Starting phenix.real_space_refine on Fri Jul 3 17:52:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plh_13489/07_2026/7plh_13489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plh_13489/07_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_13489/07_2026/7plh_13489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plh_13489/07_2026/7plh_13489_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plh_13489/07_2026/7plh_13489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plh_13489/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 3.48, 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: 1.45 Conformation dependent library (CDL) restraints added in 648.1 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: 1.91 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: 2.58 Time building geometry restraints manager: 1.86 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: 21089 4.84 - 9.69: 462 9.69 - 14.53: 39 14.53 - 19.38: 0 19.38 - 24.22: 7 Bond angle restraints: 21597 Sorted by residual: 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 angle pdb=" N PHE D 204 " pdb=" CA PHE D 204 " pdb=" C PHE D 204 " ideal model delta sigma weight residual 111.36 101.97 9.39 1.09e+00 8.42e-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: 1926 0.103 - 0.205: 357 0.205 - 0.308: 114 0.308 - 0.410: 18 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.110 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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= 0.681 Angle : 1.658 24.221 21597 Z= 1.096 Chirality : 0.100 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/Z covalent geometry : bond 0.01119 / 0.68 (15867) covalent geometry : angle 1.65755 / 1.10 (21597) hydrogen bonds : bond 0.16048 / 10.85 ( 763) hydrogen bonds : angle 6.59997 / 4.72 ( 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 : 0.536 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: 0.1823 time to fit residues: 169.4166 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 : 0.571 ------------------------------------------------------------------------------- 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... A 38 GLN A 43 HIS B 43 HIS B 185 GLN B 213 GLN D 43 HIS E 43 HIS E 185 GLN F 43 HIS F 77 HIS F 81 GLN F 98 GLN G 37 GLN G 43 HIS G 97 HIS G 206 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.112191 restraints weight = 26108.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115432 restraints weight = 13884.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117589 restraints weight = 9434.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118990 restraints weight = 7410.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119721 restraints weight = 6355.873| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15867 Z= 0.245 Angle : 0.824 14.990 21597 Z= 0.425 Chirality : 0.050 0.336 2430 Planarity : 0.006 0.057 2577 Dihedral : 22.173 119.091 2822 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 5.92 % Allowed : 20.01 % Favored : 74.07 % 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: -1.06 (0.19), residues: 1806 helix: 0.04 (0.15), residues: 1099 sheet: -1.89 (0.53), residues: 105 loop : -1.73 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 57 TYR 0.017 0.002 TYR E 73 PHE 0.013 0.002 PHE A 196 TRP 0.021 0.003 TRP F 211 HIS 0.008 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (15867) covalent geometry : angle 0.82369 / 0.42 (21597) hydrogen bonds : bond 0.05850 / 3.84 ( 763) hydrogen bonds : angle 4.28216 / 3.07 ( 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 428 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 339 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8134 (tp30) cc_final: 0.7926 (tp30) REVERT: A 159 ASP cc_start: 0.7311 (m-30) cc_final: 0.7046 (m-30) REVERT: A 185 GLN cc_start: 0.8004 (mt0) cc_final: 0.7714 (mt0) REVERT: B 37 GLN cc_start: 0.7840 (tp40) cc_final: 0.7411 (tm-30) REVERT: C 32 SER cc_start: 0.9004 (t) cc_final: 0.8721 (t) REVERT: C 229 MET cc_start: 0.8115 (mmm) cc_final: 0.7466 (mmt) REVERT: D 81 GLN cc_start: 0.6792 (mp10) cc_final: 0.6548 (mt0) REVERT: E 214 MET cc_start: 0.8501 (tpp) cc_final: 0.8154 (tpp) REVERT: F 66 LYS cc_start: 0.8425 (mtmt) cc_final: 0.8210 (mtmm) REVERT: F 162 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: G 206 ASN cc_start: 0.8190 (m-40) cc_final: 0.7805 (m110) REVERT: G 241 ILE cc_start: 0.9195 (mm) cc_final: 0.8833 (mp) REVERT: G 256 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8798 (mm) outliers start: 89 outliers final: 57 residues processed: 406 average time/residue: 0.1482 time to fit residues: 85.2052 Evaluate side-chains 335 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 276 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 122 VAL 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 163 ASP Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR 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 34 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 276 LYS 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 185 GLN 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 255 SER Chi-restraints excluded: chain E residue 276 LYS 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 153 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 199 LEU 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 199 LEU Chi-restraints excluded: chain G residue 232 ILE Chi-restraints excluded: chain G residue 255 SER Chi-restraints excluded: chain G residue 256 LEU 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: 20.0000 chunk 97 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS B 43 HIS B 98 GLN D 98 GLN ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN F 43 HIS F 77 HIS G 43 HIS G 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.106032 restraints weight = 26271.