Starting phenix.real_space_refine on Sun Jul 5 21:08:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rku_19283/07_2026/8rku_19283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rku_19283/07_2026/8rku_19283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rku_19283/07_2026/8rku_19283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rku_19283/07_2026/8rku_19283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rku_19283/07_2026/8rku_19283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rku_19283/07_2026/8rku_19283.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.080 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 82 5.49 5 Mg 14 5.21 5 S 112 5.16 5 C 18818 2.51 5 N 5491 2.21 5 O 6209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30726 Number of models: 1 Model: "" Number of chains: 46 Chain: "2" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "3" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "M" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "N" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "O" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "P" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "Q" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "I" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "K" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "O" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "P" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 6.48, per 1000 atoms: 0.21 Number of scatterers: 30726 At special positions: 0 Unit cell: (130.312, 147.056, 157.976, 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 112 16.00 P 82 15.00 Mg 14 11.99 O 6209 8.00 N 5491 7.00 C 18818 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: 2.54 Conformation dependent library (CDL) restraints added in 965.4 milliseconds 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 14 sheets defined 62.6% alpha, 6.9% beta 13 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 3.36 Creating SS restraints... Processing helix chain 'D' and resid 19 through 29 removed outlier: 3.811A pdb=" N ALA D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 52 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 101 through 113 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 151 No H-bonds generated for 'chain 'D' and resid 150 through 151' Processing helix chain 'D' and resid 152 through 165 removed outlier: 3.677A pdb=" N ASP D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.777A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 3.710A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 76 removed outlier: 3.572A pdb=" N ARG E 74 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR E 75 " --> pdb=" O ASP E 71 " (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 145 through 149 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 182 removed outlier: 3.860A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 Processing helix chain 'E' and resid 240 through 258 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 30 removed outlier: 3.839A pdb=" N GLY F 30 " --> pdb=" O ALA F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 75 removed outlier: 3.513A pdb=" N ARG F 74 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 146 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 173 through 182 removed outlier: 3.814A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 200 through 215 Processing helix chain 'F' and resid 226 through 238 Processing helix chain 'F' and resid 240 through 258 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 146 through 149 Processing helix chain 'G' and resid 152 through 164 removed outlier: 4.172A pdb=" N ASP G 156 " --> pdb=" O GLU G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.944A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.634A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 146 through 149 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 173 through 182 removed outlier: 3.903A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 Processing helix chain 'H' and resid 240 through 258 Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'I' and resid 20 through 30 removed outlier: 3.785A pdb=" N GLY I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 101 through 113 Processing helix chain 'I' and resid 121 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 3.676A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 188 Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 30 removed outlier: 3.847A pdb=" N GLY J 30 " --> pdb=" O ALA J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 151 No H-bonds generated for 'chain 'J' and resid 150 through 151' Processing helix chain 'J' and resid 152 through 164 removed outlier: 4.300A pdb=" N ASP J 156 " --> pdb=" O GLU J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 182 removed outlier: 3.715A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS J 181 " --> pdb=" O ASP J 177 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.594A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 Processing helix chain 'J' and resid 240 through 258 Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 101 through 113 Processing helix chain 'K' and resid 121 through 134 Processing helix chain 'K' and resid 146 through 149 Processing helix chain 'K' and resid 152 through 164 removed outlier: 4.089A pdb=" N ASP K 156 " --> pdb=" O GLU K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 182 removed outlier: 3.878A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing helix chain 'K' and resid 200 through 215 Processing helix chain 'K' and resid 226 through 238 Processing helix chain 'K' and resid 240 through 258 Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'L' and resid 20 through 29 Processing helix chain 'L' and resid 36 through 53 Processing helix chain 'L' and resid 65 through 77 Processing helix chain 'L' and resid 101 through 113 Processing helix chain 'L' and resid 121 through 134 Processing helix chain 'L' and resid 145 through 149 Processing helix chain 'L' and resid 153 through 164 Processing helix chain 'L' and resid 173 through 