Starting phenix.real_space_refine on Tue Dec 31 10:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plh_13489/12_2024/7plh_13489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plh_13489/12_2024/7plh_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_13489/12_2024/7plh_13489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plh_13489/12_2024/7plh_13489.map" model { file = "/net/cci-nas-00/data/ceres_data/7plh_13489/12_2024/7plh_13489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plh_13489/12_2024/7plh_13489_neut.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: {'GLU:plan': 1, 'ASN:plan1': 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: 10.28, per 1000 atoms: 0.66 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: 4.14 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.06 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: 4.49 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2492 1.30 - 1.42: 3898 1.42 - 1.55: 9226 1.55 - 1.68: 160 1.68 - 1.80: 91 Bond restraints: 15867 Sorted by residual: bond pdb=" O3A ANP A 301 " pdb=" PB ANP A 301 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP F 301 " pdb=" PB ANP F 301 " ideal model delta sigma weight residual 1.700 1.542 0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" O3A ANP G 301 " pdb=" PB ANP G 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3A ANP E 301 " pdb=" PB ANP E 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.20e+01 bond pdb=" O3A ANP D 301 " pdb=" PB ANP D 301 " ideal model delta sigma weight residual 1.700 1.543 0.157 2.00e-02 2.50e+03 6.18e+01 ... (remaining 15862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 21085 4.84 - 9.69: 462 9.69 - 14.53: 42 14.53 - 19.38: 1 19.38 - 24.22: 7 Bond angle restraints: 21597 Sorted by residual: angle pdb=" O3' DA H 13 " pdb=" C3' DA H 13 " pdb=" C2' DA H 13 " ideal model delta sigma weight residual 111.50 96.51 14.99 1.50e+00 4.44e-01 9.99e+01 angle pdb=" N LEU E 244 " pdb=" CA LEU E 244 " pdb=" C LEU E 244 " ideal model delta sigma weight residual 111.14 100.41 10.73 1.08e+00 8.57e-01 9.87e+01 angle pdb=" N PHE F 204 " pdb=" CA PHE F 204 " pdb=" C PHE F 204 " ideal model delta sigma weight residual 111.36 101.95 9.41 1.09e+00 8.42e-01 7.46e+01 angle pdb=" N PHE B 204 " pdb=" CA PHE B 204 " pdb=" C PHE B 204 " ideal model delta sigma weight residual 111.36 101.96 9.40 1.09e+00 8.42e-01 7.43e+01 angle pdb=" N LEU B 244 " pdb=" CA LEU B 244 " pdb=" C LEU B 244 " ideal model delta sigma weight residual 111.69 101.09 10.60 1.23e+00 6.61e-01 7.43e+01 ... (remaining 21592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 8455 24.16 - 48.33: 919 48.33 - 72.49: 383 72.49 - 96.66: 72 96.66 - 120.82: 7 Dihedral angle restraints: 9836 sinusoidal: 4558 harmonic: 5278 Sorted by residual: dihedral pdb=" C ARG C 76 " pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" CB ARG C 76 " ideal model delta harmonic sigma weight residual -122.60 -109.39 -13.21 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C ARG F 76 " pdb=" N ARG F 76 " pdb=" CA ARG F 76 " pdb=" CB ARG F 76 " ideal model delta harmonic sigma weight residual -122.60 -109.42 -13.18 0 2.50e+00 1.60e-01 2.78e+01 dihedral pdb=" C ARG G 76 " pdb=" N ARG G 76 " pdb=" CA ARG G 76 " pdb=" CB ARG G 76 " ideal model delta harmonic sigma weight residual -122.60 -109.43 -13.17 0 2.50e+00 1.60e-01 2.78e+01 ... (remaining 9833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1919 0.103 - 0.205: 357 0.205 - 0.308: 120 0.308 - 0.410: 19 0.410 - 0.513: 15 Chirality restraints: 2430 Sorted by residual: chirality pdb=" CA ARG F 76 " pdb=" N ARG F 76 " pdb=" C ARG F 76 " pdb=" CB ARG F 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CA ARG D 76 " pdb=" N ARG D 76 " pdb=" C ARG D 76 " pdb=" CB ARG D 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.55e+00 chirality pdb=" CA ARG B 76 " pdb=" N ARG B 76 " pdb=" C ARG B 76 " pdb=" CB ARG B 76 " both_signs ideal model delta sigma weight residual False 2.51 3.02 -0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 2427 not shown) Planarity restraints: 2577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 241 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C ILE A 241 " -0.093 2.00e-02 2.50e+03 pdb=" O ILE A 241 " 0.035 2.00e-02 2.50e+03 pdb=" N GLY A 242 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 242 " -0.026 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C GLY C 242 " 0.089 2.00e-02 2.50e+03 pdb=" O GLY C 242 " -0.034 2.00e-02 2.50e+03 pdb=" N ARG C 243 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 242 " 0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLY F 242 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY F 242 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG F 243 " 0.020 2.00e-02 2.50e+03 ... (remaining 2574 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 121 2.50 - 3.10: 11515 3.10 - 3.70: 24471 3.70 - 4.30: 34724 4.30 - 4.90: 55938 Nonbonded interactions: 126769 Sorted by model distance: nonbonded pdb=" O1B ANP A 301 " pdb="MG MG A 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP B 301 " pdb="MG MG B 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP D 301 " pdb="MG MG D 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP F 301 " pdb="MG MG F 302 " model vdw 1.901 2.170 nonbonded pdb=" O1B ANP G 301 " pdb="MG MG G 302 " model vdw 1.902 2.170 ... (remaining 126764 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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 276 or resid 301 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: 4.600 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: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 38.960 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.158 15867 Z= 0.699 Angle : 1.667 24.221 21597 Z= 1.103 Chirality : 0.101 0.513 2430 Planarity : 0.006 0.054 2577 Dihedral : 22.702 120.821 6420 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.020 0.003 TRP G 45 HIS 0.004 0.002 HIS F 43 PHE 0.017 0.002 PHE B 196 TYR 0.012 0.002 TYR D 275 ARG 0.025 0.001 ARG A 57 *********************** 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 : 1.708 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: 0.8134 (m-40) cc_final: 0.7846 (m-40) REVERT: A 234 THR cc_start: 0.9384 (m) cc_final: 0.9021 (p) REVERT: B 209 GLU cc_start: 0.7632 (tp30) cc_final: 0.6917 (tp30) REVERT: C 32 SER cc_start: 0.8442 (t) cc_final: 0.8231 (t) REVERT: C 260 LEU cc_start: 0.6918 (mp) cc_final: 0.6376 (tp) REVERT: D 250 GLU cc_start: 0.8359 (tp30) cc_final: 0.8106 (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: 0.6428 (m-30) REVERT: G 63 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5679 (mtm180) REVERT: G 234 THR cc_start: 0.8845 (m) cc_final: 0.8432 (p) REVERT: G 241 ILE cc_start: 0.8907 (mm) cc_final: 0.8696 (mp) outliers start: 135 outliers final: 17 residues processed: 697 average time/residue: 0.4020 time to fit residues: 369.6412 Evaluate side-chains 340 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 321 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 157 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN A 98 GLN B 43 HIS B 77 HIS B 213 GLN D 43 HIS E 43 HIS F 43 HIS F 77 HIS G 37 GLN G 43 HIS G 97 HIS G 206 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15867 Z= 0.247 Angle : 0.693 10.330 21597 Z= 0.360 Chirality : 0.043 0.162 2430 Planarity : 0.005 0.051 2577 Dihedral : 20.551 128.337 2822 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 4.59 % Allowed : 20.28 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1806 helix: 0.47 (0.15), residues: 1106 sheet: -1.72 (0.53), residues: 105 loop : -1.87 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 211 HIS 0.003 0.001 HIS E 97 PHE 0.012 0.002 PHE D 196 TYR 0.017 0.002 TYR E 73 ARG 0.008 0.001 ARG B 57 *********************** 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 429 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 360 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.7108 (mt) cc_final: 0.6783 (mt) REVERT: A 230 LEU cc_start: 0.9117 (tp) cc_final: 0.8839 (tt) REVERT: B 37 GLN cc_start: 0.7595 (tp40) cc_final: 0.7303 (tm-30) REVERT: C 229 MET cc_start: 0.7645 (mmm) cc_final: 0.6958 (mmt) REVERT: D 187 LEU cc_start: 0.7896 (tp) cc_final: 0.7678 (tp) REVERT: E 63 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7983 (tpt170) REVERT: E 213 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: F 36 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7952 (pt) REVERT: F 71 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: F 159 ASP cc_start: 0.7236 (m-30) cc_final: 0.7003 (m-30) REVERT: F 163 ASP cc_start: 0.7229 (m-30) cc_final: 0.7017 (m-30) REVERT: G 210 MET cc_start: 0.7710 (tpp) cc_final: 0.7363 (tpp) outliers start: 69 outliers final: 38 residues processed: 409 average time/residue: 0.3309 time to fit residues: 189.8976 Evaluate side-chains 318 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 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 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 253 ILE Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 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 213 GLN Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain E residue 276 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 71 ASP 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 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 117 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 267 VAL Chi-restraints excluded: chain G residue 276 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 30.0000 chunk 167 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 HIS D 97 HIS D 98 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS E 206 ASN F 43 HIS F 77 HIS G 97 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15867 Z= 0.291 Angle : 0.661 10.272 21597 Z= 0.340 Chirality : 0.043 0.159 2430 Planarity : 0.005 0.054 2577 Dihedral : 19.173 124.070 2806 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.85 % Allowed : 21.94 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 1806 helix: 0.83 (0.15), residues: 1113 sheet: -1.83 (0.49), residues: 105 loop : -1.64 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 45 HIS 0.008 0.001 HIS E 97 PHE 0.013 0.001 PHE G 190 TYR 0.013 0.002 TYR A 93 ARG 0.008 0.001 ARG G 249 *********************** 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 383 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 310 