Starting phenix.real_space_refine on Sat Sep 12 10:54:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plh_13489/09_2026/7plh_13489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plh_13489/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7plh_13489/09_2026/7plh_13489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plh_13489/09_2026/7plh_13489.map" model { file = "/net/cci-nas-00/data/ceres_data/7plh_13489/09_2026/7plh_13489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plh_13489/09_2026/7plh_13489_neut.cif" } 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-2.2.1-6174/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: 4.09, per 1000 atoms: 0.26 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: 1.06 Conformation dependent library (CDL) restraints added in 721.5 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: 1.62 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: 2.78 Time building geometry restraints manager: 1.54 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.960 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.670 ------------------------------------------------------------------------------- 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= 0.685 Angle : 1.658 24.221 21597 Z= 1.097 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 1.65811 / 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 : 0.659 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: 0.1707 time to fit residues: 159.0690 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 : 0.463 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.138892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112094 restraints weight = 26108.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115335 restraints weight = 13898.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117516 restraints weight = 9444.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.118900 restraints weight = 7393.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.119716 restraints weight = 6363.665| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15867 Z= 0.239 Angle : 0.820 15.056 21597 Z= 0.418 Chirality : 0.049 0.337 2430 Planarity : 0.006 0.052 2577 Dihedral : 22.110 119.208 2822 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 5.85 % Allowed : 20.08 % 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: -1.03 (0.19), residues: 1806 helix: 0.06 (0.15), residues: 1099 sheet: -1.89 (0.53), residues: 105 loop : -1.72 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 189 TYR 0.016 0.002 TYR A 93 PHE 0.012 0.002 PHE E 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 0.00545 / 0.24 (15867) covalent geometry : angle 0.82013 / 0.42 (21597) hydrogen bonds : bond 0.05843 / 3.84 ( 763) hydrogen bonds : angle 4.27611 / 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 425 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 337 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 GLU cc_start: 0.8134 (tp30) cc_final: 0.7908 (tp30) REVERT: A 159 ASP cc_start: 0.7304 (m-30) cc_final: 0.7022 (m-30) REVERT: A 185 GLN cc_start: 0.8012 (mt0) cc_final: 0.7732 (mt0) REVERT: B 37 GLN cc_start: 0.7851 (tp40) cc_final: 0.7426 (tm-30) REVERT: C 32 SER cc_start: 0.9009 (t) cc_final: 0.8724 (t) REVERT: C 229 MET cc_start: 0.8146 (mmm) cc_final: 0.7491 (mmt) REVERT: D 33 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8664 (mm) REVERT: D 81 GLN cc_start: 0.6804 (mp10) cc_final: 0.6559 (mt0) REVERT: E 214 MET cc_start: 0.8494 (tpp) cc_final: 0.8154 (tpp) REVERT: F 66 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8214 (mtmm) REVERT: F 127 ASP cc_start: 0.7611 (m-30) cc_final: 0.7411 (m-30) REVERT: F 162 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7528 (mt-10) REVERT: G 206 ASN cc_start: 0.8190 (m-40) cc_final: 0.7796 (m110) REVERT: G 241 ILE cc_start: 0.9197 (mm) cc_final: 0.8835 (mp) REVERT: G 256 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8805 (mm) outliers start: 88 outliers final: 56 residues processed: 404 average time/residue: 0.1512 time to fit residues: 86.3953 Evaluate side-chains 336 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL 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 33 ILE 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: 3.9990 chunk 22 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.110684 restraints weight = 25840.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113758 restraints weight = 13396.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115798 restraints weight = 8933.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117130 restraints weight = 6939.