181 removed outlier: 3.780A pdb=" N ASP L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 removed outlier: 3.543A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 215 Processing helix chain 'L' and resid 226 through 238 removed outlier: 3.894A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 258 Processing helix chain 'L' and resid 264 through 273 Processing helix chain 'M' and resid 20 through 29 Processing helix chain 'M' and resid 36 through 53 Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 101 through 113 Processing helix chain 'M' and resid 121 through 134 Processing helix chain 'M' and resid 146 through 149 Processing helix chain 'M' and resid 150 through 151 No H-bonds generated for 'chain 'M' and resid 150 through 151' Processing helix chain 'M' and resid 152 through 164 removed outlier: 4.265A pdb=" N ASP M 156 " --> pdb=" O GLU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 removed outlier: 3.993A pdb=" N ASP M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 190 Processing helix chain 'M' and resid 200 through 215 Processing helix chain 'M' and resid 226 through 238 removed outlier: 4.002A pdb=" N ILE M 232 " --> pdb=" O GLU M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 240 through 258 Processing helix chain 'M' and resid 264 through 274 removed outlier: 3.876A pdb=" N GLU M 274 " --> pdb=" O GLU M 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 36 through 53 Processing helix chain 'N' and resid 65 through 77 Processing helix chain 'N' and resid 101 through 113 Processing helix chain 'N' and resid 121 through 134 Processing helix chain 'N' and resid 146 through 149 Processing helix chain 'N' and resid 150 through 152 No H-bonds generated for 'chain 'N' and resid 150 through 152' Processing helix chain 'N' and resid 153 through 164 Processing helix chain 'N' and resid 173 through 181 removed outlier: 3.832A pdb=" N ASP N 177 " --> pdb=" O THR N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 190 Processing helix chain 'N' and resid 200 through 215 removed outlier: 3.853A pdb=" N GLU N 212 " --> pdb=" O VAL N 208 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN N 213 " --> pdb=" O GLU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 238 removed outlier: 4.087A pdb=" N ILE N 232 " --> pdb=" O GLU N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 240 through 258 Processing helix chain 'N' and resid 264 through 273 Processing helix chain 'O' and resid 20 through 30 Processing helix chain 'O' and resid 36 through 53 Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'O' and resid 121 through 134 Processing helix chain 'O' and resid 146 through 149 Processing helix chain 'O' and resid 152 through 164 removed outlier: 4.125A pdb=" N ASP O 156 " --> pdb=" O GLU O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 182 removed outlier: 3.839A pdb=" N ASP O 177 " --> pdb=" O THR O 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG O 182 " --> pdb=" O ALA O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 190 Processing helix chain 'O' and resid 201 through 215 Processing helix chain 'O' and resid 226 through 238 Processing helix chain 'O' and resid 240 through 258 removed outlier: 3.694A pdb=" N GLU O 246 " --> pdb=" O GLY O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 264 through 273 removed outlier: 3.992A pdb=" N GLU O 270 " --> pdb=" O ALA O 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 29 Processing helix chain 'P' and resid 36 through 53 Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 101 through 113 Processing helix chain 'P' and resid 121 through 134 Processing helix chain 'P' and resid 145 through 149 Processing helix chain 'P' and resid 153 through 164 Processing helix chain 'P' and resid 173 through 182 removed outlier: 3.833A pdb=" N ASP P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL P 179 " --> pdb=" O ARG P 175 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 190 Processing helix chain 'P' and resid 200 through 214 Processing helix chain 'P' and resid 228 through 238 removed outlier: 3.955A pdb=" N ILE P 232 " --> pdb=" O GLU P 228 " (cutoff:3.500A) Processing helix chain 'P' and resid 240 through 259 removed outlier: 4.483A pdb=" N GLU P 246 " --> pdb=" O GLY P 242 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG P 249 " --> pdb=" O ASP P 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 264 through 273 removed outlier: 3.645A pdb=" N GLU P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 30 removed outlier: 4.026A pdb=" N ARG Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 53 Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 101 through 113 Processing helix chain 'Q' and resid 121 through 134 Processing helix chain 'Q' and resid 146 through 149 Processing helix chain 'Q' and resid 152 through 164 removed outlier: 3.889A pdb=" N ASP Q 156 " --> pdb=" O GLU Q 152 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU Q 164 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 182 removed outlier: 3.873A pdb=" N ASP Q 177 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG Q 182 " --> pdb=" O ALA Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 190 Processing helix chain 'Q' and resid 200 through 215 removed outlier: 3.954A pdb=" N GLU Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 238 removed outlier: 3.648A pdb=" N ALA Q 236 " --> pdb=" O ILE Q 232 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU Q 238 " --> pdb=" O THR Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 240 through 257 removed outlier: 4.305A pdb=" N GLU Q 246 " --> pdb=" O GLY Q 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 273 Processing sheet with id=AA1, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.542A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ASP F 144 " --> pdb=" O VAL F 92 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE F 94 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.551A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP G 144 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE G 94 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.550A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP H 144 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE H 94 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.500A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP I 144 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE I 94 " --> pdb=" O ASP I 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.530A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.504A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP K 144 " --> pdb=" O VAL K 92 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE K 94 " --> pdb=" O ASP K 144 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL K 59 " --> pdb=" O PHE K 196 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 91 through 94 removed outlier: 6.614A pdb=" N VAL L 92 " --> pdb=" O ILE L 142 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU L 141 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N VAL L 171 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE L 143 " --> pdb=" O VAL L 171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 91 through 94 removed outlier: 6.521A pdb=" N VAL M 92 " --> pdb=" O ILE M 142 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ASP M 144 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE M 94 " --> pdb=" O ASP M 144 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU M 141 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N VAL M 171 " --> pdb=" O LEU M 141 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE M 143 " --> pdb=" O VAL M 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 91 through 94 removed outlier: 6.547A pdb=" N VAL N 92 " --> pdb=" O ILE N 142 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ASP N 144 " --> pdb=" O VAL N 92 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE N 94 " --> pdb=" O ASP N 144 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 141 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL N 171 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE N 143 " --> pdb=" O VAL N 171 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 91 through 94 removed outlier: 6.512A pdb=" N VAL O 92 " --> pdb=" O ILE O 142 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP O 144 " --> pdb=" O VAL O 92 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE O 94 " --> pdb=" O ASP O 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'P' and resid 91 through 94 removed outlier: 6.549A pdb=" N VAL P 92 " --> pdb=" O ILE P 142 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG P 57 " --> pdb=" O LEU P 194 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N PHE P 196 " --> pdb=" O ARG P 57 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL P 59 " --> pdb=" O PHE P 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 91 through 94 1590 hydrogen bonds defined for protein. 4671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 5.69 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8846 1.33 - 1.45: 4052 1.45 - 1.57: 17538 1.57 - 1.69: 129 1.69 - 1.81: 168 Bond restraints: 30733 Sorted by residual: bond pdb=" C3' DT 2 46 " pdb=" C2' DT 2 46 " ideal model delta sigma weight residual 1.516 1.557 -0.041 8.00e-03 1.56e+04 2.59e+01 bond pdb=" C3' DA 3 99 " pdb=" C2' DA 3 99 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.78e+01 bond pdb=" C3' DT 3 96 " pdb=" C2' DT 3 96 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.78e+01 bond pdb=" C3' DT 2 36 " pdb=" C2' DT 2 36 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.61e+01 bond pdb=" C3' DT 3 94 " pdb=" C2' DT 3 94 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 ... (remaining 30728 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 39320 1.69 - 3.37: 2024 3.37 - 5.06: 190 5.06 - 6.75: 30 6.75 - 8.43: 5 Bond angle restraints: 41569 Sorted by residual: angle pdb=" O5' DA 3 84 " pdb=" C5' DA 3 84 " pdb=" C4' DA 3 84 " ideal model delta sigma weight residual 109.40 115.96 -6.56 8.00e-01 1.56e+00 6.73e+01 angle pdb=" O5' DA 3 87 " pdb=" C5' DA 3 87 " pdb=" C4' DA 3 87 " ideal model delta sigma weight residual 109.40 114.48 -5.08 8.00e-01 1.56e+00 4.03e+01 angle pdb=" O5' DT 2 35 " pdb=" C5' DT 2 35 " pdb=" C4' DT 2 35 " ideal model delta sigma weight residual 109.40 114.43 -5.03 8.00e-01 1.56e+00 3.95e+01 angle pdb=" O5' DT 2 50 " pdb=" C5' DT 2 50 " pdb=" C4' DT 2 50 " ideal model delta sigma weight residual 109.40 114.09 -4.69 8.00e-01 1.56e+00 3.43e+01 angle pdb=" O4' DT 3 90 " pdb=" C4' DT 3 90 " pdb=" C3' DT 3 90 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.80e+01 ... (remaining 41564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 18445 35.41 - 70.81: 756 70.81 - 106.22: 57 106.22 - 141.63: 0 141.63 - 177.04: 2 Dihedral angle restraints: 19260 sinusoidal: 8830 harmonic: 10430 Sorted by residual: dihedral pdb=" CA GLY M 135 " pdb=" C GLY M 135 " pdb=" N CYS M 136 " pdb=" CA CYS M 136 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA THR F 118 " pdb=" C THR F 118 " pdb=" N LYS F 119 " pdb=" CA LYS F 119 " ideal model delta harmonic sigma weight residual 180.00 153.41 26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA TYR N 112 " pdb=" C TYR N 112 " pdb=" N LEU N 113 " pdb=" CA LEU N 113 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 19257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 4013 0.081 - 0.163: 632 0.163 - 0.244: 20 0.244 - 0.325: 1 0.325 - 0.406: 2 Chirality restraints: 4668 Sorted by residual: chirality pdb=" C3' DA 3 98 " pdb=" C4' DA 3 98 " pdb=" O3' DA 3 98 " pdb=" C2' DA 3 98 " both_signs ideal model delta sigma weight residual False -2.73 -2.32 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1' DT 2 35 " pdb=" O4' DT 2 35 " pdb=" C2' DT 2 35 " pdb=" N1 DT 2 35 " both_signs ideal model delta sigma weight residual False 2.43 2.10 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C3' ATP M 300 " pdb=" C2' ATP M 300 " pdb=" C4' ATP M 300 " pdb=" O3' ATP M 300 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 4665 not shown) Planarity restraints: 5066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP P 300 " -0.036 2.00e-02 2.50e+03 2.82e-02 2.18e+01 pdb=" C2 ATP P 300 