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.109098 restraints weight = 14130.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111124 restraints weight = 9677.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.112424 restraints weight = 7659.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113224 restraints weight = 6622.009| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 15867 Z= 0.250 Angle : 0.778 13.566 21597 Z= 0.394 Chirality : 0.048 0.325 2430 Planarity : 0.005 0.054 2577 Dihedral : 21.028 124.974 2809 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.98 % Allowed : 20.55 % Favored : 73.47 % 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: -0.78 (0.19), residues: 1806 helix: 0.39 (0.15), residues: 1113 sheet: -2.54 (0.36), residues: 175 loop : -1.57 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 249 TYR 0.020 0.002 TYR A 73 PHE 0.016 0.002 PHE A 204 TRP 0.016 0.002 TRP F 211 HIS 0.011 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 (15867) covalent geometry : angle 0.77843 / 0.39 (21597) hydrogen bonds : bond 0.05518 / 3.65 ( 763) hydrogen bonds : angle 3.98096 / 2.88 ( 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 380 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 290 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7351 (m-30) cc_final: 0.7043 (m-30) REVERT: A 185 GLN cc_start: 0.8023 (mt0) cc_final: 0.7801 (mt0) REVERT: B 37 GLN cc_start: 0.7930 (tp40) cc_final: 0.7477 (tm-30) REVERT: B 196 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: C 229 MET cc_start: 0.8179 (mmm) cc_final: 0.7501 (mmt) REVERT: D 81 GLN cc_start: 0.6949 (mp10) cc_final: 0.6668 (mt0) REVERT: E 27 ARG cc_start: 0.8266 (ttp80) cc_final: 0.8027 (ttp80) REVERT: E 40 LYS cc_start: 0.8680 (tppt) cc_final: 0.8374 (tptp) REVERT: E 63 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8137 (tpt170) REVERT: E 188 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7635 (mm-30) REVERT: E 196 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: E 214 MET cc_start: 0.8535 (tpp) cc_final: 0.8140 (tpp) REVERT: F 66 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8268 (mtmm) REVERT: F 214 MET cc_start: 0.7753 (mmp) cc_final: 0.7370 (mmm) REVERT: G 196 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.8264 (m-80) REVERT: G 241 ILE cc_start: 0.9239 (mm) cc_final: 0.8893 (mp) REVERT: G 256 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8782 (mm) outliers start: 90 outliers final: 62 residues processed: 362 average time/residue: 0.1363 time to fit residues: 72.1033 Evaluate side-chains 317 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 250 time to evaluate : 0.649 ------------------------------------------------------------------------------- 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 199 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 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 179 VAL Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 256 LEU 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 196 PHE Chi-restraints excluded: chain C residue 211 TRP 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 34 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 31 LYS 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 68 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 199 LEU 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 34 VAL Chi-restraints excluded: chain F residue 55 SER 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 177 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 253 ILE 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 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: 3.9990 chunk 142 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 98 GLN C 77 HIS ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 81 GLN 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 = 0.3746 r_free = 0.3746 target = 0.133529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.106738 restraints weight = 25931.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109791 restraints weight = 14038.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111822 restraints weight = 9641.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113134 restraints weight = 7612.