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 GLN cc_start: 0.7333 (mt0) cc_final: 0.7060 (mt0) REVERT: B 37 GLN cc_start: 0.7564 (tp40) cc_final: 0.7242 (tm-30) REVERT: B 185 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7676 (mp10) REVERT: B 196 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: C 229 MET cc_start: 0.7602 (mmm) cc_final: 0.7037 (mmt) REVERT: D 85 ARG cc_start: 0.7194 (mmm160) cc_final: 0.6752 (ttm170) REVERT: D 273 LYS cc_start: 0.7320 (ptmt) cc_final: 0.7000 (pttp) REVERT: E 27 ARG cc_start: 0.8276 (ttp80) cc_final: 0.8060 (ttp80) REVERT: E 63 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8079 (mpt180) REVERT: E 210 MET cc_start: 0.8051 (tpp) cc_final: 0.7681 (ttm) REVERT: F 36 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8061 (pt) REVERT: G 196 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7902 (m-10) outliers start: 73 outliers final: 45 residues processed: 369 average time/residue: 0.3217 time to fit residues: 171.3852 Evaluate side-chains 304 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 1.754 ------------------------------------------------------------------------------- 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 209 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 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 185 GLN Chi-restraints excluded: chain B residue 196 PHE 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 198 LYS 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 36 LEU Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 247 ILE 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 41 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 232 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 ASN C 213 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS F 97 HIS G 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15867 Z= 0.212 Angle : 0.598 11.160 21597 Z= 0.311 Chirality : 0.041 0.142 2430 Planarity : 0.004 0.039 2577 Dihedral : 17.970 117.725 2789 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.52 % Allowed : 22.61 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1806 helix: 1.09 (0.15), residues: 1113 sheet: -2.23 (0.36), residues: 175 loop : -1.32 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 45 HIS 0.007 0.001 HIS E 97 PHE 0.027 0.002 PHE E 204 TYR 0.010 0.001 TYR A 93 ARG 0.006 0.001 ARG C 254 *********************** 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 369 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 301 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: B 185 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: C 229 MET cc_start: 0.7526 (mmm) cc_final: 0.7114 (mmt) REVERT: D 85 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6953 (ttm170) REVERT: D 232 ILE cc_start: 0.8281 (tt) cc_final: 0.8024 (tp) REVERT: E 63 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7984 (mpt180) REVERT: F 36 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7850 (pp) outliers start: 68 outliers final: 46 residues processed: 348 average time/residue: 0.2987 time to fit residues: 150.1716 Evaluate side-chains 312 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 263 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 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 232 ILE Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 248 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 186 VAL Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 124 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN C 77 HIS C 213 GLN D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS F 77 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15867 Z= 0.297 Angle : 0.633 10.321 21597 Z= 0.330 Chirality : 0.042 0.153 2430 Planarity : 0.004 0.046 2577 Dihedral : 17.630 116.383 2787 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.32 % Allowed : 23.67 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1806 helix: 1.09 (0.15), residues: 1113 sheet: -1.90 (0.47), residues: 105 loop : -1.39 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 211 HIS 0.006 0.001 HIS E 97 PHE 0.017 0.002 PHE E 106 TYR 0.011 0.002 TYR A 93 ARG 0.006 0.001 ARG C 254 *********************** 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 365 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 285 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6746 (ttmt) REVERT: B 115 TYR cc_start: 0.8135 (m-80) cc_final: 0.7919 (m-80) REVERT: B 185 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: C 229 MET cc_start: 0.7662 (mmm) cc_final: 0.7266 (mmt) REVERT: D 85 ARG cc_start: 0.7425 (mmm160) cc_final: 0.7049 (mmt90) REVERT: E 63 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8213 (mpt180) REVERT: G 196 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8035 (m-10) REVERT: G 206 ASN cc_start: 0.7642 (m-40) cc_final: 0.7421 (m110) outliers start: 80 outliers final: 54 residues processed: 343 average time/residue: 0.2903 time to fit residues: 144.5100 Evaluate side-chains 320 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 262 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 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 185 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 212 GLU 