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ATP P 300 " -0.012 2.00e-02 2.50e+03 pdb=" C5 ATP P 300 " 0.001 2.00e-02 2.50e+03 pdb=" C6 ATP P 300 " -0.002 2.00e-02 2.50e+03 pdb=" C8 ATP P 300 " -0.028 2.00e-02 2.50e+03 pdb=" N1 ATP P 300 " -0.002 2.00e-02 2.50e+03 pdb=" N3 ATP P 300 " 0.003 2.00e-02 2.50e+03 pdb=" N6 ATP P 300 " -0.002 2.00e-02 2.50e+03 pdb=" N7 ATP P 300 " 0.002 2.00e-02 2.50e+03 pdb=" N9 ATP P 300 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT 2 35 " 0.044 2.00e-02 2.50e+03 2.12e-02 1.12e+01 pdb=" N1 DT 2 35 " -0.046 2.00e-02 2.50e+03 pdb=" C2 DT 2 35 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT 2 35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT 2 35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT 2 35 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT 2 35 " 0.014 2.00e-02 2.50e+03 pdb=" C5 DT 2 35 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT 2 35 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT 2 35 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ATP O 300 " -0.025 2.00e-02 2.50e+03 1.94e-02 1.03e+01 pdb=" C2 ATP O 300 " 0.001 2.00e-02 2.50e+03 pdb=" C4 ATP O 300 " -0.014 2.00e-02 2.50e+03 pdb=" C5 ATP O 300 " -0.001 2.00e-02 2.50e+03 pdb=" C6 ATP O 300 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ATP O 300 " -0.015 2.00e-02 2.50e+03 pdb=" N1 ATP O 300 " -0.001 2.00e-02 2.50e+03 pdb=" N3 ATP O 300 " 0.002 2.00e-02 2.50e+03 pdb=" N6 ATP O 300 " -0.001 2.00e-02 2.50e+03 pdb=" N7 ATP O 300 " 0.001 2.00e-02 2.50e+03 pdb=" N9 ATP O 300 " 0.055 2.00e-02 2.50e+03 ... (remaining 5063 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 128 2.37 - 3.00: 16362 3.00 - 3.64: 47813 3.64 - 4.27: 77297 4.27 - 4.90: 124031 Nonbonded interactions: 265631 Sorted by model distance: nonbonded pdb=" O2B ATP O 300 " pdb="MG MG O 301 " model vdw 1.738 2.170 nonbonded pdb="MG MG D 301 " pdb=" O2B ATP D 302 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR E 67 " pdb="MG MG E 301 " model vdw 1.998 2.170 nonbonded pdb=" OG1 THR D 67 " pdb="MG MG D 301 " model vdw 1.999 2.170 nonbonded pdb=" OG1 THR F 67 " pdb="MG MG F 301 " model vdw 2.011 2.170 ... (remaining 265626 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 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) selection = (chain 'I' and resid 19 through 275) selection = (chain 'J' and resid 19 through 275) selection = (chain 'K' and resid 19 through 275) selection = (chain 'L' and resid 19 through 275) selection = (chain 'M' and resid 19 through 275) selection = (chain 'N' and resid 19 through 275) selection = (chain 'O' and resid 19 through 275) selection = (chain 'P' and resid 19 through 275) selection = (chain 'Q' and resid 19 through 275) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.080 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.050 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 : 0.006 0.062 30733 Z= 0.287 Angle : 0.820 8.432 41569 Z= 0.517 Chirality : 0.056 0.406 4668 Planarity : 0.012 0.111 5066 Dihedral : 17.117 177.037 12512 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.38 % Allowed : 5.01 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 3570 helix: -0.90 (0.10), residues: 2142 sheet: 0.49 (0.31), residues: 210 loop : -0.12 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG M 158 TYR 0.028 0.005 TYR P 240 PHE 0.019 0.002 PHE J 190 TRP 0.037 0.004 TRP M 45 HIS 0.011 0.002 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.29 (30733) covalent geometry : angle 0.82024 / 0.52 (41569) hydrogen bonds : bond 0.18215 / 16.71 ( 1619) hydrogen bonds : angle 7.22393 / 6.52 ( 4729) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 566 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 184 GLU cc_start: 0.6516 (tp30) cc_final: 0.5933 (tt0) REVERT: D 189 ARG cc_start: 0.7051 (ptp-110) cc_final: 0.6708 (ptp90) REVERT: D 214 MET cc_start: 0.7847 (mtm) cc_final: 0.7599 (mtm) REVERT: D 229 MET cc_start: 0.7004 (mmt) cc_final: 0.6589 (mmt) REVERT: E 127 ASP cc_start: 0.6740 (m-30) cc_final: 0.6489 (m-30) REVERT: E 140 MET cc_start: 0.9210 (ttm) cc_final: 0.8805 (ttm) REVERT: E 225 LYS cc_start: 0.7027 (tptp) cc_final: 0.6798 (ttpp) REVERT: E 227 LYS cc_start: 0.7292 (ttpp) cc_final: 0.7014 (ttmm) REVERT: E 231 ARG cc_start: 0.7772 (ttp80) cc_final: 0.7035 (tpp-160) REVERT: F 128 ARG cc_start: 0.8308 (mmm160) cc_final: 0.8087 (tpt170) REVERT: F 131 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7476 (mm-30) REVERT: F 202 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7490 (mm-30) REVERT: F 205 LYS cc_start: 0.8291 (tttm) cc_final: 0.8083 (tttm) REVERT: F 209 GLU cc_start: 0.7945 (tt0) cc_final: 0.7738 (tp30) REVERT: F 210 MET cc_start: 0.8151 (mtp) cc_final: 0.7717 (mtp) REVERT: G 152 GLU cc_start: 0.8700 (pt0) cc_final: 0.8494 (pm20) REVERT: G 223 ASN cc_start: 0.6982 (m-40) cc_final: 0.6425 (m-40) REVERT: G 269 GLN cc_start: 0.7257 (mm110) cc_final: 0.6764 (mt0) REVERT: G 270 GLU cc_start: 0.7677 (tt0) cc_final: 0.7463 (tt0) REVERT: H 202 GLU cc_start: 0.7244 (tp30) cc_final: 0.7040 (tp30) REVERT: H 209 GLU cc_start: 0.6827 (tt0) cc_final: 0.6619 (tm-30) REVERT: H 261 LYS cc_start: 0.7656 (mptt) cc_final: 0.7020 (mmtm) REVERT: I 37 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7728 (tp40) REVERT: I 99 LYS cc_start: 0.8649 (mttm) cc_final: 0.8408 (mttm) REVERT: I 107 LYS cc_start: 0.8746 (mtpm) cc_final: 0.8458 (mtpt) REVERT: I 231 ARG cc_start: 0.7562 (ttp-170) cc_final: 0.7175 (ttp80) REVERT: J 196 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: J 206 ASN cc_start: 0.8199 (m110) cc_final: 0.7534 (m110) REVERT: J 227 LYS cc_start: 0.7121 (tmmt) cc_final: 0.6857 (tmmt) REVERT: J 228 GLU cc_start: 0.7204 (mp0) cc_final: 0.6962 (mp0) REVERT: J 231 ARG cc_start: 0.7330 (tpm170) cc_final: 0.7082 (tpp-160) REVERT: J 269 GLN cc_start: 0.7305 (mt0) cc_final: 0.7071 (mt0) REVERT: K 22 GLN cc_start: 0.7348 (mp10) cc_final: 0.7068 (mp10) REVERT: K 175 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7897 (ttp80) REVERT: K 231 ARG cc_start: 0.7212 (tmm160) cc_final: 0.6793 (tmm160) REVERT: L 37 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7843 (tp40) REVERT: L 103 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8397 (ttpp) REVERT: L 175 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7649 (ttm170) REVERT: L 188 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7417 (tp30) REVERT: M 37 GLN cc_start: 0.7427 (tp40) cc_final: 0.6978 (tp40) REVERT: M 82 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6363 (tt0) REVERT: M 184 GLU cc_start: 0.7824 (tt0) cc_final: 0.7086 (pt0) REVERT: M 194 LEU cc_start: 0.8949 (tp) cc_final: 0.8722 (tt) REVERT: M 205 LYS cc_start: 0.7328 (mtpp) cc_final: 0.6745 (mttt) REVERT: N 40 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7825 (tptt) REVERT: N 116 ARG cc_start: 0.8322 (mmp-170) cc_final: 0.8122 (mmp-170) REVERT: N 131 GLU cc_start: 0.8275 (tt0) cc_final: 0.7882 (tm-30) REVERT: N 246 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6086 (tp30) REVERT: O 37 GLN cc_start: 0.7513 (mm-40) cc_final: 0.7111 (tm130) REVERT: O 78 LYS cc_start: 0.6763 (pttt) cc_final: 0.6346 (mttm) REVERT: O 238 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: O 265 LYS cc_start: 0.5749 (ttmt) cc_final: 0.5507 (tmtt) REVERT: O 269 GLN cc_start: 0.6806 (tp40) cc_final: 0.6483 (tp-100) REVERT: O 274 GLU cc_start: 0.7637 (tt0) cc_final: 0.7339 (tt0) REVERT: P 47 ASP cc_start: 0.7470 (m-30) cc_final: 0.7196 (m-30) REVERT: Q 143 ILE cc_start: 0.7323 (mt) cc_final: 0.6865 (mt) REVERT: Q 229 MET cc_start: 0.2661 (mpt) cc_final: 0.1529 (tpp) outliers start: 12 outliers final: 2 residues processed: 574 average time/residue: 0.9098 time to fit residues: 588.8315 Evaluate side-chains 427 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 421 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain L residue 103 LYS Chi-restraints excluded: chain L residue 255 SER Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain O residue 238 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 206 ASN D 269 GLN F 213 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 38 GLN G 206 ASN H 38 GLN H 213 GLN J 38 GLN K 206 ASN N 81 GLN N 213 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.195484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.152437 restraints weight = 29768.131| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.44 r_work: 0.3718 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30733 Z= 0.214 Angle : 0.674 8.614 41569 Z= 0.366 Chirality : 0.048 0.283 4668 Planarity : 0.006 0.052 5066 Dihedral : 16.176 178.822 4966 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.85 % Allowed : 8.99 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.13), residues: 3570 helix: 0.53 (0.11), residues: 2198 sheet: 0.12 (0.29), residues: 210 loop : 0.44 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 63 TYR 0.021 0.002 TYR O 75 PHE 0.016 0.002 PHE J 190 TRP 0.024 0.003 TRP M 45 HIS 0.010 0.002 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (30733) covalent geometry : angle 0.67438 / 0.37 (41569) hydrogen bonds : bond 0.05867 / 5.55 ( 1619) hydrogen bonds : angle 5.14819 / 4.71 ( 4729) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 433 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: D 184 GLU cc_start: 0.6518 (tp30) cc_final: 0.5683 (tt0) REVERT: D 189 ARG cc_start: 0.6949 (ptp-110) cc_final: 0.6540 (ptp90) REVERT: D 214 MET cc_start: 0.7561 (mtm) cc_final: 0.7273 (mtm) REVERT: E 38 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8152 (tp-100) REVERT: E 140 MET cc_start: 0.9154 (ttm) cc_final: 0.8805 (ttm) REVERT: E 227 LYS cc_start: 0.6890 (ttpp) cc_final: 0.6606 (ttmm) REVERT: F 202 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7523 (tp30) REVERT: F 210 MET cc_start: 0.8208 (mtp) cc_final: 0.7951 (mtp) REVERT: F 265 LYS cc_start: 0.8206 (mtpm) cc_final: 0.7486 (mtmm) REVERT: G 217 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7287 (mtmp) REVERT: G 223 ASN cc_start: 0.7249 (m-40) cc_final: 0.6710 (m-40) REVERT: G 269 GLN cc_start: 0.7557 (mm110) cc_final: 0.7083 (mt0) REVERT: H 202 GLU cc_start: 0.7540 (tp30) cc_final: 0.7304 (tp30) REVERT: H 261 LYS cc_start: 0.7903 (mptt) cc_final: 0.7433 (mmtm) REVERT: J 22 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7075 (mp10) REVERT: J 196 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: J 206 ASN cc_start: 0.8238 (m110) cc_final: 0.7793 (m110) REVERT: K 22 GLN cc_start: 0.7475 (mp10) cc_final: 0.7119 (mm-40) REVERT: K 225 LYS cc_start: 0.7145 (ttpm) cc_final: 0.6558 (tttm) REVERT: K 231 ARG cc_start: 0.7389 (tmm160) cc_final: 0.7039 (tmm160) REVERT: L 37 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7826 (tp40) REVERT: L 149 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8449 (mp) REVERT: L 175 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7633 (ttm170) REVERT: L 210 MET cc_start: 0.7031 (ttp) cc_final: 0.6734 (ttp) REVERT: M 37 GLN cc_start: 0.7428 (tp40) cc_final: 0.7012 (tp40) REVERT: M 184 GLU cc_start: 0.7747 (tt0) cc_final: 0.7484 (pt0) REVERT: M 205 LYS cc_start: 0.7373 (mtpp) cc_final: 0.6774 (mttt) REVERT: N 116 ARG cc_start: 0.8309 (mmp-170) cc_final: 0.8091 (mmp-170) REVERT: N 131 GLU cc_start: 0.8251 (tt0) cc_final: 0.7939 (tm-30) REVERT: N 182 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7354 (mtp180) REVERT: N 229 MET cc_start: 0.3675 (OUTLIER) cc_final: 0.2902 (mmt) REVERT: O 37 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7209 (tm130) REVERT: O 78 LYS cc_start: 0.6711 (pttt) cc_final: 0.6276 (mttm) REVERT: O 210 MET cc_start: 0.6461 (mtp) cc_final: 0.6223 (mtp) REVERT: O 269 GLN cc_start: 0.6600 (tp40) cc_final: 0.6391 (tp40) REVERT: O 274 GLU cc_start: 0.7519 (tt0) cc_final: 0.7304 (tt0) REVERT: P 182 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5898 (mtp180) REVERT: Q 40 LYS cc_start: 0.6212 (ttpp) cc_final: 0.5849 (tttt) REVERT: Q 94 ILE cc_start: 0.7295 (pt) cc_final: 0.7089 (pt) REVERT: Q 143 ILE cc_start: 0.6733 (mt) cc_final: 0.6415 (mt) REVERT: Q 229 MET cc_start: 0.2601 (mpt) cc_final: 0.1507 (tpp) outliers start: 58 outliers final: 18 residues processed: 466 average time/residue: 1.0120 time to fit residues: 529.9983 Evaluate side-chains 409 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 