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113935 restraints weight = 6584.477| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15867 Z= 0.162 Angle : 0.682 12.688 21597 Z= 0.347 Chirality : 0.045 0.309 2430 Planarity : 0.004 0.036 2577 Dihedral : 20.066 122.598 2798 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.78 % Allowed : 22.81 % Favored : 71.41 % 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: -0.43 (0.19), residues: 1806 helix: 0.61 (0.15), residues: 1113 sheet: -2.15 (0.47), residues: 105 loop : -1.58 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 243 TYR 0.012 0.002 TYR E 112 PHE 0.022 0.001 PHE E 106 TRP 0.012 0.002 TRP D 45 HIS 0.008 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (15867) covalent geometry : angle 0.68198 / 0.35 (21597) hydrogen bonds : bond 0.04960 / 3.28 ( 763) hydrogen bonds : angle 3.76320 / 2.72 ( 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 368 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 281 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7303 (m-30) cc_final: 0.7023 (m-30) REVERT: B 37 GLN cc_start: 0.7857 (tp40) cc_final: 0.7442 (tm-30) REVERT: B 196 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: C 61 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7155 (mt-10) REVERT: C 229 MET cc_start: 0.8082 (mmm) cc_final: 0.7428 (mmt) REVERT: C 273 LYS cc_start: 0.7757 (pttt) cc_final: 0.7454 (tmtt) REVERT: D 81 GLN cc_start: 0.6962 (mp10) cc_final: 0.6650 (mt0) REVERT: D 115 TYR cc_start: 0.7400 (m-80) cc_final: 0.7096 (m-80) REVERT: E 27 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7912 (ttp80) REVERT: E 40 LYS cc_start: 0.8605 (tppt) cc_final: 0.8325 (tptp) REVERT: E 63 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.8129 (tpt170) REVERT: E 213 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8293 (mp10) REVERT: E 214 MET cc_start: 0.8453 (tpp) cc_final: 0.8178 (tpp) REVERT: F 162 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: G 196 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: G 206 ASN cc_start: 0.8301 (m-40) cc_final: 0.7858 (m110) REVERT: G 241 ILE cc_start: 0.9263 (mm) cc_final: 0.8896 (mp) REVERT: G 256 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8773 (mm) outliers start: 87 outliers final: 61 residues processed: 346 average time/residue: 0.1298 time to fit residues: 66.0763 Evaluate side-chains 318 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 251 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER 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 176 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 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 196 PHE Chi-restraints excluded: chain B residue 199 LEU 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 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 253 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 257 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 129 THR Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 31 LYS 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 177 ASP Chi-restraints excluded: chain F residue 196 PHE Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 32 SER 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 196 PHE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 232 ILE 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: 0.9990 chunk 61 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 98 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.109456 restraints weight = 25789.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112536 restraints weight = 13300.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114588 restraints weight = 8828.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.115837 restraints weight = 6836.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116706 restraints weight = 5865.777| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15867 Z= 0.132 Angle : 0.643 11.744 21597 Z= 0.327 Chirality : 0.043 0.300 2430 Planarity : 0.004 0.034 2577 Dihedral : 19.352 119.061 2790 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.65 % Allowed : 24.00 % 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: -0.15 (0.19), residues: 1806 helix: 0.83 (0.15), residues: 1113 sheet: -1.96 (0.46), residues: 105 loop : -1.45 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 249 TYR 0.012 0.001 TYR D 112 PHE 0.024 0.001 PHE E 106 TRP 0.017 0.002 TRP D 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15867) covalent geometry : angle 0.64341 / 0.33 (21597) hydrogen bonds : bond 0.04641 / 3.09 ( 763) hydrogen bonds : angle 3.62073 / 2.63 ( 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 351 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 281 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7321 (m-30) cc_final: 0.6991 (m-30) REVERT: A 185 GLN cc_start: 0.7952 (mt0) cc_final: 0.7682 (mt0) REVERT: B 115 TYR cc_start: 0.8092 (m-80) cc_final: 0.7751 (m-10) REVERT: B 196 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: C 229 MET cc_start: 0.8023 (mmm) cc_final: 0.7436 (mmt) REVERT: C 250 GLU cc_start: 0.8037 (tp30) cc_final: 0.7834 (tp30) REVERT: C 273 LYS cc_start: 0.7814 (pttt) cc_final: 0.7532 (tmtt) REVERT: D 81 GLN cc_start: 0.6998 (mp10) cc_final: 0.6691 (mt0) REVERT: D 85 ARG cc_start: 0.7740 (mmm160) cc_final: 0.6865 (ttm170) REVERT: D 115 TYR cc_start: 0.7448 (m-80) cc_final: 0.7137 (m-80) REVERT: D 210 MET cc_start: 0.8450 (ttm) cc_final: 0.8135 (ttp) REVERT: E 27 ARG cc_start: 0.8262 (ttp80) cc_final: 0.8001 (ttp80) REVERT: E 40 LYS cc_start: 0.8533 (tppt) cc_final: 0.8272 (tptp) REVERT: E 63 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8022 (mpt180) REVERT: E 209 GLU cc_start: 0.7814 (tp30) cc_final: 0.7115 (tp30) REVERT: E 210 MET cc_start: 0.8271 (tpp) cc_final: 0.7975 (ttm) REVERT: E 213 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: E 229 MET cc_start: 0.7425 (mmp) cc_final: 0.7041 (mmm) REVERT: F 162 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7527 (mt-10) REVERT: G 196 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7848 (m-10) REVERT: G 206 ASN cc_start: 0.8339 (m-40) cc_final: 0.7875 (m110) REVERT: G 241 ILE cc_start: 0.9252 (mm) cc_final: 0.8877 (mp) REVERT: G 256 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8757 (mm) outliers start: 70 outliers final: 47 residues processed: 333 average time/residue: 0.1301 time to fit residues: 63.7618 Evaluate side-chains 307 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 254 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER 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 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain C residue 32 SER 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 196 PHE Chi-restraints excluded: chain C residue 211 TRP 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 34 VAL Chi-restraints excluded: chain D residue 36 LEU 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 213 GLN Chi-restraints excluded: chain E residue 232 ILE 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 117 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 32 SER 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 196 PHE 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: 3.9990 chunk 24 optimal weight: 20.0000 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN B 98 GLN E 43 HIS E 77 HIS F 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.133899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108227 restraints weight = 25529.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111228 restraints weight = 13249.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113227 restraints weight = 8849.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114520 restraints weight = 6863.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115242 restraints weight = 5872.802| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15867 Z= 0.144 Angle : 0.642 11.733 21597 Z= 0.327 Chirality : 0.044 0.296 2430 Planarity : 0.004 0.032 2577 Dihedral : 18.707 118.556 2789 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.92 % Allowed : 24.87 % Favored : 70.21 % 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: 0.10 (0.19), residues: 1806 helix: 1.03 (0.15), residues: 1113 sheet: -1.97 (0.45), residues: 105 loop : -1.35 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 254 TYR 0.020 0.001 TYR C 73 PHE 0.024 0.001 PHE E 106 TRP 0.016 0.002 TRP G 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15867) covalent geometry : angle 0.64226 / 0.33 (21597) hydrogen bonds : bond 0.04458 / 2.97 ( 763) hydrogen bonds : angle 3.54390 / 2.58 ( 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 352 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7213 (m-30) cc_final: 0.6883 (m-30) REVERT: B 196 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: C 229 MET cc_start: 0.8026 (mmm) cc_final: 0.7476 (mmt) REVERT: C 273 LYS cc_start: 0.7983 (pttt) cc_final: 0.7706 (tmtt) REVERT: D 81 GLN cc_start: 0.7084 (mp10) cc_final: 0.6751 (mt0) REVERT: D 85 ARG cc_start: 0.7790 (mmm160) cc_final: 0.6981 (ttt180) REVERT: D 115 TYR cc_start: 0.7558 (m-80) cc_final: 0.7288 (m-80) REVERT: D 210 MET cc_start: 0.8410 (ttm) cc_final: 0.8027 (ttp) REVERT: E 27 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7946 (ttp80) REVERT: E 63 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8055 (mpt180) REVERT: E 210 MET cc_start: 0.8164 (tpp) cc_final: 0.7812 (ttm) REVERT: E 213 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8067 (mp10) REVERT: E 229 MET cc_start: 0.7546 (mmp) cc_final: 0.7023 (mmm) REVERT: F 162 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7520 (mt-10) REVERT: G 196 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7927 (m-10) REVERT: G 241 ILE cc_start: 0.9255 (mm) cc_final: 0.8885 (mp) REVERT: G 256 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8739 (mm) outliers start: 74 outliers final: 52 residues processed: 329 average time/residue: 0.1308 time to fit residues: 63.3199 Evaluate side-chains 323 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 176 LEU 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 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 199 LEU 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 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL 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 34 VAL Chi-restraints excluded: chain D residue 36 LEU 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 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 162 GLU Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 32 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 196 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 68 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 154 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 GLN D 77 HIS D 213 GLN E 43 HIS F 77 HIS F 98 GLN G 43 HIS G 206 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.131803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104847 restraints weight = 25812.