044 0.231 2060 Planarity : 0.005 0.051 2250 Dihedral : 3.900 15.156 1742 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.18 % Allowed : 9.47 % Favored : 88.35 % 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: 3.02 (0.15), residues: 1085 sheet: 1.36 (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 0.020 0.002 PHE A 86 TYR 0.026 0.003 TYR B 299 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 184 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7332 (mpt180) REVERT: A 391 ARG cc_start: 0.7418 (ttm-80) cc_final: 0.7039 (ttt180) REVERT: B 292 MET cc_start: 0.8878 (tpp) cc_final: 0.8379 (tpp) REVERT: B 390 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7111 (mpt180) REVERT: B 391 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6803 (tmt170) REVERT: C 329 ASP cc_start: 0.8261 (m-30) cc_final: 0.8058 (m-30) REVERT: C 390 ARG cc_start: 0.7625 (mtt180) cc_final: 0.7061 (mpt180) REVERT: C 391 ARG cc_start: 0.7327 (ttm-80) cc_final: 0.6844 (tmt170) REVERT: D 253 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8054 (mm-30) REVERT: D 261 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7586 (mp0) REVERT: D 383 MET cc_start: 0.7916 (mmp) cc_final: 0.7707 (mpp) REVERT: D 390 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7253 (mpt180) REVERT: D 391 ARG cc_start: 0.7398 (ttm-80) cc_final: 0.6732 (ttt180) REVERT: E 390 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7250 (mpt180) REVERT: E 391 ARG cc_start: 0.7358 (ttm-80) cc_final: 0.6945 (ttt180) outliers start: 31 outliers final: 11 residues processed: 177 average time/residue: 1.1426 time to fit residues: 222.3524 Evaluate side-chains 151 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 383 MET 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: 0.6980 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.003 0.030 13160 Z= 0.223 Angle : 0.511 9.478 17790 Z= 0.258 Chirality : 0.040 0.245 2060 Planarity : 0.004 0.051 2250 Dihedral : 3.755 14.071 1740 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.11 % Allowed : 10.67 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.06 (0.15), residues: 1090 sheet: 1.34 (0.38), residues: 145 loop : 0.80 (0.38), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 375 HIS 0.004 0.001 HIS A 122 PHE 0.015 0.001 PHE E 352 TYR 0.024 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 191 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.714 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7666 (mtt180) cc_final: 0.7294 (mpt180) REVERT: A 391 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.7001 (ttt180) REVERT: B 390 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7038 (mpt180) REVERT: B 391 ARG cc_start: 0.7256 (ttm-80) cc_final: 0.6794 (tmt170) REVERT: C 336 MET cc_start: 0.8939 (mtp) cc_final: 0.8707 (ttm) REVERT: C 390 ARG cc_start: 0.7596 (mtt180) cc_final: 0.7034 (mpt180) REVERT: C 391 ARG cc_start: 0.7347 (ttm-80) cc_final: 0.6881 (tmt170) REVERT: D 253 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8017 (mm-30) REVERT: D 261 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7581 (mp0) REVERT: D 390 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7208 (mpt180) REVERT: D 391 ARG cc_start: 0.7367 (ttm-80) cc_final: 0.6728 (ttt180) REVERT: E 390 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7265 (mpt180) REVERT: E 391 ARG cc_start: 0.7383 (ttm-80) cc_final: 0.6991 (ttt180) outliers start: 30 outliers final: 13 residues processed: 180 average time/residue: 1.1781 time to fit residues: 233.0366 Evaluate side-chains 169 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.559 ------------------------------------------------------------------------------- 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 A residue 342 LEU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 106 GLU 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: 2.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13160 Z= 0.241 Angle : 0.510 9.642 17790 Z= 0.258 Chirality : 0.040 0.254 2060 Planarity : 0.004 0.050 2250 Dihedral : 3.722 14.171 1740 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.18 % Allowed : 10.53 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.01 (0.15), residues: 1105 sheet: 1.43 (0.38), residues: 145 loop : 0.60 (0.39), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.015 0.001 PHE D 352 TYR 0.033 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 192 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7654 (mtt180) cc_final: 0.7287 (mpt180) REVERT: A 391 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.6968 (ttt180) REVERT: B 390 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7031 (mpt180) REVERT: B 391 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6842 (tmt170) REVERT: C 390 ARG cc_start: 0.7611 (mtt180) cc_final: 0.7043 (mpt180) REVERT: C 391 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.6922 (tmt170) REVERT: D 137 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8832 (mtp) REVERT: D 253 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8049 (mm-30) REVERT: D 261 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7586 (mp0) REVERT: D 297 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: D 390 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7190 (mpt180) REVERT: D 391 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.6730 (ttt180) REVERT: E 390 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7257 (mpt180) REVERT: E 391 ARG cc_start: 0.7377 (ttm-80) cc_final: 0.6984 (ttt180) outliers start: 31 outliers final: 17 residues processed: 179 average time/residue: 1.1551 time to fit residues: 227.5067 Evaluate side-chains 165 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 78 optimal weight: 0.0270 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13160 Z= 0.155 Angle : 0.484 9.970 17790 Z= 0.242 Chirality : 0.039 0.260 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.597 13.968 1740 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.54 % Allowed : 12.28 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.21), residues: 1595 helix: 3.13 (0.15), residues: 1105 sheet: 1.55 (0.39), residues: 145 loop : 0.59 (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 0.015 0.001 PHE E 352 TYR 0.034 0.002 TYR E 154 ARG 0.005 0.000 ARG A 301 *********************** 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 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.662 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7213 (mpt180) REVERT: A 391 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7019 (ttt180) REVERT: B 390 ARG cc_start: 0.7551 (mtt180) cc_final: 0.7026 (mpt180) REVERT: B 391 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6806 (tmt170) REVERT: C 267 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8381 (mt-10) REVERT: C 390 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7051 (mpt180) REVERT: C 391 ARG cc_start: 0.7284 (ttm-80) cc_final: 0.6838 (tmt170) REVERT: D 253 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7967 (mm-30) REVERT: D 261 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7567 (mp0) REVERT: D 292 MET cc_start: 0.8860 (tpp) cc_final: 0.8518 (tpp) REVERT: D 297 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: D 390 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7169 (mpt180) REVERT: D 391 ARG cc_start: 0.7366 (ttm-80) cc_final: 0.6756 (tmt170) REVERT: E 390 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7151 (mpt180) REVERT: E 391 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.6964 (ttt180) outliers start: 22 outliers final: 9 residues processed: 171 average time/residue: 1.1623 time to fit residues: 218.4347 Evaluate side-chains 160 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 150 time to evaluate : 1.455 ------------------------------------------------------------------------------- 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 101 GLU Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.7995 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13160 Z= 0.192 Angle : 0.496 9.584 17790 Z= 0.249 Chirality : 0.040 0.264 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.597 14.222 1740 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.75 % Allowed : 12.63 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.77 (0.21), residues: 1595 helix: 3.17 (0.15), residues: 1085 sheet: 1.63 (0.39), residues: 145 loop : 0.72 (0.38), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 389 HIS 0.003 0.001 HIS A 122 PHE 0.026 0.001 PHE A 374 TYR 0.033 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 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.493 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7231 (mpt180) REVERT: A 391 ARG cc_start: 0.7425 (ttm-80) cc_final: 0.7045 (ttt180) REVERT: B 390 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7009 (mpt180) REVERT: B 391 ARG cc_start: 0.7247 (ttm-80) cc_final: 0.6856 (tmt170) REVERT: C 267 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 390 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7008 (mpt180) REVERT: C 391 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6845 (tmt170) REVERT: D 137 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8886 (mtp) REVERT: D 253 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8036 (mm-30) REVERT: D 261 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7523 (mp0) REVERT: D 292 MET cc_start: 0.8832 (tpp) cc_final: 0.8487 (tpp) REVERT: D 297 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: D 390 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7210 (mpt180) REVERT: D 391 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.6728 (ttt180) REVERT: E 390 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7209 (mpt180) REVERT: E 391 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.6942 (ttt180) outliers start: 25 outliers final: 12 residues processed: 169 average time/residue: 1.1677 time to fit residues: 216.9716 Evaluate side-chains 163 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 124 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: 0.9990 chunk 17 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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: 0.8027 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13160 Z= 0.349 Angle : 0.565 9.616 17790 Z= 0.282 Chirality : 0.042 0.263 2060 Planarity : 0.004 0.049 2250 Dihedral : 3.805 15.750 1740 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.04 % Allowed : 12.14 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.21), residues: 1595 helix: 2.90 (0.15), residues: 1105 sheet: 1.67 (0.38), residues: 145 loop : 0.53 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 389 HIS 0.003 0.001 HIS A 122 PHE 0.024 0.002 PHE A 374 TYR 0.036 0.003 TYR B 154 ARG 0.006 0.001 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 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 149 time to evaluate : 1.700 Fit side-chains REVERT: A 390 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7349 (mpt180) REVERT: A 391 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.6961 (ttt180) REVERT: B 292 MET cc_start: 0.8861 (tpp) cc_final: 0.8325 (tpp) REVERT: B 390 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7009 (mpt180) REVERT: B 391 ARG cc_start: 0.7282 (ttm-80) cc_final: 0.6885 (tmt170) REVERT: C 335 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8746 (mtm) REVERT: C 390 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7025 (mpt180) REVERT: C 391 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.6826 (tmt170) REVERT: D 261 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7540 (mp0) REVERT: D 390 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7219 (mpt180) REVERT: D 391 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.6760 (ttt180) REVERT: E 390 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7271 (mpt180) REVERT: E 391 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.6943 (ttt180) outliers start: 29 outliers final: 13 residues processed: 167 average time/residue: 1.1576 time to fit residues: 212.8237 Evaluate side-chains 163 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 1.561 ------------------------------------------------------------------------------- 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 355 MET Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 385 SER 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: 0.8980 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13160 Z= 0.276 Angle : 0.544 10.192 17790 Z= 0.271 Chirality : 0.041 0.279 2060 Planarity : 0.004 0.050 2250 Dihedral : 3.768 15.354 1740 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.33 % Allowed : 13.26 % Favored : 85.40 % 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: 2.89 (0.15), residues: 1105 sheet: 1.69 (0.38), residues: 145 loop : 0.50 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.024 0.002 PHE A 374 TYR 0.036 0.003 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 168 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.375 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7338 (mpt180) REVERT: A 391 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6942 (ttt180) REVERT: B 390 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6999 (mpt180) REVERT: B 391 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6858 (tmt170) REVERT: C 390 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7002 (mpt180) REVERT: C 391 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6809 (tmt170) REVERT: D 261 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7542 (mp0) REVERT: D 390 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7202 (mpt180) REVERT: D 391 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.6749 (ttt180) REVERT: E 390 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7254 (mpt180) REVERT: E 391 ARG cc_start: 0.7310 (ttm-80) cc_final: 0.6926 (ttt180) outliers start: 19 outliers final: 13 residues processed: 161 average time/residue: 1.1475 time to fit residues: 203.7567 Evaluate side-chains 160 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2165 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= 0.182 Angle : 0.492 9.485 17790 Z= 0.249 Chirality : 0.040 0.275 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.641 14.556 1740 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.12 % Allowed : 13.54 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.61 (0.21), residues: 1595 helix: 3.02 (0.15), residues: 1105 sheet: 1.71 (0.39), residues: 145 loop : 0.52 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.024 0.001 PHE A 374 TYR 0.033 0.002 TYR B 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 