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 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 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 231 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 GLN D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 GLN E 43 HIS F 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15867 Z= 0.205 Angle : 0.590 10.883 21597 Z= 0.307 Chirality : 0.041 0.167 2430 Planarity : 0.004 0.043 2577 Dihedral : 17.370 110.089 2787 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.99 % Allowed : 25.93 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.20), residues: 1806 helix: 1.26 (0.16), residues: 1113 sheet: -1.96 (0.46), residues: 105 loop : -1.31 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 20 HIS 0.007 0.001 HIS E 97 PHE 0.016 0.001 PHE B 190 TYR 0.010 0.001 TYR A 93 ARG 0.006 0.001 ARG C 254 *********************** 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 350 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 290 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6778 (ttmt) REVERT: B 185 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: B 245 ASP cc_start: 0.8134 (t70) cc_final: 0.7816 (t0) REVERT: C 229 MET cc_start: 0.7563 (mmm) cc_final: 0.7279 (mmt) REVERT: D 85 ARG cc_start: 0.7525 (mmm160) cc_final: 0.7209 (mmt90) REVERT: D 127 ASP cc_start: 0.6533 (m-30) cc_final: 0.6012 (m-30) REVERT: D 232 ILE cc_start: 0.8436 (tt) cc_final: 0.8158 (tp) REVERT: E 63 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8035 (mpt180) REVERT: G 206 ASN cc_start: 0.7683 (m-40) cc_final: 0.7446 (m110) outliers start: 60 outliers final: 46 residues processed: 333 average time/residue: 0.3099 time to fit residues: 150.6993 Evaluate side-chains 307 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 258 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 185 GLN Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain 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 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN C 213 GLN D 206 ASN E 43 HIS E 206 ASN F 77 HIS G 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15867 Z= 0.248 Angle : 0.607 10.597 21597 Z= 0.315 Chirality : 0.042 0.197 2430 Planarity : 0.004 0.048 2577 Dihedral : 17.229 107.698 2785 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.79 % Allowed : 25.93 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1806 helix: 1.27 (0.16), residues: 1113 sheet: -2.33 (0.34), residues: 175 loop : -1.17 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 20 HIS 0.005 0.001 HIS E 97 PHE 0.024 0.001 PHE E 106 TYR 0.018 0.001 TYR C 73 ARG 0.007 0.000 ARG A 95 *********************** 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 340 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.6779 (ttmt) REVERT: B 245 ASP cc_start: 0.8263 (t70) cc_final: 0.7937 (t0) REVERT: C 229 MET cc_start: 0.7586 (mmm) cc_final: 0.7309 (mmt) REVERT: D 85 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7250 (mmt90) REVERT: E 63 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8128 (mpt180) REVERT: G 196 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7814 (m-10) outliers start: 72 outliers final: 53 residues processed: 317 average time/residue: 0.3012 time to fit residues: 138.0834 Evaluate side-chains 312 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 256 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 255 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 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 231 ARG Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 255 SER 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 110 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 77 HIS D 206 ASN E 43 HIS F 77 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.6732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15867 Z= 0.215 Angle : 0.593 10.818 21597 Z= 0.309 Chirality : 0.041 0.257 2430 Planarity : 0.004 0.047 2577 Dihedral : 17.098 102.818 2785 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.06 % Allowed : 26.80 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1806 helix: 1.35 (0.16), residues: 1106 sheet: -2.26 (0.34), residues: 175 loop : -1.15 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 20 HIS 0.006 0.001 HIS E 97 PHE 0.015 0.001 PHE D 106 TYR 0.015 0.001 TYR C 73 ARG 0.007 0.000 ARG C 254 *********************** 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 336 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6812 (ttmt) REVERT: A 209 GLU cc_start: 0.7666 (pt0) cc_final: 0.7453 (mt-10) REVERT: B 245 ASP cc_start: 0.8247 (t70) cc_final: 0.7925 (t0) REVERT: C 229 MET cc_start: 0.7533 (mmm) cc_final: 0.7292 (mmt) REVERT: D 85 ARG cc_start: 0.7660 (mmm160) cc_final: 0.7383 (ttt180) REVERT: D 232 ILE cc_start: 0.8450 (tt) cc_final: 0.8177 (tp) REVERT: E 27 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8070 (ttp80) REVERT: E 63 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8058 (mpt180) outliers start: 61 outliers final: 48 residues processed: 320 average time/residue: 0.3166 time to fit residues: 144.6134 Evaluate side-chains 306 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 256 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 