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.107852 restraints weight = 13908.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.109831 restraints weight = 9514.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.111116 restraints weight = 7519.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.111815 restraints weight = 6494.557| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15867 Z= 0.173 Angle : 0.662 10.866 21597 Z= 0.336 Chirality : 0.044 0.296 2430 Planarity : 0.004 0.032 2577 Dihedral : 18.260 118.742 2787 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.65 % Allowed : 25.47 % Favored : 69.88 % 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: 1.13 (0.15), residues: 1113 sheet: -2.05 (0.44), residues: 105 loop : -1.28 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 254 TYR 0.015 0.002 TYR D 112 PHE 0.015 0.001 PHE B 190 TRP 0.022 0.002 TRP G 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (15867) covalent geometry : angle 0.66174 / 0.34 (21597) hydrogen bonds : bond 0.04504 / 3.02 ( 763) hydrogen bonds : angle 3.58282 / 2.61 ( 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 344 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 274 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7279 (ttpt) REVERT: A 159 ASP cc_start: 0.7205 (m-30) cc_final: 0.6874 (m-30) REVERT: B 37 GLN cc_start: 0.7849 (tp40) cc_final: 0.7581 (tp40) REVERT: B 196 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: B 245 ASP cc_start: 0.8501 (t0) cc_final: 0.8228 (t0) REVERT: C 229 MET cc_start: 0.8056 (mmm) cc_final: 0.7514 (mmt) REVERT: D 81 GLN cc_start: 0.7128 (mp10) cc_final: 0.6821 (mt0) REVERT: D 85 ARG cc_start: 0.7847 (mmm160) cc_final: 0.6978 (ttt180) REVERT: D 210 MET cc_start: 0.8440 (ttm) cc_final: 0.8200 (ttp) REVERT: E 27 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7953 (ttp80) REVERT: E 36 LEU cc_start: 0.8318 (pt) cc_final: 0.7945 (pt) REVERT: E 40 LYS cc_start: 0.8653 (tppt) cc_final: 0.8347 (tptp) REVERT: E 63 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8155 (mpt180) REVERT: E 95 ARG cc_start: 0.7826 (ptt-90) cc_final: 0.7616 (ptt90) REVERT: E 210 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7904 (ttm) REVERT: E 213 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: F 152 GLU cc_start: 0.8069 (mp0) cc_final: 0.7747 (mp0) REVERT: F 162 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: G 80 GLN cc_start: 0.6581 (pm20) cc_final: 0.5804 (tt0) REVERT: G 196 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: G 241 ILE cc_start: 0.9275 (mm) cc_final: 0.8909 (mp) REVERT: G 256 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 70 outliers final: 49 residues processed: 328 average time/residue: 0.1287 time to fit residues: 61.8674 Evaluate side-chains 318 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 58 VAL 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 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 196 PHE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 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 203 ASP 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 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 210 MET 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 153 THR Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 32 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 196 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 106 optimal weight: 0.0870 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 50 optimal weight: 0.0470 chunk 147 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 GLN D 77 HIS E 43 HIS F 77 HIS F 97 HIS G 43 HIS G 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.109029 restraints weight = 25570.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112078 restraints weight = 13168.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114086 restraints weight = 8732.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.115254 restraints weight = 6780.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116178 restraints weight = 5834.345| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15867 Z= 0.118 Angle : 0.624 10.964 21597 Z= 0.321 Chirality : 0.042 0.288 2430 Planarity : 0.004 0.032 2577 Dihedral : 17.834 114.845 2787 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.66 % Allowed : 26.73 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.30 (0.20), residues: 1806 helix: 1.16 (0.16), residues: 1113 sheet: -2.27 (0.40), residues: 140 loop : -0.98 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 254 TYR 0.009 0.001 TYR E 112 PHE 0.017 0.001 PHE B 190 TRP 0.035 0.003 TRP F 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15867) covalent geometry : angle 0.62386 / 0.32 (21597) hydrogen bonds : bond 0.04274 / 2.87 ( 763) hydrogen bonds : angle 3.53434 / 2.55 ( 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 333 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 278 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6959 (ttmt) REVERT: A 159 