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 157 time to evaluate : 1.785 Fit side-chains revert: symmetry clash REVERT: A 190 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 390 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7275 (mpt180) REVERT: A 391 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6830 (ttt180) REVERT: B 253 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7983 (mm-30) REVERT: B 390 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6989 (mpt180) REVERT: B 391 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6876 (tmt170) REVERT: C 267 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8393 (mt-10) REVERT: C 390 ARG cc_start: 0.7532 (mtt180) cc_final: 0.6993 (mpt180) REVERT: C 391 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6847 (tmt170) REVERT: D 261 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7578 (mp0) REVERT: D 292 MET cc_start: 0.8856 (tpp) cc_final: 0.8530 (tpp) REVERT: D 297 GLU cc_start: 0.8336 (tt0) cc_final: 0.7932 (tp30) REVERT: D 390 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7195 (mpt180) REVERT: D 391 ARG cc_start: 0.7364 (ttm-80) cc_final: 0.6723 (ttt180) REVERT: E 155 ARG cc_start: 0.8664 (mmt90) cc_final: 0.8464 (mmt90) REVERT: E 390 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7240 (mpt180) REVERT: E 391 ARG cc_start: 0.7320 (ttm-80) cc_final: 0.6927 (ttt180) outliers start: 16 outliers final: 10 residues processed: 169 average time/residue: 1.1966 time to fit residues: 222.3099 Evaluate side-chains 165 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 1.422 ------------------------------------------------------------------------------- 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 190 GLU Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 338 LEU Chi-restraints excluded: chain E residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 0.0970 chunk 92 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 159 optimal weight: 0.0870 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13160 Z= 0.193 Angle : 0.518 10.530 17790 Z= 0.256 Chirality : 0.040 0.276 2060 Planarity : 0.004 0.052 2250 Dihedral : 3.631 14.871 1740 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.77 % Allowed : 14.11 % Favored : 85.12 % 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: 3.03 (0.15), residues: 1105 sheet: 1.71 (0.39), residues: 145 loop : 0.53 (0.40), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 389 HIS 0.004 0.001 HIS A 122 PHE 0.015 0.001 PHE E 352 TYR 0.034 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 164 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 153 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.7670 (mtt180) cc_final: 0.7277 (mpt180) REVERT: A 391 ARG cc_start: 0.7391 (ttm-80) cc_final: 0.7015 (ttt180) REVERT: B 253 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8001 (mm-30) REVERT: B 390 ARG cc_start: 0.7489 (mtt180) cc_final: 0.6990 (mpt180) REVERT: B 391 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6877 (tmt170) REVERT: C 267 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8380 (mt-10) REVERT: C 390 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6993 (mpt180) REVERT: C 391 ARG cc_start: 0.7315 (ttm-80) cc_final: 0.6848 (tmt170) REVERT: D 261 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7608 (mp0) REVERT: D 297 GLU cc_start: 0.8334 (tt0) cc_final: 0.7929 (tp30) REVERT: D 390 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7194 (mpt180) REVERT: D 391 ARG cc_start: 0.7379 (ttm-80) cc_final: 0.6775 (tmt170) REVERT: E 390 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7238 (mpt180) REVERT: E 391 ARG cc_start: 0.7354 (ttm-80) cc_final: 0.6970 (ttt180) outliers start: 11 outliers final: 8 residues processed: 162 average time/residue: 1.1787 time to fit residues: 210.1082 Evaluate side-chains 157 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 130 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3475 r_free = 0.3475 target = 0.103666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077785 restraints weight = 55168.497| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.08 r_work: 0.2797 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13160 Z= 0.145 Angle : 0.480 9.523 17790 Z= 0.243 Chirality : 0.039 0.273 2060 Planarity : 0.004 0.053 2250 Dihedral : 3.567 15.410 1740 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.63 % Allowed : 14.11 % Favored : 85.26 % 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: 3.76 (0.21), residues: 1595 helix: 3.15 (0.15), residues: 1085 sheet: 1.80 (0.39), residues: 145 loop : 0.67 (0.39), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 389 HIS 0.004 0.001 HIS D 122 PHE 0.017 0.001 PHE E 352 TYR 0.031 0.002 TYR B 154 ARG 0.011 0.000 ARG E 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4534.82 seconds wall clock time: 80 minutes 55.37 seconds (4855.37 seconds total)