383 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain K residue 227 LYS Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 149 LEU Chi-restraints excluded: chain M residue 208 VAL Chi-restraints excluded: chain N residue 182 ARG Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 VAL Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 162 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 304 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 HIS G 22 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN N 81 GLN Q 77 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.200919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.160866 restraints weight = 29736.882| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.26 r_work: 0.3772 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30733 Z= 0.112 Angle : 0.511 7.751 41569 Z= 0.281 Chirality : 0.042 0.251 4668 Planarity : 0.004 0.046 5066 Dihedral : 15.717 176.677 4955 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.63 % Allowed : 10.65 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3570 helix: 1.25 (0.11), residues: 2198 sheet: 0.27 (0.30), residues: 210 loop : 0.69 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 191 TYR 0.016 0.001 TYR E 115 PHE 0.011 0.001 PHE M 204 TRP 0.018 0.002 TRP K 45 HIS 0.004 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (30733) covalent geometry : angle 0.51121 / 0.28 (41569) hydrogen bonds : bond 0.04352 / 4.18 ( 1619) hydrogen bonds : angle 4.83106 / 4.40 ( 4729) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 428 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8039 (tptt) cc_final: 0.7416 (tmmt) REVERT: D 95 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7655 (ttm170) REVERT: D 184 GLU cc_start: 0.6551 (tp30) cc_final: 0.5665 (tt0) REVERT: D 189 ARG cc_start: 0.6745 (ptp-110) cc_final: 0.6315 (ptp90) REVERT: D 214 MET cc_start: 0.7452 (mtm) cc_final: 0.7211 (mtm) REVERT: E 38 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8141 (tp-100) REVERT: E 140 MET cc_start: 0.9118 (ttm) cc_final: 0.8852 (ttm) REVERT: E 227 LYS cc_start: 0.6914 (ttpp) cc_final: 0.6442 (tptp) REVERT: E 270 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6450 (mp0) REVERT: F 202 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7434 (tp30) REVERT: F 209 GLU cc_start: 0.7901 (tp30) cc_final: 0.7689 (tm-30) REVERT: F 210 MET cc_start: 0.8065 (mtp) cc_final: 0.7824 (mtp) REVERT: F 265 LYS cc_start: 0.8155 (mtpm) cc_final: 0.7412 (mtmm) REVERT: G 181 LYS cc_start: 0.8380 (mtmt) cc_final: 0.8076 (mttm) REVERT: G 223 ASN cc_start: 0.7113 (m-40) cc_final: 0.6589 (m110) REVERT: H 202 GLU cc_start: 0.7357 (tp30) cc_final: 0.7133 (tp30) REVERT: H 209 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: H 261 LYS cc_start: 0.7862 (mptt) cc_final: 0.7305 (mptm) REVERT: J 196 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: J 206 ASN cc_start: 0.8138 (m110) cc_final: 0.7684 (m110) REVERT: J 214 MET cc_start: 0.7991 (mtm) cc_final: 0.7789 (mtm) REVERT: K 22 GLN cc_start: 0.7418 (mp10) cc_final: 0.7030 (mm-40) REVERT: K 54 LYS cc_start: 0.8413 (tppt) cc_final: 0.8044 (tmtt) REVERT: K 61 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7710 (mp0) REVERT: K 196 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8661 (t80) REVERT: K 221 SER cc_start: 0.7596 (m) cc_final: 0.7329 (p) REVERT: L 37 GLN cc_start: 0.7884 (tp-100) cc_final: 0.7626 (tp40) REVERT: L 175 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7534 (ttm170) REVERT: L 210 MET cc_start: 0.6925 (ttp) cc_final: 0.6667 (ttp) REVERT: M 37 GLN cc_start: 0.7289 (tp40) cc_final: 0.6893 (tp40) REVERT: M 184 GLU cc_start: 0.7664 (tt0) cc_final: 0.7341 (pt0) REVERT: M 205 LYS cc_start: 0.7374 (mtpp) cc_final: 0.7147 (mtpp) REVERT: N 116 ARG cc_start: 0.8242 (mmp-170) cc_final: 0.7995 (mmp-170) REVERT: N 131 GLU cc_start: 0.7962 (tt0) cc_final: 0.7657 (tm-30) REVERT: N 181 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7602 (mtmt) REVERT: N 229 MET cc_start: 0.3663 (OUTLIER) cc_final: 0.2893 (mmt) REVERT: O 71 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7281 (t70) REVERT: O 75 TYR cc_start: 0.7466 (m-10) cc_final: 0.6880 (m-80) REVERT: O 78 LYS cc_start: 0.6652 (pttt) cc_final: 0.6198 (mttm) REVERT: O 273 LYS cc_start: 0.7567 (tttp) cc_final: 0.7240 (ttpt) REVERT: O 274 GLU cc_start: 0.7463 (tt0) cc_final: 0.6961 (tt0) REVERT: P 182 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.5971 (mtp180) REVERT: Q 40 LYS cc_start: 0.6135 (ttpp) cc_final: 0.5783 (tttt) REVERT: Q 94 ILE cc_start: 0.7156 (pt) cc_final: 0.6911 (pt) REVERT: Q 143 ILE cc_start: 0.6605 (mt) cc_final: 0.6328 (mt) REVERT: Q 229 MET cc_start: 0.2547 (mpt) cc_final: 0.1426 (tpp) outliers start: 51 outliers final: 14 residues processed: 462 average time/residue: 0.9749 time to fit residues: 508.5165 Evaluate side-chains 411 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 388 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 227 LYS Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 261 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 246 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 240 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 160 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN G 38 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN K 269 GLN N 81 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.199886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.160046 restraints weight = 29741.851| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.28 r_work: 0.3721 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30733 Z= 0.126 Angle : 0.520 7.603 41569 Z= 0.282 Chirality : 0.042 0.263 4668 Planarity : 0.004 0.043 5066 Dihedral : 15.651 173.552 4954 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.63 % Allowed : 12.66 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.14), residues: 3570 helix: 1.46 (0.11), residues: 2198 sheet: 0.33 (0.30), residues: 210 loop : 0.72 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 175 TYR 0.014 0.001 TYR E 115 PHE 0.009 0.001 PHE Q 125 TRP 0.014 0.002 TRP G 45 HIS 