ASP cc_start: 0.7155 (m-30) cc_final: 0.6831 (m-30) REVERT: A 185 GLN cc_start: 0.8117 (mt0) cc_final: 0.7883 (mt0) REVERT: B 245 ASP cc_start: 0.8368 (t0) cc_final: 0.8073 (t0) REVERT: C 229 MET cc_start: 0.7988 (mmm) cc_final: 0.7460 (mmt) REVERT: D 33 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7453 (tp) REVERT: D 81 GLN cc_start: 0.7144 (mp10) cc_final: 0.6819 (mt0) REVERT: D 85 ARG cc_start: 0.7855 (mmm160) cc_final: 0.7065 (ttt180) REVERT: E 27 ARG cc_start: 0.8218 (ttp80) cc_final: 0.8011 (ttp80) REVERT: E 40 LYS cc_start: 0.8621 (tppt) cc_final: 0.8307 (tptp) REVERT: E 63 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8017 (mpt180) REVERT: E 209 GLU cc_start: 0.7557 (tp30) cc_final: 0.7229 (tp30) REVERT: E 210 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7838 (ttm) REVERT: E 229 MET cc_start: 0.7553 (mmp) cc_final: 0.6958 (mmm) REVERT: F 127 ASP cc_start: 0.7616 (m-30) cc_final: 0.7409 (m-30) REVERT: F 152 GLU cc_start: 0.8018 (mp0) cc_final: 0.7727 (mp0) REVERT: F 162 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: G 80 GLN cc_start: 0.6510 (pm20) cc_final: 0.5835 (tt0) REVERT: G 241 ILE cc_start: 0.9248 (mm) cc_final: 0.8884 (mp) REVERT: G 256 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8737 (mm) outliers start: 55 outliers final: 40 residues processed: 315 average time/residue: 0.1265 time to fit residues: 57.9203 Evaluate side-chains 307 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 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 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 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 263 ILE 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 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 257 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 255 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 162 GLU Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 32 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 70 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 185 optimal weight: 50.0000 chunk 83 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 GLN D 206 ASN E 43 HIS F 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.105333 restraints weight = 25989.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108343 restraints weight = 13977.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.110361 restraints weight = 9549.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111657 restraints weight = 7548.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112368 restraints weight = 6521.257| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15867 Z= 0.159 Angle : 0.646 10.941 21597 Z= 0.331 Chirality : 0.043 0.294 2430 Planarity : 0.004 0.044 2577 Dihedral : 17.715 117.085 2787 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.52 % Allowed : 27.39 % 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: 0.34 (0.20), residues: 1806 helix: 1.21 (0.16), residues: 1106 sheet: -2.34 (0.39), residues: 140 loop : -0.97 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 95 TYR 0.012 0.001 TYR B 275 PHE 0.024 0.001 PHE E 106 TRP 0.024 0.002 TRP G 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (15867) covalent geometry : angle 0.64589 / 0.33 (21597) hydrogen bonds : bond 0.04336 / 2.90 ( 763) hydrogen bonds : angle 3.57517 / 2.59 ( 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 321 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 268 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6949 (ttmt) REVERT: A 159 ASP cc_start: 0.7187 (m-30) cc_final: 0.6846 (m-30) REVERT: A 185 GLN cc_start: 0.8117 (mt0) cc_final: 0.7885 (mt0) REVERT: B 245 ASP cc_start: 0.8383 (t0) cc_final: 0.8073 (t0) REVERT: C 229 MET cc_start: 0.8047 (mmm) cc_final: 0.7546 (mmt) REVERT: D 81 GLN cc_start: 0.7195 (mp10) cc_final: 0.6864 (mt0) REVERT: D 85 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7111 (ttt180) REVERT: E 27 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7987 (ttp80) REVERT: E 42 LEU cc_start: 0.9097 (tt) cc_final: 0.8852 (tp) REVERT: E 63 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8072 (mpt180) REVERT: E 229 MET cc_start: 0.7639 (mmp) cc_final: 0.6933 (mmm) REVERT: F 127 ASP cc_start: 0.7612 (m-30) cc_final: 0.7405 (m-30) REVERT: F 152 GLU cc_start: 0.8024 (mp0) cc_final: 0.7750 (mp0) REVERT: G 80 GLN cc_start: 0.6530 (pm20) cc_final: 0.5864 (tt0) REVERT: G 241 ILE cc_start: 0.9255 (mm) cc_final: 0.8905 (mp) REVERT: G 256 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 53 outliers final: 45 residues processed: 303 average time/residue: 0.1200 time to fit residues: 53.4215 Evaluate side-chains 309 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 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 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU 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 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 256 LEU 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 257 SER 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 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 255 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 230 LEU Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 32 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 GLN D 206 ASN E 43 HIS F 77 HIS G 206 ASN G 213 GLN 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 = 0.133766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107010 restraints weight = 25804.