Starting phenix.real_space_refine on Wed Mar 4 18:05:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plh_13489/03_2026/7plh_13489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plh_13489/03_2026/7plh_13489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7plh_13489/03_2026/7plh_13489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plh_13489/03_2026/7plh_13489_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plh_13489/03_2026/7plh_13489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plh_13489/03_2026/7plh_13489.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 P 65 5.49 5 Mg 7 5.21 5 S 56 5.16 5 C 9594 2.51 5 N 2835 2.21 5 O 2985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 133 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15542 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2056 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2060 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 250} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "I" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 451 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.41, per 1000 atoms: 0.22 Number of scatterers: 15542 At special positions: 0 Unit cell: (128.05, 139.1, 115.7, 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) S 56 16.00 P 65 15.00 Mg 7 11.99 O 2985 8.00 N 2835 7.00 C 9594 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 680.8 milliseconds 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 7 sheets defined 62.4% alpha, 5.8% beta 16 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 17 through 30 Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS A 77 " --> pdb=" O TYR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 150 through 165 removed outlier: 3.682A pdb=" N PHE A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 155 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 3.699A pdb=" N ALA A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 226 through 238 removed outlier: 3.538A pdb=" N GLU A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.865A pdb=" N GLU A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU A 268 " --> pdb=" O ASP A 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 30 Processing helix chain 'B' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA B 69 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B 77 " --> pdb=" O TYR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA B 178 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU B 238 " --> pdb=" O THR B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 Processing helix chain 'B' and resid 264 through 274 removed outlier: 3.637A pdb=" N LEU B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 30 Processing helix chain 'C' and resid 36 through 52 removed outlier: 3.522A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 113 Processing helix chain 'C' and resid 121 through 136 Processing helix chain 'C' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE C 154 " --> pdb=" O LYS C 150 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA C 155 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 3.697A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU C 188 " --> pdb=" O GLU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 226 through 238 removed outlier: 3.535A pdb=" N GLU C 238 " --> pdb=" O THR C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 Processing helix chain 'C' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 30 Processing helix chain 'D' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA D 52 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS D 77 " --> pdb=" O TYR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 121 through 136 Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.700A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.664A pdb=" N GLU D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 30 Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA E 52 " --> pdb=" O GLY E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS E 77 " --> pdb=" O TYR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 121 through 136 Processing helix chain 'E' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASP E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.665A pdb=" N GLU E 188 " --> pdb=" O GLU E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 Processing helix chain 'E' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 274 removed outlier: 3.636A pdb=" N LEU E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 30 Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.522A pdb=" N ALA F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS F 77 " --> pdb=" O TYR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE F 154 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA F 155 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 removed outlier: 3.664A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 215 Processing helix chain 'F' and resid 226 through 238 removed outlier: 3.537A pdb=" N GLU F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 264 through 274 removed outlier: 3.637A pdb=" N LEU F 268 " --> pdb=" O ASP F 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 30 Processing helix chain 'G' and resid 36 through 52 removed outlier: 3.523A pdb=" N ALA G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 removed outlier: 3.658A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS G 77 " --> pdb=" O TYR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 136 Processing helix chain 'G' and resid 150 through 165 removed outlier: 3.681A pdb=" N PHE G 154 " --> pdb=" O LYS G 150 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA G 155 