198 LYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 125 PHE 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 216 LEU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 72 optimal weight: 0.0170 chunk 131 optimal weight: 7.9990 chunk 51 optimal weight: 0.0170 chunk 150 optimal weight: 20.0000 chunk 158 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 77 HIS D 206 ASN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS F 77 HIS G 206 ASN G 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15867 Z= 0.166 Angle : 0.586 10.743 21597 Z= 0.304 Chirality : 0.040 0.225 2430 Planarity : 0.004 0.048 2577 Dihedral : 16.899 99.410 2785 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.93 % Allowed : 27.66 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1806 helix: 1.41 (0.16), residues: 1106 sheet: -2.74 (0.37), residues: 140 loop : -0.92 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 20 HIS 0.004 0.001 HIS E 97 PHE 0.018 0.001 PHE B 190 TYR 0.013 0.001 TYR B 275 ARG 0.013 0.001 ARG G 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3612 Ramachandran restraints generated. 1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7591 (pt0) cc_final: 0.7360 (mt-10) REVERT: B 245 ASP cc_start: 0.8282 (t70) cc_final: 0.8025 (t0) REVERT: C 229 MET cc_start: 0.7519 (mmm) cc_final: 0.7312 (mmt) REVERT: C 246 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7135 (mm-30) REVERT: D 31 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7622 (mttm) REVERT: D 85 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7389 (mmt90) REVERT: D 232 ILE cc_start: 0.8383 (tt) cc_final: 0.8113 (tp) REVERT: E 27 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8080 (ttp80) outliers start: 44 outliers final: 33 residues processed: 309 average time/residue: 0.2922 time to fit residues: 130.6092 Evaluate side-chains 295 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 261 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 125 PHE 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 129 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain F residue 269 GLN Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 5.9990 chunk 176 optimal weight: 30.0000 chunk 107 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 77 HIS D 206 ASN F 77 HIS G 43 HIS G 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15867 Z= 0.403 Angle : 0.726 10.187 21597 Z= 0.372 Chirality : 0.046 0.272 2430 Planarity : 0.005 0.048 2577 Dihedral : 17.181 102.704 2784 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.06 % Allowed : 27.66 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.19), residues: 1806 helix: 1.09 (0.15), residues: 1106 sheet: -2.49 (0.38), residues: 140 loop : -1.21 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 211 HIS 0.005 0.001 HIS F 43 PHE 0.016 0.002 PHE B 190 TYR 0.016 0.002 TYR E 115 ARG 0.013 0.001 ARG G 182 ********************** 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 301 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 255 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5716 (tt0) REVERT: C 229 MET cc_start: 0.7713 (mmm) cc_final: 0.7386 (mmt) REVERT: C 246 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7339 (mm-30) REVERT: D 85 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7360 (ttt180) REVERT: G 199 LEU cc_start: 0.8731 (tt) cc_final: 0.8359 (tp) outliers start: 46 outliers final: 40 residues processed: 290 average time/residue: 0.3071 time to fit residues: 130.0447 Evaluate side-chains 283 residues out of total 1589 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 242 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 212 GLU Chi-restraints excluded: chain 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 55 SER Chi-restraints excluded: chain D residue 125 PHE 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 129 THR Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 125 PHE Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 177 ASP Chi-restraints excluded: chain F residue 255 SER Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 125 PHE Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 18 optimal weight: 0.0980 chunk 27 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN C 213 GLN D 206 ASN F 77 HIS G 43 HIS G 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107450 restraints weight = 25573.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110531 restraints weight = 13712.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.112574 restraints weight = 9310.588| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15867 Z= 0.176 Angle : 0.624 12.665 21597 Z= 0.322 Chirality : 0.041 0.231 2430 Planarity : 0.004 0.050 2577 Dihedral : 16.918 100.175 2784 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.39 % Allowed : 28.59 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1806 helix: 1.23 (0.16), residues: 1106 sheet: -2.85 (0.35), residues: 140 loop : -0.92 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 20 HIS 0.004 0.001 HIS E 97 PHE 0.019 0.001 PHE G 204 TYR 0.011 0.001 TYR C 73 ARG 0.012 0.001 ARG G 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.87 seconds wall clock time: 72 minutes 41.53 seconds (4361.53 seconds total)