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110070 restraints weight = 13661.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112108 restraints weight = 9234.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113400 restraints weight = 7253.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114179 restraints weight = 6264.890| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15867 Z= 0.116 Angle : 0.629 11.098 21597 Z= 0.324 Chirality : 0.042 0.278 2430 Planarity : 0.004 0.034 2577 Dihedral : 17.441 112.046 2787 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.99 % Allowed : 27.93 % 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: 0.38 (0.20), residues: 1806 helix: 1.22 (0.16), residues: 1106 sheet: -2.26 (0.39), residues: 140 loop : -0.92 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 254 TYR 0.009 0.001 TYR F 240 PHE 0.020 0.001 PHE E 106 TRP 0.025 0.002 TRP G 211 HIS 0.006 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (15867) covalent geometry : angle 0.62868 / 0.32 (21597) hydrogen bonds : bond 0.04129 / 2.77 ( 763) hydrogen bonds : angle 3.55692 / 2.57 ( 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 326 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7170 (m-30) cc_final: 0.6828 (m-30) REVERT: B 37 GLN cc_start: 0.7791 (tp-100) cc_final: 0.7578 (tp40) REVERT: B 115 TYR cc_start: 0.8083 (m-80) cc_final: 0.7734 (m-10) REVERT: B 245 ASP cc_start: 0.8323 (t0) cc_final: 0.7947 (t0) REVERT: C 229 MET cc_start: 0.8014 (mmm) cc_final: 0.7519 (mmt) REVERT: D 81 GLN cc_start: 0.7207 (mp10) cc_final: 0.6874 (mt0) REVERT: D 85 ARG cc_start: 0.7947 (mmm160) cc_final: 0.7244 (mmt90) REVERT: E 40 LYS cc_start: 0.8506 (tppt) cc_final: 0.8246 (tptp) REVERT: E 42 LEU cc_start: 0.9095 (tt) cc_final: 0.8864 (tp) REVERT: E 63 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7939 (mpt180) REVERT: E 229 MET cc_start: 0.7646 (mmp) cc_final: 0.6976 (mmm) REVERT: E 238 GLU cc_start: 0.8706 (mp0) cc_final: 0.8242 (mp0) REVERT: F 127 ASP cc_start: 0.7585 (m-30) cc_final: 0.7377 (m-30) REVERT: F 162 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: F 246 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7528 (mt-10) REVERT: G 61 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7814 (mt-10) REVERT: G 78 LYS cc_start: 0.7300 (ptpp) cc_final: 0.7064 (ptpt) REVERT: G 80 GLN cc_start: 0.6533 (pm20) cc_final: 0.5897 (tt0) REVERT: G 240 TYR cc_start: 0.8642 (m-10) cc_final: 0.8263 (m-10) REVERT: G 241 ILE cc_start: 0.9228 (mm) cc_final: 0.8858 (mp) REVERT: G 256 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8726 (mm) outliers start: 45 outliers final: 38 residues processed: 313 average time/residue: 0.1256 time to fit residues: 57.2276 Evaluate side-chains 304 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU 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 125 PHE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 153 THR 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 183 ASP Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL 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 255 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 162 GLU Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 230 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 255 SER Chi-restraints excluded: chain G residue 256 LEU 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: 4.9990 chunk 152 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 176 optimal weight: 30.0000 chunk 122 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 213 GLN D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS E 206 ASN F 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108665 restraints weight = 25400.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111665 restraints weight = 12975.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.113637 restraints weight = 8543.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.114897 restraints weight = 6628.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115603 restraints weight = 5664.851| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.6163 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= 0.123 Angle : 0.629 10.968 21597 Z= 0.322 Chirality : 0.042 0.263 2430 Planarity : 0.004 0.075 2577 Dihedral : 17.378 112.820 2787 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.79 % Allowed : 28.12 % 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: 0.48 (0.20), residues: 1806 helix: 1.29 (0.16), residues: 1106 sheet: -2.24 (0.38), residues: 140 loop : -0.83 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 27 TYR 0.010 0.001 TYR F 240 PHE 0.017 0.001 PHE B 190 TRP 0.029 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15867) covalent geometry : angle 0.62899 / 0.32 (21597) hydrogen bonds : bond 0.04077 / 2.74 ( 763) hydrogen bonds : angle 3.54874 / 2.57 ( 2257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3045.46 seconds wall clock time: 53 minutes 23.42 seconds (3203.42 seconds total)