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117837 restraints weight = 5921.952| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 15867 Z= 0.203 Angle : 0.727 13.555 21597 Z= 0.370 Chirality : 0.046 0.318 2430 Planarity : 0.005 0.047 2577 Dihedral : 21.048 123.171 2809 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.59 % Allowed : 21.34 % Favored : 73.07 % 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: -0.55 (0.19), residues: 1806 helix: 0.50 (0.15), residues: 1099 sheet: -2.00 (0.49), residues: 105 loop : -1.57 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 249 TYR 0.018 0.002 TYR A 73 PHE 0.017 0.002 PHE A 204 TRP 0.017 0.002 TRP F 211 HIS 0.011 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (15867) covalent geometry : angle 0.72680 / 0.37 (21597) hydrogen bonds : bond 0.05369 / 3.55 ( 763) hydrogen bonds : angle 3.94062 / 2.84 ( 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 366 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 282 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7306 (m-30) cc_final: 0.7001 (m-30) REVERT: A 185 GLN cc_start: 0.7978 (mt0) cc_final: 0.7749 (mt0) REVERT: B 37 GLN cc_start: 0.7924 (tp40) cc_final: 0.7486 (tm-30) REVERT: B 196 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8131 (m-80) REVERT: B 232 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9072 (tt) REVERT: C 32 SER cc_start: 0.9161 (t) cc_final: 0.8940 (t) REVERT: C 229 MET cc_start: 0.8099 (mmm) cc_final: 0.7381 (mmt) REVERT: D 81 GLN cc_start: 0.6909 (mp10) cc_final: 0.6640 (mt0) REVERT: D 114 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8551 (mmtt) REVERT: E 63 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8098 (tpt170) REVERT: E 188 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7501 (mm-30) REVERT: E 214 MET cc_start: 0.8487 (tpp) cc_final: 0.8126 (tpp) REVERT: F 127 ASP cc_start: 0.7660 (m-30) cc_final: 0.7415 (m-30) REVERT: F 162 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: F 214 MET cc_start: 0.7656 (mmp) cc_final: 0.7298 (mmm) REVERT: G 196 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8002 (m-10) REVERT: G 206 ASN cc_start: 0.8359 (m-40) cc_final: 0.8006 (m110) REVERT: G 241 ILE cc_start: 0.9227 (mm) cc_final: 0.8870 (mp) REVERT: G 256 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8797 (mm) outliers start: 84 outliers final: 56 residues processed: 349 average time/residue: 0.1379 time to fit residues: 70.4250 Evaluate side-chains 322 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 232 ILE Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 260 LEU 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 D residue 276 LYS Chi-restraints excluded: chain E residue 31 LYS 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 122 VAL Chi-restraints excluded: chain E residue 129 THR 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 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 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 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: 0.9990 chunk 142 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109657 restraints weight = 25575.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.112733 restraints weight = 13230.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.114784 restraints weight = 8809.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.116087 restraints weight = 6837.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116974 restraints weight = 5854.001| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15867 Z= 0.160 Angle : 0.676 12.611 21597 Z= 0.342 Chirality : 0.045 0.303 2430 Planarity : 0.005 0.074 2577 Dihedral : 19.998 121.741 2802 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.39 % Allowed : 22.34 % Favored : 72.27 % 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: -0.37 (0.19), residues: 1806 helix: 0.66 (0.15), residues: 1113 sheet: -2.08 (0.47), residues: 105 loop : -1.56 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 27 TYR 0.017 0.002 TYR C 240 PHE 0.026 0.002 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 0.67576 / 0.34 (21597) hydrogen bonds : bond 0.04855 / 3.22 ( 763) hydrogen bonds : angle 3.78113 / 2.73 ( 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 367 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 286 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7310 (m-30) cc_final: 0.7005 (m-30) REVERT: A 185 GLN cc_start: 0.7961 (mt0) cc_final: 0.7637 (mt0) REVERT: B 37 GLN cc_start: 0.7872 (tp40) cc_final: 0.7460 (tm-30) REVERT: B 196 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: C 229 MET cc_start: 0.8039 (mmm) cc_final: 0.7361 (mmt) REVERT: C 273 LYS cc_start: 0.7656 (pttt) cc_final: 0.7330 (tmtt) REVERT: D 81 GLN cc_start: 0.6906 (mp10) cc_final: 0.6619 (mt0) REVERT: E 27 