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 3.698A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 190 removed outlier: 3.664A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.536A pdb=" N GLU G 238 " --> pdb=" O THR G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 274 removed outlier: 3.637A pdb=" N LEU G 268 " --> pdb=" O ASP G 264 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.424A pdb=" N LEU A 141 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL A 171 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE A 143 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS A 56 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N GLY A 172 " --> pdb=" O CYS A 56 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL A 58 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL B 92 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 141 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL B 171 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 143 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS B 56 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY B 172 " --> pdb=" O CYS B 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 58 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 141 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE C 143 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS C 56 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY C 172 " --> pdb=" O CYS C 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.565A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS D 56 " --> pdb=" O LEU D 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY D 172 " --> pdb=" O CYS D 56 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU E 141 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL E 171 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE E 143 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS E 56 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY E 172 " --> pdb=" O CYS E 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.566A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU F 141 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL F 171 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE F 143 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N CYS F 56 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N GLY F 172 " --> pdb=" O CYS F 56 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.564A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL G 171 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE G 143 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS G 56 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N GLY G 172 " --> pdb=" O CYS G 56 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL G 58 " --> pdb=" O GLY G 172 " (cutoff:3.500A) 731 hydrogen bonds defined for protein. 2193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2492 1.30 - 1.42: 3898 1.42 - 1.55: 9226 1.55 - 1.68: 160 1.68 - 1.80: 91 Bond restraints: 15867 Sorted by residual: bond pdb=" O3A ANP A 301 " pdb=" PB ANP A 301 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP F 301 " pdb=" PB ANP F 301 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP G 301 " pdb=" PB ANP G 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3A ANP E 301 " pdb=" PB ANP E 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.18e+01 ... (remaining 15862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 21085 4.84 - 9.69: 462 9.69 - 14.53: 42 14.53 - 19.38: 1 19.38 - 24.22: 7 Bond angle restraints: 21597 Sorted by residual: angle pdb=" O3' DA H 13 " pdb=" C3' DA H 13 " pdb=" C2' DA H 13 " ideal model delta sigma weight residual 111.50 96.51 14.99 1.50e+00 4.44e-01 9.99e+01 angle pdb=" N LEU E 244 " pdb=" CA LEU E 244 " pdb=" C LEU E 244 " ideal model delta sigma weight residual 111.14 100.41 10.73 1.08e+00 8.57e-01 9.87e+01 angle pdb=" N PHE F 204 " pdb=" CA PHE F 204 " pdb=" C PHE F 204 " ideal model delta sigma weight residual 111.36 101.95 9.41 1.09e+00 8.42e-01 7.46e+01 angle pdb=" N PHE B 204 " pdb=" CA PHE B 204 " pdb=" C PHE B 204 " ideal model delta sigma weight residual 111.36 101.96 9.40 1.09e+00 8.42e-01 7.43e+01 angle pdb=" N LEU B 244 " pdb=" CA LEU B 244 " pdb=" C LEU B 244 " ideal model delta sigma weight residual 111.69 101.09 10.60 1.23e+00 6.61e-01 7.43e+01 ... (remaining 21592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 8455 24.16 - 48.33: 919 48.33 - 72.49: 383 72.49 - 96.66: 72 96.66 - 120.82: 7 Dihedral angle restraints: 9836 sinusoidal: 4558 harmonic: 5278 Sorted by residual: dihedral pdb=" C ARG C 76 " pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" CB ARG C 76 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C ARG F 76 " pdb=" N ARG F 76 " pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " ideal model delta harmonic sigma weight residual -122.60 -109.42 -13.18 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C ARG G 76 " pdb=" N ARG G 76 " pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " ideal model delta harmonic sigma weight residual -122.60 -109.43 -13.17 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 9833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1919 0.103 - 0.205: 357 0.205 - 0.308: 120 0.308 - 0.410: 19 0.410 - 0.513: 15 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CA ARG F 76 " pdb=" N ARG F 76 " pdb=" C ARG F 76 " pdb=" CB ARG F 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA ARG D 76 " pdb=" N ARG D 76 " pdb=" C ARG D 76 " pdb=" CB ARG D 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA ARG B 76 " pdb=" N ARG B 76 " pdb=" C ARG B 76 " pdb=" CB ARG B 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 2427 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 241 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C ILE A 241 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE A 241 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY A 242 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 242 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLY C 242 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY C 242 " -0.034 2.00e-02 2.50e+03 pdb=" N ARG C 243 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 242 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLY F 242 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY F 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG F 243 " 0.020 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 121 2.50 - 3.10: 11515 3.10 - 3.70: 24471 3.70 - 4.30: 34724 4.30 - 4.90: 55938 Nonbonded interactions: 126769 Sorted by model distance: nonbonded pdb=" O1B ANP A 301 " pdb="MG MG A 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP B 301 " pdb="MG MG B 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP D 301 " pdb="MG MG D 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP F 301 " pdb="MG MG F 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP G 301 " pdb="MG MG G 302 " model vdw 1.902 2.170 ... (remaining 126764 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 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'B' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'C' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'D' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = (chain 'E' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) selection = chain 'F' selection = (chain 'G' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 302)) } ncs_group { reference = chain 'H' selection = chain 'I' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.130 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: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.750 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.011 0.158 15867 Z= 0.675 Angle : 1.667 24.221 21597 Z= 1.103 Chirality : 0.101 0.513 2430 Planarity : 0.006 0.054 2577 Dihedral : 22.702 120.821 6420 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 8.98 % Allowed : 12.10 % Favored : 78.92 % Cbeta Deviations : 0.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.18), residues: 1806 helix: -0.98 (0.14), residues: 1078 sheet: -1.95 (0.49), residues: 119 loop : -2.19 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 57 TYR 0.012 0.002 TYR D 275 PHE 0.017 0.002 PHE B 196 TRP 0.020 0.003 TRP G 45 HIS 0.004 0.002 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.01124 (15867) covalent geometry : angle 1.66746 (21597) hydrogen bonds : bond 0.16048 ( 763) hydrogen bonds : angle 6.59997 ( 2257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 611 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASN cc_start: 0.8135 (m-40) cc_final: 0.7852 (m-40) REVERT: A 234 THR cc_start: 0.9384 (m) cc_final: 0.9019 (p) REVERT: B 209 GLU cc_start: 0.7632 (tp30) cc_final: 0.6916 (tp30) REVERT: C 32 SER cc_start: 0.8442 (t) cc_final: 0.8230 (t) REVERT: C 260 LEU cc_start: 0.6918 (mp) cc_final: 0.6371 (tp) REVERT: D 250 GLU cc_start: 0.8359 (tp30) cc_final: 0.8105 (tp30) REVERT: E 153 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (t) REVERT: E 206 ASN cc_start: 0.8150 (m-40) cc_final: 0.7746 (t0) REVERT: F 163 ASP cc_start: 0.7160 (m-30) cc_final: 0.6427 (m-30) REVERT: G 63 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5674 (mtm180) REVERT: G 234 THR cc_start: 0.8845 (m) cc_final: 0.8435 (p) REVERT: G 241 ILE cc_start: 0.8907 (mm) cc_final: 0.8694 (mp) outliers start: 135 outliers final: 17 residues processed: 697 average time/residue: 0.1785 time to fit residues: 164.7219 Evaluate side-chains 337 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 318 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 276 LYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain G residue 63 ARG Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 77 HIS B 185 GLN B 213 GLN D 43 HIS ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 81 GLN G 37 GLN G 43 HIS G 97 HIS G 206 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.108216 restraints weight = 26041.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111368 restraints weight = 13940.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113492 restraints weight = 9517.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114836 restraints weight = 7491.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.115678 restraints weight = 6470.425| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15867 Z= 0.236 Angle : 0.748 10.411 21597 Z= 0.387 Chirality : 0.045 0.166 2430 Planarity : 0.005 0.047 2577 Dihedral : 20.916 129.152 2822 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.39 % Allowed : 20.68 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.19), residues: 1806 helix: 0.30 (0.15), residues: 1113 sheet: -1.68 (0.69), residues: 70 loop : -1.74 (0.22), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 57 TYR 0.015 0.002 TYR A 93 PHE 0.018 0.002 PHE D 196 TRP 0.015 0.002 TRP D 211 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00557 (15867) covalent geometry : angle 0.74815 (21597) hydrogen bonds : bond 0.04990 ( 763) hydrogen bonds : angle 3.97226 ( 2257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 341 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7259 (m-30) cc_final: 0.6980 (m-30) REVERT: A 216 LEU cc_start: 0.7743 (mt) cc_final: 0.7310 (mt) REVERT: B 37 GLN cc_start: 0.7904 (tp40) cc_final: 0.7418 (tm-30) REVERT: C 32 SER cc_start: 0.9158 (t) cc_final: 0.8908 (t) REVERT: C 44 ASP cc_start: 0.7666 (m-30) cc_final: 0.7462 (m-30) REVERT: C 163 ASP cc_start: 0.8111 (m-30) cc_final: 0.7868 (m-30) REVERT: C 229 MET cc_start: 0.8145 (mmm) cc_final: 0.7503 (mmt) REVERT: D 81 GLN cc_start: 0.6946 (mp10) cc_final: 0.6701 (mt0) REVERT: D 98 GLN cc_start: 0.8415 (tp40) cc_final: 0.8073 (tp40) REVERT: D 246 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7695 (mt-10) REVERT: E 63 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8076 (tpt170) REVERT: E 188 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7646 (mm-30) REVERT: E 214 MET cc_start: 0.8433 (tpp) cc_final: 0.8089 (tpp) REVERT: F 36 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8099 (pt) REVERT: F 159 ASP cc_start: 0.8131 (m-30) cc_final: 0.7609 (m-30) REVERT: F 162 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7603 (mt-10) REVERT: F 163 ASP cc_start: 0.7870 (m-30) cc_final: 0.7534 (m-30) REVERT: G 196 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: G 210 MET cc_start: 0.8233 (tpp) cc_final: 0.7720 (tpp) REVERT: G 241 ILE cc_start: 0.9236 (mm) cc_final: 0.8865 (mp) REVERT: G 256 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8770 (mm) REVERT: G 276 LYS cc_start: 0.6640 (OUTLIER) cc_final: 0.6169 (ttmt) outliers start: 81 outliers final: 56 residues processed: 406 average time/residue: 0.1417 time to fit residues: 80.6445 Evaluate side-chains 323 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 261 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 211 TRP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 276 LYS Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 136 optimal weight: 0.0770 chunk 97 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 98 GLN E 43 HIS E 77 HIS E 206 ASN F 43 HIS F 77 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111361 restraints weight = 25541.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114508 restraints weight = 12987.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116605 restraints weight = 8567.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.117963 restraints weight = 6604.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.118682 restraints weight = 5616.757| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15867 Z= 0.123 Angle : 0.609 11.378 21597 Z= 0.315 Chirality : 0.040 0.157 2430 Planarity : 0.004 0.044 2577 Dihedral : 19.059 119.308 2805 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.45 % Allowed : 22.14 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 1806 helix: 0.94 (0.15), residues: 1113 sheet: -1.76 (0.51), residues: 105 loop : -1.66 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 249 TYR 0.013 0.001 TYR A 93 PHE 0.021 0.001 PHE E 106 TRP 0.017 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00274 (15867) covalent geometry : angle 0.60900 (21597) hydrogen bonds : bond 0.04158 ( 763) hydrogen bonds : angle 3.58973 ( 2257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 307 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7220 (m-30) cc_final: 0.6885 (m-30) REVERT: A 185 GLN cc_start: 0.7905 (mt0) cc_final: 0.7635 (mt0) REVERT: A 250 GLU cc_start: 0.8565 (tp30) cc_final: 0.8169 (mt-10) REVERT: C 44 ASP cc_start: 0.7688 (m-30) cc_final: 0.7393 (m-30) REVERT: C 229 MET cc_start: 0.7940 (mmm) cc_final: 0.7398 (mmt) REVERT: D 81 GLN cc_start: 0.6995 (mp10) cc_final: 0.6698 (mt0) REVERT: D 85 ARG cc_start: 0.7643 (mmm160) cc_final: 0.6846 (ttt180) REVERT: D 115 TYR cc_start: 0.7462 (m-80) cc_final: 0.7183 (m-80) REVERT: D 246 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7728 (mt-10) REVERT: E 40 LYS cc_start: 0.8625 (tppt) cc_final: 0.8292 (tptp) REVERT: E 63 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7756 (mpt180) REVERT: E 210 MET cc_start: 0.8315 (tpp) cc_final: 0.8096 (ttm) REVERT: F 36 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7867 (pt) REVERT: F 162 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: G 37 GLN cc_start: 0.7485 (mm110) cc_final: 0.7212 (mm-40) REVERT: G 241 ILE cc_start: 0.9225 (mm) cc_final: 0.8844 (mp) REVERT: G 256 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8749 (mm) outliers start: 67 outliers final: 40 residues processed: 355 average time/residue: 0.1286 time to fit residues: 66.6768 Evaluate side-chains 310 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 40 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 98 optimal weight: 20.0000 chunk 143 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN D 97 HIS D 98 GLN F 43 HIS F 77 HIS G 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.134424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.107582 restraints weight = 25781.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.110648 restraints weight = 13754.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112724 restraints weight = 9300.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114065 restraints weight = 7288.