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8014 (ttp80) REVERT: E 40 LYS cc_start: 0.8573 (tppt) cc_final: 0.8278 (tptp) REVERT: E 42 LEU cc_start: 0.9129 (tt) cc_final: 0.8871 (tp) REVERT: E 63 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8081 (tpt170) REVERT: E 214 MET cc_start: 0.8449 (tpp) cc_final: 0.8127 (tpp) REVERT: F 127 ASP cc_start: 0.7620 (m-30) cc_final: 0.7404 (m-30) REVERT: G 196 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: G 206 ASN cc_start: 0.8438 (m-40) cc_final: 0.8091 (m110) REVERT: G 241 ILE cc_start: 0.9242 (mm) cc_final: 0.8882 (mp) REVERT: G 256 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8787 (mm) outliers start: 81 outliers final: 56 residues processed: 346 average time/residue: 0.1344 time to fit residues: 68.4241 Evaluate side-chains 311 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 251 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 SER 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 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 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 215 VAL 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 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 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 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 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 255 SER Chi-restraints excluded: chain G residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 179 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 98 GLN C 213 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS G 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107597 restraints weight = 26127.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110691 restraints weight = 14031.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112738 restraints weight = 9582.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114067 restraints weight = 7560.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114822 restraints weight = 6529.340| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15867 Z= 0.140 Angle : 0.649 11.822 21597 Z= 0.329 Chirality : 0.043 0.293 2430 Planarity : 0.004 0.045 2577 Dihedral : 19.252 119.628 2790 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.99 % Allowed : 23.54 % Favored : 71.48 % 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: 0.86 (0.15), residues: 1113 sheet: -1.89 (0.47), residues: 105 loop : -1.42 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 249 TYR 0.014 0.001 TYR D 112 PHE 0.024 0.001 PHE E 106 TRP 0.018 0.002 TRP D 211 HIS 0.008 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15867) covalent geometry : angle 0.64901 / 0.33 (21597) hydrogen bonds : bond 0.04609 / 3.09 ( 763) hydrogen bonds : angle 3.66492 / 2.66 ( 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 358 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7270 (m-30) cc_final: 0.6961 (m-30) REVERT: C 229 MET cc_start: 0.8039 (mmm) cc_final: 0.7417 (mmt) REVERT: C 273 LYS cc_start: 0.7790 (pttt) cc_final: 0.7468 (tmtt) REVERT: D 81 GLN cc_start: 0.6967 (mp10) cc_final: 0.6661 (mt0) REVERT: D 85 ARG cc_start: 0.7676 (mmm160) cc_final: 0.6800 (ttm170) REVERT: D 159 ASP cc_start: 0.7201 (m-30) cc_final: 0.7000 (m-30) REVERT: E 27 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7976 (ttp80) REVERT: E 63 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8035 (mpt180) REVERT: E 196 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7965 (m-80) REVERT: E 209 GLU cc_start: 0.7801 (tp30) cc_final: 0.7241 (tp30) REVERT: E 210 MET cc_start: 0.8281 (tpp) cc_final: 0.8021 (ttm) REVERT: E 213 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: E 229 MET cc_start: 0.7465 (mmp) cc_final: 0.7042 (mmm) REVERT: F 66 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8265 (mtmm) REVERT: F 113 LEU cc_start: 0.9256 (mt) cc_final: 0.9053 (mt) REVERT: F 127 ASP cc_start: 0.7635 (m-30) cc_final: 0.7422 (m-30) REVERT: F 162 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: G 196 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: G 204 PHE cc_start: 0.8472 (t80) cc_final: 0.8265 (t80) REVERT: G 206 ASN cc_start: 0.8475 (m-40) cc_final: 0.8086 (m110) REVERT: G 241 ILE cc_start: 0.9255 (mm) cc_final: 0.8898 (mp) REVERT: G 256 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 75 outliers final: 47 residues processed: 340 average time/residue: 0.1398 time to fit residues: 69.4732 Evaluate side-chains 318 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 264 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 125 PHE 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 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 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 196 PHE 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 66 LYS 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 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 255 SER Chi-restraints excluded: chain G residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 82 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN B 37 GLN B 98 GLN C 213 GLN E 77 HIS F 77 HIS G 43 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106416 restraints weight = 25818.