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.114886 restraints weight = 6253.659| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15867 Z= 0.129 Angle : 0.591 10.633 21597 Z= 0.304 Chirality : 0.040 0.138 2430 Planarity : 0.004 0.048 2577 Dihedral : 17.902 116.792 2792 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.65 % Allowed : 22.87 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.20), residues: 1806 helix: 1.22 (0.15), residues: 1113 sheet: -2.10 (0.37), residues: 175 loop : -1.33 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 27 TYR 0.011 0.001 TYR A 93 PHE 0.021 0.001 PHE E 204 TRP 0.021 0.002 TRP G 211 HIS 0.006 0.001 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00295 (15867) covalent geometry : angle 0.59121 (21597) hydrogen bonds : bond 0.03853 ( 763) hydrogen bonds : angle 3.41341 ( 2257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 296 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7144 (m-30) cc_final: 0.6746 (m-30) REVERT: A 250 GLU cc_start: 0.8589 (tp30) cc_final: 0.8216 (mt-10) REVERT: B 210 MET cc_start: 0.8213 (ttm) cc_final: 0.7898 (ttp) REVERT: B 245 ASP cc_start: 0.8425 (t0) cc_final: 0.8094 (t0) REVERT: C 40 LYS cc_start: 0.8669 (tptm) cc_final: 0.8299 (tptp) REVERT: C 44 ASP cc_start: 0.7698 (m-30) cc_final: 0.7198 (m-30) REVERT: C 229 MET cc_start: 0.7969 (mmm) cc_final: 0.7476 (mmt) REVERT: C 273 LYS cc_start: 0.7816 (pttt) cc_final: 0.7545 (tmtt) REVERT: D 81 GLN cc_start: 0.7060 (mp10) cc_final: 0.6770 (mt0) REVERT: D 85 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7023 (mmt90) REVERT: D 232 ILE cc_start: 0.8478 (tt) cc_final: 0.8244 (tp) REVERT: D 246 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7741 (mt-10) REVERT: E 63 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7845 (mpt180) REVERT: E 210 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7892 (ttm) REVERT: E 213 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: E 229 MET cc_start: 0.7592 (mmp) cc_final: 0.7044 (mmm) REVERT: F 36 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7688 (pp) REVERT: F 127 ASP cc_start: 0.7537 (m-30) cc_final: 0.7321 (m-30) REVERT: F 152 GLU cc_start: 0.8080 (mp0) cc_final: 0.7769 (mp0) REVERT: G 37 GLN cc_start: 0.7475 (mm110) cc_final: 0.7225 (mm-40) REVERT: G 185 GLN cc_start: 0.8312 (mp10) cc_final: 0.8009 (mt0) REVERT: G 241 ILE cc_start: 0.9245 (mm) cc_final: 0.8856 (mp) REVERT: G 246 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7144 (tt0) REVERT: G 256 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8749 (mm) outliers start: 70 outliers final: 50 residues processed: 347 average time/residue: 0.1274 time to fit residues: 64.8865 Evaluate side-chains 317 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 262 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 137 optimal weight: 0.0060 chunk 74 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN C 77 HIS D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS F 77 HIS G 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107801 restraints weight = 25676.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110797 restraints weight = 13345.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.112810 restraints weight = 8907.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114112 restraints weight = 6903.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.114930 restraints weight = 5879.304| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15867 Z= 0.156 Angle : 0.598 10.242 21597 Z= 0.312 Chirality : 0.041 0.161 2430 Planarity : 0.004 0.044 2577 Dihedral : 17.542 115.237 2790 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.39 % Allowed : 24.87 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1806 helix: 1.36 (0.16), residues: 1113 sheet: -2.06 (0.37), residues: 175 loop : -1.17 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 27 TYR 0.012 0.001 TYR A 93 PHE 0.021 0.001 PHE E 106 TRP 0.021 0.002 TRP G 211 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00368 (15867) covalent geometry : angle 0.59817 (21597) hydrogen bonds : bond 0.03996 ( 763) hydrogen bonds : angle 3.35508 ( 2257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 TYR cc_start: 0.7966 (m-80) cc_final: 0.7735 (m-80) REVERT: A 159 ASP cc_start: 0.7141 (m-30) cc_final: 0.6725 (m-30) REVERT: A 250 GLU cc_start: 0.8654 (tp30) cc_final: 0.8326 (mt-10) REVERT: B 37 GLN cc_start: 0.7896 (tp40) cc_final: 0.7635 (tp-100) REVERT: B 115 TYR cc_start: 0.8164 (m-80) cc_final: 0.7854 (m-10) REVERT: C 40 LYS cc_start: 0.8674 (tptm) cc_final: 0.8443 (tptp) REVERT: C 44 ASP cc_start: 0.7716 (m-30) cc_final: 0.7325 (m-30) REVERT: C 229 MET cc_start: 0.7947 (mmm) cc_final: 0.7475 (mmt) REVERT: D 81 GLN cc_start: 0.7219 (mp10) cc_final: 0.6926 (mt0) REVERT: D 85 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7029 (ttt180) REVERT: D 98 GLN cc_start: 0.8463 (tp40) cc_final: 0.8186 (tp40) REVERT: D 232 ILE cc_start: 0.8605 (tt) cc_final: 0.8391 (tp) REVERT: D 246 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7771 (mt-10) REVERT: D 269 GLN cc_start: 0.8787 (mm110) cc_final: 0.8551 (mp10) REVERT: E 27 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7929 (ttp80) REVERT: E 63 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7955 (mpt180) REVERT: E 213 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8109 (mp10) REVERT: F 127 ASP cc_start: 0.7567 (m-30) cc_final: 0.7354 (m-30) REVERT: G 206 ASN cc_start: 0.8316 (m-40) cc_final: 0.7866 (m110) REVERT: G 241 ILE cc_start: 0.9265 (mm) cc_final: 0.8902 (mp) REVERT: G 246 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7341 (tt0) REVERT: G 256 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8753 (mm) outliers start: 66 outliers final: 47 residues processed: 335 average time/residue: 0.1327 time to fit residues: 64.3220 Evaluate side-chains 319 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.133255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106802 restraints weight = 25635.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109855 restraints weight = 13587.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.111852 restraints weight = 9183.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113149 restraints weight = 7207.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113585 restraints weight = 6193.567| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15867 Z= 0.130 Angle : 0.573 10.733 21597 Z= 0.298 Chirality : 0.040 0.150 2430 Planarity : 0.004 0.041 2577 Dihedral : 17.296 111.279 2788 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.26 % Allowed : 24.40 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 1806 helix: 1.42 (0.16), residues: 1113 sheet: -2.09 (0.36), residues: 175 loop : -1.12 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 27 TYR 0.011 0.001 TYR A 93 PHE 0.031 0.001 PHE E 106 TRP 0.014 0.002 TRP A 20 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00302 (15867) covalent geometry : angle 0.57266 (21597) hydrogen bonds : bond 0.03751 ( 763) hydrogen bonds : angle 3.31120 ( 2257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 TYR cc_start: 0.7938 (m-80) cc_final: 0.7681 (m-80) REVERT: A 145 GLU cc_start: 0.7981 (tp30) cc_final: 0.7751 (tp30) REVERT: A 159 ASP cc_start: 0.7143 (m-30) cc_final: 0.6723 (m-30) REVERT: A 182 ARG cc_start: 0.7482 (mtm110) cc_final: 0.7248 (mtm180) REVERT: A 250 GLU cc_start: 0.8614 (tp30) cc_final: 0.8156 (mt-10) REVERT: B 115 TYR cc_start: 0.8160 (m-80) cc_final: 0.7812 (m-80) REVERT: B 245 ASP cc_start: 0.8475 (t70) cc_final: 0.8033 (t0) REVERT: C 40 LYS cc_start: 0.8649 (tptm) cc_final: 0.8412 (tptp) REVERT: C 44 ASP cc_start: 0.7691 (m-30) cc_final: 0.7271 (m-30) REVERT: C 229 MET cc_start: 0.7956 (mmm) cc_final: 0.7558 (mmt) REVERT: C 250 GLU cc_start: 0.8054 (tp30) cc_final: 0.7815 (tp30) REVERT: D 31 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7814 (mttm) REVERT: D 75 TYR cc_start: 0.8470 (m-10) cc_final: 0.8249 (m-10) REVERT: D 81 GLN cc_start: 0.7309 (mp10) cc_final: 0.6934 (mt0) REVERT: D 85 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7221 (mmt90) REVERT: D 232 ILE cc_start: 0.8617 (tt) cc_final: 0.8401 (tp) REVERT: D 246 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7735 (mt-10) REVERT: E 27 ARG cc_start: 0.8321 (ttp80) cc_final: 0.7971 (ttp80) REVERT: E 63 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7893 (mpt180) REVERT: E 213 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8111 (mp10) REVERT: E 229 MET cc_start: 0.7643 (mmp) cc_final: 0.6965 (mmm) REVERT: F 127 ASP cc_start: 0.7575 (m-30) cc_final: 0.7354 (m-30) REVERT: G 206 ASN cc_start: 0.8397 (m-40) cc_final: 0.7919 (m110) REVERT: G 240 TYR cc_start: 0.8629 (m-10) cc_final: 0.8352 (m-10) REVERT: G 241 ILE cc_start: 0.9262 (mm) cc_final: 0.8888 (mp) REVERT: G 246 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7388 (tt0) REVERT: G 256 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8827 (mm) outliers start: 64 outliers final: 48 residues processed: 340 average time/residue: 0.1369 time to fit residues: 67.7181 Evaluate side-chains 319 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN F 77 HIS F 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106275 restraints weight = 25605.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109334 restraints weight = 13555.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111365 restraints weight = 9151.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.112668 restraints weight = 7173.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113538 restraints weight = 6160.969| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.6393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15867 Z= 0.124 Angle : 0.567 10.454 21597 Z= 0.296 Chirality : 0.040 0.182 2430 Planarity : 0.004 0.055 2577 Dihedral : 17.118 107.835 2788 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.45 % Allowed : 25.73 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1806 helix: 1.52 (0.16), residues: 1113 sheet: -2.06 (0.35), residues: 175 loop : -1.03 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 53 TYR 0.018 0.001 TYR C 73 PHE 0.018 0.001 PHE E 106 TRP 0.013 0.002 TRP A 20 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00286 (15867) covalent geometry : angle 0.56680 (21597) hydrogen bonds : bond 0.03660 ( 763) hydrogen bonds : angle 3.28774 ( 2257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7303 (ttmt) REVERT: A 115 TYR cc_start: 0.7919 (m-80) cc_final: 0.7659 (m-80) REVERT: A 159 ASP cc_start: 0.7090 (m-30) cc_final: 0.6649 (m-30) REVERT: A 250 GLU cc_start: 0.8634 (tp30) cc_final: 0.8171 (mt-10) REVERT: B 115 TYR cc_start: 0.8162 (m-80) cc_final: 0.7849 (m-80) REVERT: C 40 LYS cc_start: 0.8655 (tptm) cc_final: 0.8409 (tptp) REVERT: C 44 ASP cc_start: 0.7737 (m-30) cc_final: 0.7288 (m-30) REVERT: C 124 ASP cc_start: 0.7600 (t0) cc_final: 0.6884 (m-30) REVERT: C 229 MET cc_start: 0.7953 (mmm) cc_final: 0.7587 (mmt) REVERT: D 31 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7826 (mttm) REVERT: D 75 TYR cc_start: 0.8477 (m-10) cc_final: 0.8255 (m-10) REVERT: D 81 GLN cc_start: 0.7341 (mp10) cc_final: 0.7015 (mt0) REVERT: D 85 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7278 (mmt90) REVERT: D 232 ILE cc_start: 0.8650 (tt) cc_final: 0.8380 (tp) REVERT: D 246 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7737 (mt-10) REVERT: E 27 ARG cc_start: 0.8293 (ttp80) cc_final: 0.7959 (ttp80) REVERT: E 63 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7838 (mpt180) REVERT: E 85 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7762 (mmm-85) REVERT: E 213 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: E 229 MET cc_start: 0.7786 (mmp) cc_final: 0.6985 (mmm) REVERT: F 27 ARG cc_start: 0.6593 (tmm-80) cc_final: 0.6389 (tmm-80) REVERT: F 127 ASP cc_start: 0.7588 (m-30) cc_final: 0.7365 (m-30) REVERT: F 231 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7812 (ttm-80) REVERT: G 116 ARG cc_start: 0.7838 (tpp-160) cc_final: 0.7565 (tpp-160) REVERT: G 241 ILE cc_start: 0.9242 (mm) cc_final: 0.8850 (mp) REVERT: G 246 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7403 (tt0) REVERT: G 256 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8849 (mm) outliers start: 67 outliers final: 50 residues processed: 327 average time/residue: 0.1364 time to fit residues: 63.7417 Evaluate side-chains 325 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 210 MET Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 118 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 50 optimal weight: 20.0000 chunk 147 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 77 HIS D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN F 77 HIS G 43 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103726 restraints weight = 26104.