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109486 restraints weight = 13789.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111519 restraints weight = 9380.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112843 restraints weight = 7395.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113653 restraints weight = 6369.346| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15867 Z= 0.152 Angle : 0.654 12.039 21597 Z= 0.330 Chirality : 0.044 0.285 2430 Planarity : 0.004 0.042 2577 Dihedral : 18.695 118.961 2789 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.72 % Allowed : 24.34 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.20), residues: 1806 helix: 1.04 (0.15), residues: 1113 sheet: -2.29 (0.34), residues: 175 loop : -1.24 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 254 TYR 0.021 0.002 TYR C 73 PHE 0.016 0.001 PHE E 106 TRP 0.016 0.002 TRP G 211 HIS 0.008 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (15867) covalent geometry : angle 0.65377 / 0.33 (21597) hydrogen bonds : bond 0.04451 / 2.98 ( 763) hydrogen bonds : angle 3.55682 / 2.59 ( 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 364 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 293 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7197 (m-30) cc_final: 0.6862 (m-30) REVERT: B 196 PHE cc_start: 0.8603 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: C 229 MET cc_start: 0.8056 (mmm) cc_final: 0.7475 (mmt) REVERT: C 273 LYS cc_start: 0.7962 (pttt) cc_final: 0.7676 (tmtt) REVERT: D 81 GLN cc_start: 0.7048 (mp10) cc_final: 0.6734 (mt0) REVERT: D 85 ARG cc_start: 0.7750 (mmm160) cc_final: 0.6881 (ttm170) REVERT: D 183 ASP cc_start: 0.7479 (m-30) cc_final: 0.7248 (m-30) REVERT: E 27 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7997 (ttp80) REVERT: E 40 LYS cc_start: 0.8648 (tppt) cc_final: 0.8310 (tptp) REVERT: E 63 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8125 (mpt180) REVERT: E 213 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: E 229 MET cc_start: 0.7557 (mmp) cc_final: 0.7013 (mmm) REVERT: F 113 LEU cc_start: 0.9254 (mt) cc_final: 0.9044 (mt) REVERT: F 127 ASP cc_start: 0.7642 (m-30) cc_final: 0.7431 (m-30) REVERT: F 152 GLU cc_start: 0.8065 (mp0) cc_final: 0.7705 (mp0) REVERT: F 162 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: G 196 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8041 (m-10) REVERT: G 206 ASN cc_start: 0.8495 (m-40) cc_final: 0.8099 (m110) REVERT: G 241 ILE cc_start: 0.9257 (mm) cc_final: 0.8889 (mp) REVERT: G 256 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8717 (mm) outliers start: 71 outliers final: 50 residues processed: 342 average time/residue: 0.1317 time to fit residues: 66.8187 Evaluate side-chains 331 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 275 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 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 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 125 PHE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 211 TRP Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 186 VAL 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 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 199 LEU 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: 2.9990 chunk 63 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 154 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 98 GLN C 213 GLN D 77 HIS ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 97 HIS F 98 GLN G 43 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.107510 restraints weight = 25379.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110537 restraints weight = 13009.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112556 restraints weight = 8580.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.113862 restraints weight = 6631.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114577 restraints weight = 5650.329| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15867 Z= 0.124 Angle : 0.633 11.316 21597 Z= 0.324 Chirality : 0.043 0.276 2430 Planarity : 0.004 0.041 2577 Dihedral : 18.146 115.700 2787 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.92 % Allowed : 25.53 % Favored : 70.55 % 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: 0.24 (0.20), residues: 1806 helix: 1.20 (0.15), residues: 1113 sheet: -2.17 (0.35), residues: 175 loop : -1.17 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 254 TYR 0.015 0.001 TYR D 112 PHE 0.046 0.001 PHE E 106 TRP 0.021 0.002 TRP G 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15867) covalent geometry : angle 0.63264 / 0.32 (21597) hydrogen bonds : bond 0.04261 / 2.85 ( 763) hydrogen bonds : angle 3.51924 / 2.56 ( 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 349 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 290 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ASP cc_start: 0.7149 (m-30) cc_final: 0.6794 (m-30) REVERT: B 37 GLN cc_start: 0.7768 (tp40) cc_final: 0.7493 (tp40) REVERT: B 196 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: C 229 MET cc_start: 0.7999 (mmm) cc_final: 0.7736 (mmt) REVERT: C 273 LYS cc_start: 0.7960 (pttt) cc_final: 0.7667 (tmtt) REVERT: D 81 GLN cc_start: 0.7058 (mp10) cc_final: 0.6744 (mt0) REVERT: D 85 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7061 (mmt90) REVERT: D 183 ASP cc_start: 0.7426 (m-30) cc_final: 0.7186 (m-30) REVERT: D 210 MET cc_start: 0.8387 (ttm) cc_final: 0.8170 (ttp) REVERT: E 36 LEU cc_start: 0.8203 (pt) cc_final: 0.7853 (pt) REVERT: E 40 LYS cc_start: 0.8621 (tppt) cc_final: 0.8294 (tptp) REVERT: E 63 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7973 (mpt180) REVERT: E 209 GLU cc_start: 0.7679 (tp30) cc_final: 0.7309 (tp30) REVERT: E 213 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: E 229 MET cc_start: 0.7582 (mmp) cc_final: 0.7042 (mmm) REVERT: F 113 LEU cc_start: 0.9225 (mt) cc_final: 0.9007 (mt) REVERT: F 127 ASP cc_start: 0.7637 (m-30) cc_final: 0.7404 (m-30) REVERT: F 152 GLU cc_start: 0.8025 (mp0) cc_final: 0.7711 (mp0) REVERT: F 162 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: F 238 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7638 (mm-30) REVERT: G 241 ILE cc_start: 0.9249 (mm) cc_final: 0.8897 (mp) REVERT: G 256 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8722 (mm) outliers start: 59 outliers final: 46 residues processed: 331 average time/residue: 0.1324 time to fit residues: 64.5807 Evaluate side-chains 330 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 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 125 PHE Chi-restraints excluded: chain B residue 196 PHE 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 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 89 VAL Chi-restraints excluded: chain D residue 125 PHE 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 176 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 F residue 34 VAL 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 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 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: 4.9990 chunk 73 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 106 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 43 HIS F 77 HIS G 43 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.133404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.108544 restraints weight = 25750.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111543 restraints weight = 13124.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.113555 restraints weight = 8633.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114849 restraints weight = 6638.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.115662 restraints weight = 5639.698| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15867 Z= 0.138 Angle : 0.623 11.324 21597 Z= 0.319 Chirality : 0.043 0.272 2430 Planarity : 0.004 0.085 2577 Dihedral : 17.804 116.683 2787 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.92 % Allowed : 25.86 % 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: 0.42 (0.20), residues: 1806 helix: 1.26 (0.16), residues: 1113 sheet: -2.31 (0.40), residues: 140 loop : -0.93 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 27 TYR 0.016 0.001 TYR D 112 PHE 0.009 0.001 PHE D 204 TRP 0.035 0.002 TRP F 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (15867) covalent geometry : angle 0.62290 / 0.32 (21597) hydrogen bonds : bond 0.04238 / 2.84 ( 763) hydrogen bonds : angle 3.49826 / 2.54 ( 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 347 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 288 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6946 (ttmt) REVERT: A 159 ASP cc_start: 0.7135 (m-30) cc_final: 0.6761 (m-30) REVERT: B 196 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: C 229 MET cc_start: 0.7991 (mmm) cc_final: 0.7451 (mmt) REVERT: C 261 LYS cc_start: 0.3888 (tptt) cc_final: 0.3241 (tmtt) REVERT: C 273 LYS cc_start: 0.7997 (pttt) cc_final: 0.7746 (tmtt) REVERT: D 33 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7632 (tp) REVERT: D 81 GLN cc_start: 0.7119 (mp10) cc_final: 0.6832 (mt0) REVERT: D 85 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7014 (ttt180) REVERT: D 183 ASP cc_start: 0.7331 (m-30) cc_final: 0.7111 (m-30) REVERT: D 210 MET cc_start: 0.8305 (ttm) cc_final: 0.8025 (ttp) REVERT: E 40 LYS cc_start: 0.8571 (tppt) cc_final: 0.8279 (tptp) REVERT: E 63 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8024 (mpt180) REVERT: E 209 GLU cc_start: 0.7581 (tp30) cc_final: 0.7268 (tp30) REVERT: F 127 ASP cc_start: 0.7632 (m-30) cc_final: 0.7394 (m-30) REVERT: F 162 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7571 (mt-10) REVERT: G 80 GLN cc_start: 0.6487 (pm20) cc_final: 0.5807 (tt0) REVERT: G 241 ILE cc_start: 0.9262 (mm) cc_final: 0.8909 (mp) REVERT: G 256 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8736 (mm) outliers start: 59 outliers final: 41 residues processed: 331 average time/residue: 0.1312 time to fit residues: 63.9951 Evaluate side-chains 318 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 271 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 SER 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 125 PHE Chi-restraints excluded: chain C residue 186 VAL 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 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 231 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL 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 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: 10.0000 chunk 108 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 185 optimal weight: 50.0000 chunk 83 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 206 ASN E 43 HIS F 77 HIS G 43 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107023 restraints weight = 25826.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110094 restraints weight = 13679.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112164 restraints weight = 9235.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.113492 restraints weight = 7221.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114335 restraints weight = 6209.688| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15867 Z= 0.118 Angle : 0.624 11.423 21597 Z= 0.320 Chirality : 0.042 0.264 2430 Planarity : 0.004 0.050 2577 Dihedral : 17.558 113.568 2787 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.12 % Allowed : 26.99 % 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: 0.49 (0.20), residues: 1806 helix: 1.30 (0.15), residues: 1113 sheet: -2.29 (0.39), residues: 140 loop : -0.85 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 27 TYR 0.013 0.001 TYR D 112 PHE 0.011 0.001 PHE E 106 TRP 0.026 0.002 TRP G 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (15867) covalent geometry : angle 0.62418 / 0.32 (21597) hydrogen bonds : bond 0.04122 / 2.77 ( 763) hydrogen bonds : angle 3.49567 / 2.54 ( 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 331 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 284 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6976 (ttmt) REVERT: A 159 ASP cc_start: 0.7123 (m-30) cc_final: 0.6736 (m-30) REVERT: B 37 GLN cc_start: 0.7763 (tp40) cc_final: 0.7440 (tp40) REVERT: B 196 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: C 229 MET cc_start: 0.7997 (mmm) cc_final: 0.7777 (mmt) REVERT: C 261 LYS cc_start: 0.3919 (tptt) cc_final: 0.3269 (tmtt) REVERT: C 273 LYS cc_start: 0.7995 (pttt) cc_final: 0.7749 (tttp) REVERT: D 81 GLN cc_start: 0.7158 (mp10) cc_final: 0.6863 (mt0) REVERT: D 85 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7061 (ttt180) REVERT: D 210 MET cc_start: 0.8353 (ttm) cc_final: 0.8149 (ttp) REVERT: E 40 LYS cc_start: 0.8577 (tppt) cc_final: 0.8294 (tptp) REVERT: E 63 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7922 (mpt180) REVERT: E 229 MET cc_start: 0.7606 (mmp) cc_final: 0.6970 (mmm) REVERT: F 113 LEU cc_start: 0.9231 (mt) cc_final: 0.9003 (mt) REVERT: F 127 ASP cc_start: 0.7632 (m-30) cc_final: 0.7415 (m-30) REVERT: F 162 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7622 (mt-10) REVERT: G 241 ILE cc_start: 0.9253 (mm) cc_final: 0.8892 (mp) REVERT: G 256 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8730 (mm) outliers start: 47 outliers final: 35 residues processed: 318 average time/residue: 0.1310 time to fit residues: 61.2830 Evaluate side-chains 305 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 265 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 SER 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 C residue 125 PHE Chi-restraints excluded: chain C residue 186 VAL 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 255 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 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 166 optimal weight: 0.4980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 206 ASN E 43 HIS E 206 ASN F 77 HIS G 43 HIS G 213 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107491 restraints weight = 25833.