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106671 restraints weight = 14080.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108660 restraints weight = 9634.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109945 restraints weight = 7593.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.110651 restraints weight = 6550.065| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15867 Z= 0.180 Angle : 0.621 9.799 21597 Z= 0.323 Chirality : 0.042 0.188 2430 Planarity : 0.004 0.053 2577 Dihedral : 17.116 105.267 2786 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.45 % Allowed : 26.46 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1806 helix: 1.46 (0.16), residues: 1106 sheet: -2.19 (0.34), residues: 175 loop : -1.10 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 53 TYR 0.016 0.002 TYR C 73 PHE 0.011 0.001 PHE F 204 TRP 0.022 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00428 (15867) covalent geometry : angle 0.62065 (21597) hydrogen bonds : bond 0.04083 ( 763) hydrogen bonds : angle 3.41549 ( 2257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7198 (m-30) cc_final: 0.6791 (m-30) REVERT: A 250 GLU cc_start: 0.8658 (tp30) cc_final: 0.8321 (tt0) REVERT: B 37 GLN cc_start: 0.7871 (tp40) cc_final: 0.7653 (tp-100) REVERT: B 115 TYR cc_start: 0.8227 (m-80) cc_final: 0.7887 (m-80) REVERT: C 44 ASP cc_start: 0.7729 (m-30) cc_final: 0.7442 (m-30) REVERT: C 229 MET cc_start: 0.7994 (mmm) cc_final: 0.7625 (mmt) REVERT: C 246 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7756 (mm-30) REVERT: D 33 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7569 (tp) REVERT: D 75 TYR cc_start: 0.8492 (m-10) cc_final: 0.8269 (m-10) REVERT: D 81 GLN cc_start: 0.7438 (mp10) cc_final: 0.7059 (mt0) REVERT: D 85 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7387 (mmt90) REVERT: D 246 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7805 (mt-10) REVERT: E 27 ARG cc_start: 0.8368 (ttp80) cc_final: 0.7892 (ttp80) REVERT: E 63 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7961 (mpt180) REVERT: E 246 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6512 (mt-10) REVERT: F 127 ASP cc_start: 0.7636 (m-30) cc_final: 0.7386 (m-30) REVERT: F 231 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7887 (ttm-80) REVERT: F 246 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7468 (mt-10) REVERT: G 116 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7563 (tpp-160) REVERT: G 185 GLN cc_start: 0.8533 (mt0) cc_final: 0.8318 (mt0) REVERT: G 241 ILE cc_start: 0.9262 (mm) cc_final: 0.8895 (mp) REVERT: G 246 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7343 (tt0) REVERT: G 256 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8890 (mm) outliers start: 67 outliers final: 56 residues processed: 329 average time/residue: 0.1353 time to fit residues: 64.1761 Evaluate side-chains 326 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 266 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.0020 chunk 185 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN C 213 GLN D 77 HIS D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS G 43 HIS G 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.106065 restraints weight = 25749.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.109065 restraints weight = 13845.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.111036 restraints weight = 9424.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.112310 restraints weight = 7423.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113106 restraints weight = 6400.252| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15867 Z= 0.132 Angle : 0.601 10.631 21597 Z= 0.312 Chirality : 0.041 0.183 2430 Planarity : 0.004 0.048 2577 Dihedral : 16.939 100.213 2786 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.12 % Allowed : 26.80 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1806 helix: 1.52 (0.16), residues: 1106 sheet: -2.12 (0.34), residues: 175 loop : -1.05 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 85 TYR 0.013 0.001 TYR C 73 PHE 0.013 0.001 PHE D 106 TRP 0.017 0.002 TRP B 20 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00307 (15867) covalent geometry : angle 0.60136 (21597) hydrogen bonds : bond 0.03765 ( 763) hydrogen bonds : angle 3.38334 ( 2257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 283 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7158 (m-30) cc_final: 0.6765 (m-30) REVERT: A 250 GLU cc_start: 0.8623 (tp30) cc_final: 0.8339 (mt-10) REVERT: B 115 TYR cc_start: 0.8178 (m-80) cc_final: 0.7838 (m-80) REVERT: C 44 ASP cc_start: 0.7633 (m-30) cc_final: 0.7413 (m-30) REVERT: C 124 ASP cc_start: 0.7655 (t0) cc_final: 0.6859 (m-30) REVERT: C 229 MET cc_start: 0.7942 (mmm) cc_final: 0.7623 (mmt) REVERT: C 246 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7951 (mm-30) REVERT: D 75 TYR cc_start: 0.8439 (m-10) cc_final: 0.8233 (m-10) REVERT: D 81 GLN cc_start: 0.7487 (mp10) cc_final: 0.7270 (mt0) REVERT: D 85 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7476 (mmt90) REVERT: D 246 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7810 (mt-10) REVERT: E 27 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8055 (ttp80) REVERT: E 63 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7819 (mpt180) REVERT: E 213 GLN cc_start: 0.8378 (pm20) cc_final: 0.8018 (pm20) REVERT: E 229 MET cc_start: 0.7673 (mmp) cc_final: 0.7041 (mmm) REVERT: E 246 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6501 (mt-10) REVERT: F 127 ASP cc_start: 0.7595 (m-30) cc_final: 0.7368 (m-30) REVERT: F 231 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7864 (ttm-80) REVERT: F 246 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7410 (mt-10) REVERT: F 275 TYR cc_start: 0.8071 (m-80) cc_final: 0.7783 (m-80) REVERT: G 116 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7576 (tpp-160) REVERT: G 241 ILE cc_start: 0.9265 (mm) cc_final: 0.8883 (mp) outliers start: 62 outliers final: 48 residues processed: 325 average time/residue: 0.1287 time to fit residues: 60.7434 Evaluate side-chains 319 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 77 HIS D 206 ASN D 213 GLN F 77 HIS G 43 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.104417 restraints weight = 25980.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107399 restraints weight = 13975.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.109391 restraints weight = 9470.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110539 restraints weight = 7432.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111420 restraints weight = 6461.437| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15867 Z= 0.186 Angle : 0.639 10.226 21597 Z= 0.330 Chirality : 0.043 0.178 2430 Planarity : 0.005 0.057 2577 Dihedral : 17.000 99.529 2786 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.72 % Allowed : 26.86 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1806 helix: 1.42 (0.16), residues: 1106 sheet: -2.23 (0.33), residues: 175 loop : -1.10 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 254 TYR 0.014 0.002 TYR C 73 PHE 0.018 0.002 PHE E 106 TRP 0.030 0.002 TRP G 211 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00444 (15867) covalent geometry : angle 0.63883 (21597) hydrogen bonds : bond 0.04143 ( 763) hydrogen bonds : angle 3.49647 ( 2257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7145 (ttmt) REVERT: A 159 ASP cc_start: 0.7212 (m-30) cc_final: 0.6801 (m-30) REVERT: A 250 GLU cc_start: 0.8660 (tp30) cc_final: 0.8312 (mt-10) REVERT: B 115 TYR cc_start: 0.8236 (m-80) cc_final: 0.7883 (m-80) REVERT: C 44 ASP cc_start: 0.7655 (m-30) cc_final: 0.7453 (m-30) REVERT: C 229 MET cc_start: 0.7961 (mmm) cc_final: 0.7639 (mmt) REVERT: C 246 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7929 (mm-30) REVERT: D 33 ILE cc_start: 0.7925 (mm) cc_final: 0.7571 (tp) REVERT: D 58 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8808 (m) REVERT: D 75 TYR cc_start: 0.8475 (m-10) cc_final: 0.8262 (m-10) REVERT: D 85 ARG cc_start: 0.8117 (mmm160) cc_final: 0.7432 (ttt180) REVERT: D 232 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8519 (tp) REVERT: D 246 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7831 (mt-10) REVERT: E 27 ARG cc_start: 0.8423 (ttp80) cc_final: 0.7953 (ttp80) REVERT: E 40 LYS cc_start: 0.8811 (tptp) cc_final: 0.8605 (tppt) REVERT: E 63 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7971 (mpt180) REVERT: E 213 GLN cc_start: 0.8363 (pm20) cc_final: 0.8004 (pm20) REVERT: E 229 MET cc_start: 0.7698 (mmp) cc_final: 0.7081 (mmm) REVERT: E 246 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6495 (mt-10) REVERT: F 196 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: F 231 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7866 (ttm-80) REVERT: F 246 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7454 (mt-10) REVERT: G 116 ARG cc_start: 0.7948 (tpp-160) cc_final: 0.7622 (tpp-160) REVERT: G 185 GLN cc_start: 0.8525 (mt0) cc_final: 0.8319 (mt0) REVERT: G 241 ILE cc_start: 0.9294 (mm) cc_final: 0.8914 (mp) REVERT: G 257 SER cc_start: 0.9050 (t) cc_final: 0.8688 (m) outliers start: 56 outliers final: 46 residues processed: 317 average time/residue: 0.1392 time to fit residues: 63.3467 Evaluate side-chains 316 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 8.9990 chunk 152 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 176 optimal weight: 30.0000 chunk 122 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 77 HIS F 77 HIS G 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103680 restraints weight = 25820.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106607 restraints weight = 13931.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108553 restraints weight = 9505.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109802 restraints weight = 7480.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110581 restraints weight = 6457.845| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15867 Z= 0.213 Angle : 0.667 10.217 21597 Z= 0.344 Chirality : 0.044 0.206 2430 Planarity : 0.005 0.050 2577 Dihedral : 17.055 98.657 2786 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.19 % Allowed : 26.60 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.19), residues: 1806 helix: 1.30 (0.15), residues: 1106 sheet: -2.30 (0.33), residues: 175 loop : -1.13 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 182 TYR 0.013 0.002 TYR C 73 PHE 0.041 0.002 PHE E 106 TRP 0.028 0.002 TRP G 211 HIS 0.004 0.001 HIS B 77 Details of bonding type rmsd covalent geometry : bond 0.00512 (15867) covalent geometry : angle 0.66719 (21597) hydrogen bonds : bond 0.04260 ( 763) hydrogen bonds : angle 3.58913 ( 2257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.56 seconds wall clock time: 52 minutes 45.35 seconds (3165.35 seconds total)