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.110538 restraints weight = 13646.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112613 restraints weight = 9224.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113928 restraints weight = 7218.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.114643 restraints weight = 6218.254| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15867 Z= 0.119 Angle : 0.618 11.368 21597 Z= 0.319 Chirality : 0.042 0.355 2430 Planarity : 0.004 0.041 2577 Dihedral : 17.440 113.016 2787 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.73 % Allowed : 27.33 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1806 helix: 1.32 (0.15), residues: 1106 sheet: -2.27 (0.39), residues: 140 loop : -0.82 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 95 TYR 0.014 0.001 TYR D 112 PHE 0.024 0.001 PHE F 204 TRP 0.028 0.002 TRP G 211 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15867) covalent geometry : angle 0.61757 / 0.32 (21597) hydrogen bonds : bond 0.04150 / 2.83 ( 763) hydrogen bonds : angle 3.55338 / 2.58 ( 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 310 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 269 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7411 (ptpt) cc_final: 0.7035 (ttmt) REVERT: A 159 ASP cc_start: 0.7087 (m-30) cc_final: 0.6714 (m-30) REVERT: C 229 MET cc_start: 0.8006 (mmm) cc_final: 0.7791 (mmt) REVERT: C 261 LYS cc_start: 0.3916 (tptt) cc_final: 0.3290 (tmtt) REVERT: C 273 LYS cc_start: 0.8017 (pttt) cc_final: 0.7755 (tttp) REVERT: D 81 GLN cc_start: 0.7166 (mp10) cc_final: 0.6860 (mt0) REVERT: D 85 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7172 (mmt90) REVERT: E 63 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7941 (mpt180) REVERT: E 229 MET cc_start: 0.7654 (mmp) cc_final: 0.6957 (mmm) REVERT: F 113 LEU cc_start: 0.9231 (mt) cc_final: 0.9008 (mt) REVERT: F 127 ASP cc_start: 0.7637 (m-30) cc_final: 0.7409 (m-30) REVERT: F 162 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7629 (mt-10) REVERT: G 240 TYR cc_start: 0.8668 (m-10) cc_final: 0.8293 (m-10) REVERT: G 241 ILE cc_start: 0.9248 (mm) cc_final: 0.8893 (mp) REVERT: G 256 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8798 (mm) outliers start: 41 outliers final: 35 residues processed: 301 average time/residue: 0.1311 time to fit residues: 58.3507 Evaluate side-chains 299 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 261 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 186 VAL 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 255 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 255 SER Chi-restraints excluded: chain E residue 275 TYR 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 F residue 263 ILE 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 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 181 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 176 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 125 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 206 ASN E 43 HIS F 77 HIS G 43 HIS ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106826 restraints weight = 25596.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.109840 restraints weight = 13631.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.111872 restraints weight = 9261.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.113183 restraints weight = 7276.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114032 restraints weight = 6258.457| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15867 Z= 0.128 Angle : 0.630 11.141 21597 Z= 0.323 Chirality : 0.043 0.280 2430 Planarity : 0.004 0.039 2577 Dihedral : 17.358 112.457 2787 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.79 % Allowed : 27.59 % 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: 0.57 (0.20), residues: 1806 helix: 1.36 (0.16), residues: 1106 sheet: -2.28 (0.39), residues: 140 loop : -0.77 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 27 TYR 0.014 0.001 TYR D 112 PHE 0.023 0.001 PHE E 106 TRP 0.028 0.002 TRP G 211 HIS 0.007 0.001 HIS E 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15867) covalent geometry : angle 0.63014 / 0.32 (21597) hydrogen bonds : bond 0.04069 / 2.75 ( 763) hydrogen bonds : angle 3.56966 / 2.60 ( 2257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.21 seconds wall clock time: 56 minutes 10.87 seconds (3370.87 seconds total)