0.006 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (30733) covalent geometry : angle 0.51983 / 0.28 (41569) hydrogen bonds : bond 0.04317 / 4.16 ( 1619) hydrogen bonds : angle 4.71900 / 4.31 ( 4729) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 404 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8068 (tptt) cc_final: 0.7650 (ttmt) REVERT: D 184 GLU cc_start: 0.6584 (tp30) cc_final: 0.5751 (tt0) REVERT: D 189 ARG cc_start: 0.6719 (ptp-110) cc_final: 0.6404 (ptp90) REVERT: D 214 MET cc_start: 0.7468 (mtm) cc_final: 0.7023 (mtp) REVERT: E 38 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8152 (tp-100) REVERT: E 140 MET cc_start: 0.9121 (ttm) cc_final: 0.8897 (ttm) REVERT: E 225 LYS cc_start: 0.6259 (tptt) cc_final: 0.6056 (tmmt) REVERT: E 227 LYS cc_start: 0.7000 (ttpp) cc_final: 0.6550 (tptp) REVERT: F 202 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7431 (tp30) REVERT: F 209 GLU cc_start: 0.7968 (tp30) cc_final: 0.7738 (tm-30) REVERT: F 265 LYS cc_start: 0.8141 (mtpm) cc_final: 0.7381 (mtmm) REVERT: G 181 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8108 (mttm) REVERT: G 223 ASN cc_start: 0.7085 (m-40) cc_final: 0.6558 (m110) REVERT: H 202 GLU cc_start: 0.7356 (tp30) cc_final: 0.7129 (tp30) REVERT: H 209 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: H 261 LYS cc_start: 0.7881 (mptt) cc_final: 0.7345 (mptm) REVERT: I 33 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8400 (mm) REVERT: J 196 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7607 (m-80) REVERT: J 206 ASN cc_start: 0.8139 (m110) cc_final: 0.7746 (m110) REVERT: K 22 GLN cc_start: 0.7407 (mp10) cc_final: 0.6992 (mm-40) REVERT: K 196 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8791 (t80) REVERT: K 221 SER cc_start: 0.7646 (m) cc_final: 0.7340 (p) REVERT: L 37 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7631 (tp40) REVERT: L 175 ARG cc_start: 0.7924 (ttp80) cc_final: 0.7554 (ttm170) REVERT: M 37 GLN cc_start: 0.7307 (tp40) cc_final: 0.6913 (tp40) REVERT: M 184 GLU cc_start: 0.7678 (tt0) cc_final: 0.7279 (pt0) REVERT: M 205 LYS cc_start: 0.7344 (mtpp) cc_final: 0.7107 (mtpp) REVERT: M 211 TRP cc_start: 0.7181 (t-100) cc_final: 0.6797 (t-100) REVERT: M 263 ILE cc_start: 0.3345 (OUTLIER) cc_final: 0.2865 (mp) REVERT: N 131 GLU cc_start: 0.8037 (tt0) cc_final: 0.7697 (tm-30) REVERT: N 181 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7567 (mtmt) REVERT: O 71 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7229 (t70) REVERT: O 75 TYR cc_start: 0.7449 (m-10) cc_final: 0.6883 (m-80) REVERT: O 78 LYS cc_start: 0.6622 (pttt) cc_final: 0.6159 (mttm) REVERT: O 210 MET cc_start: 0.6516 (mtp) cc_final: 0.6040 (mtt) REVERT: O 229 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.4941 (mtp) REVERT: O 273 LYS cc_start: 0.7526 (tttp) cc_final: 0.7279 (ttpt) REVERT: O 274 GLU cc_start: 0.7486 (tt0) cc_final: 0.7013 (tt0) REVERT: P 175 ARG cc_start: 0.6478 (OUTLIER) cc_final: 0.5998 (ttt-90) REVERT: P 182 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.5940 (mtp180) REVERT: Q 40 LYS cc_start: 0.6177 (ttpp) cc_final: 0.5839 (tttt) REVERT: Q 94 ILE cc_start: 0.7141 (pt) cc_final: 0.6885 (pt) REVERT: Q 143 ILE cc_start: 0.6553 (mt) cc_final: 0.6270 (mt) REVERT: Q 214 MET cc_start: 0.2263 (OUTLIER) cc_final: 0.0852 (tpt) REVERT: Q 229 MET cc_start: 0.2468 (mpt) cc_final: 0.1312 (tpp) outliers start: 51 outliers final: 19 residues processed: 437 average time/residue: 0.9773 time to fit residues: 481.8578 Evaluate side-chains 419 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 388 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain M residue 263 ILE Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 236 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN N 81 GLN N 213 GLN Q 77 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.200603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.159292 restraints weight = 29773.850| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.46 r_work: 0.3755 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30733 Z= 0.113 Angle : 0.491 7.402 41569 Z= 0.269 Chirality : 0.041 0.268 4668 Planarity : 0.004 0.041 5066 Dihedral : 15.522 173.679 4954 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.75 % Allowed : 13.20 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.14), residues: 3570 helix: 1.58 (0.11), residues: 2198 sheet: 0.37 (0.31), residues: 210 loop : 0.75 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 175 TYR 0.013 0.001 TYR E 115 PHE 0.013 0.001 PHE M 204 TRP 0.013 0.002 TRP L 45 HIS 0.005 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (30733) covalent geometry : angle 0.49100 / 0.27 (41569) hydrogen bonds : bond 0.04013 / 3.88 ( 1619) hydrogen bonds : angle 4.65543 / 4.23 ( 4729) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 410 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8116 (tptt) cc_final: 0.7717 (ttmt) REVERT: D 95 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7553 (ttm170) REVERT: D 116 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.5809 (mpp-170) REVERT: D 184 GLU cc_start: 0.6633 (tp30) cc_final: 0.5748 (tt0) REVERT: D 189 ARG cc_start: 0.6713 (ptp-110) cc_final: 0.6394 (ptp90) REVERT: D 214 MET cc_start: 0.7502 (mtm) cc_final: 0.7059 (mtp) REVERT: E 38 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8159 (tp-100) REVERT: E 140 MET cc_start: 0.9117 (ttm) cc_final: 0.8903 (ttm) REVERT: E 225 LYS cc_start: 0.6206 (tptt) cc_final: 0.5983 (tmmt) REVERT: E 227 LYS cc_start: 0.6979 (ttpp) cc_final: 0.6553 (tptp) REVERT: E 229 MET cc_start: 0.7602 (mmm) cc_final: 0.7231 (mmm) REVERT: F 202 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7462 (tp30) REVERT: F 265 LYS cc_start: 0.8141 (mtpm) cc_final: 0.7398 (mtmm) REVERT: G 181 LYS cc_start: 0.8409 (mtmt) cc_final: 0.8124 (mttm) REVERT: G 223 ASN cc_start: 0.7089 (m-40) cc_final: 0.6569 (m110) REVERT: H 202 GLU cc_start: 0.7375 (tp30) cc_final: 0.7154 (tp30) REVERT: H 241 ILE cc_start: 0.8631 (tp) cc_final: 0.8430 (tp) REVERT: H 261 LYS cc_start: 0.7862 (mptt) cc_final: 0.7364 (mptm) REVERT: I 33 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8390 (mm) REVERT: J 196 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7576 (m-80) REVERT: J 206 ASN cc_start: 0.8156 (m110) cc_final: 0.7787 (m110) REVERT: K 22 GLN cc_start: 0.7428 (mp10) cc_final: 0.7055 (mm-40) REVERT: K 182 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7457 (mtp180) REVERT: K 196 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8781 (t80) REVERT: K 221 SER cc_start: 0.7684 (m) cc_final: 0.7392 (p) REVERT: L 37 GLN cc_start: 0.7912 (tp-100) cc_final: 0.7610 (tp40) REVERT: L 175 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7566 (ttm170) REVERT: L 273 LYS cc_start: 0.7115 (pptt) cc_final: 0.6596 (tmmt) REVERT: M 37 GLN cc_start: 0.7287 (tp40) cc_final: 0.6874 (tp40) REVERT: M 184 GLU cc_start: 0.7738 (tt0) cc_final: 0.7346 (pt0) REVERT: M 205 LYS cc_start: 0.7362 (mtpp) cc_final: 0.7127 (mtpp) REVERT: M 209 GLU cc_start: 0.5791 (tt0) cc_final: 0.5556 (tp30) REVERT: M 211 TRP cc_start: 0.7199 (t-100) cc_final: 0.6839 (t-100) REVERT: N 27 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.4906 (ptt-90) REVERT: N 131 GLU cc_start: 0.8039 (tt0) cc_final: 0.7718 (tm-30) REVERT: N 181 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7591 (mtmt) REVERT: N 229 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.2865 (mmt) REVERT: O 38 GLN cc_start: 0.7425 (tp40) cc_final: 0.7135 (tt0) REVERT: O 71 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7255 (t70) REVERT: O 75 TYR cc_start: 0.7433 (m-10) cc_final: 0.6876 (m-80) REVERT: O 78 LYS cc_start: 0.6619 (pttt) cc_final: 0.6140 (mttm) REVERT: O 210 MET cc_start: 0.6521 (mtp) cc_final: 0.6039 (mtt) REVERT: O 214 MET cc_start: 0.5856 (mpp) cc_final: 0.5613 (pmm) REVERT: O 229 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4920 (mtp) REVERT: O 273 LYS cc_start: 0.7514 (tttp) cc_final: 0.7295 (ttpt) REVERT: O 274 GLU cc_start: 0.7481 (tt0) cc_final: 0.7001 (tt0) REVERT: P 182 ARG cc_start: 0.6771 (OUTLIER) cc_final: 0.5922 (mtp180) REVERT: Q 94 ILE cc_start: 0.7161 (pt) cc_final: 0.6879 (pt) REVERT: Q 143 ILE cc_start: 0.6614 (mt) cc_final: 0.6320 (mt) REVERT: Q 191 ARG cc_start: 0.4935 (ttp80) cc_final: 0.4589 (ptm-80) REVERT: Q 229 MET cc_start: 0.2482 (mpt) cc_final: 0.1424 (tpp) outliers start: 55 outliers final: 22 residues processed: 442 average time/residue: 0.9213 time to fit residues: 460.1220 Evaluate side-chains 425 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 181 LYS Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 248 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 210 optimal weight: 4.9990 chunk 278 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN Q 77 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.198299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154208 restraints weight = 29673.958| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.50 r_work: 0.3696 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30733 Z= 0.143 Angle : 0.525 7.553 41569 Z= 0.285 Chirality : 0.043 0.273 4668 Planarity : 0.004 0.047 5066 Dihedral : 15.641 172.969 4954 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.79 % Allowed : 13.52 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.14), residues: 3570 helix: 1.56 (0.11), residues: 2198 sheet: 0.29 (0.31), residues: 210 loop : 0.69 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 175 TYR 0.013 0.001 TYR E 115 PHE 0.012 0.001 PHE M 204 TRP 0.012 0.002 TRP J 45 HIS 0.007 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (30733) covalent geometry : angle 0.52517 / 0.28 (41569) hydrogen bonds : bond 0.04386 / 4.22 ( 1619) hydrogen bonds : angle 4.66583 / 4.25 ( 4729) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 398 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8096 (tptt) cc_final: 0.7667 (ttmt) REVERT: D 74 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.5970 (ttm170) REVERT: D 95 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: D 116 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.5834 (mpp-170) REVERT: D 184 GLU cc_start: 0.6606 (tp30) cc_final: 0.5701 (tt0) REVERT: D 189 ARG cc_start: 0.6723 (ptp-110) cc_final: 0.6381 (ptp90) REVERT: D 214 MET cc_start: 0.7500 (mtm) cc_final: 0.7057 (mtp) REVERT: E 38 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8167 (tp-100) REVERT: E 140 MET cc_start: 0.9140 (ttm) cc_final: 0.8883 (ttm) REVERT: E 225 LYS cc_start: 0.6209 (tptt) cc_final: 0.5936 (tmmt) REVERT: E 227 LYS cc_start: 0.6959 (ttpp) cc_final: 0.6535 (tptp) REVERT: E 229 MET cc_start: 0.7608 (mmm) cc_final: 0.7286 (mmm) REVERT: F 74 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.7534 (ppt-90) REVERT: F 202 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7434 (tp30) REVERT: F 209 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7251 (tm-30) REVERT: F 265 LYS cc_start: 0.8156 (mtpm) cc_final: 0.7411 (mtmm) REVERT: G 181 LYS cc_start: 0.8452 (mtmt) cc_final: 0.8131 (mttm) REVERT: G 223 ASN cc_start: 0.7103 (m-40) cc_final: 0.6573 (m110) REVERT: H 202 GLU cc_start: 0.7378 (tp30) cc_final: 0.7145 (tp30) REVERT: H 241 ILE cc_start: 0.8665 (tp) cc_final: 0.8460 (tp) REVERT: H 261 LYS cc_start: 0.7873 (mptt) cc_final: 0.7368 (mptm) REVERT: I 33 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8453 (mm) REVERT: I 99 LYS cc_start: 0.8643 (mttm) cc_final: 0.8425 (mttm) REVERT: J 76 ARG cc_start: 0.7181 (ttp-170) cc_final: 0.6571 (ptm-80) REVERT: J 163 ASP cc_start: 0.8397 (m-30) cc_final: 0.8174 (m-30) REVERT: J 196 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7611 (m-80) REVERT: J 206 ASN cc_start: 0.8172 (m110) cc_final: 0.7793 (m110) REVERT: K 61 GLU cc_start: 0.8617 (mt-10) cc_final: 0.7569 (mp0) REVERT: K 196 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8699 (t80) REVERT: L 37 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7662 (tp40) REVERT: L 175 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7521 (ttm170) REVERT: L 273 LYS cc_start: 0.7244 (pptt) cc_final: 0.6665 (tmmt) REVERT: M 37 GLN cc_start: 0.7309 (tp40) cc_final: 0.6868 (tp40) REVERT: M 184 GLU cc_start: 0.7700 (tt0) cc_final: 0.7238 (pt0) REVERT: M 205 LYS cc_start: 0.7361 (mtpp) cc_final: 0.7110 (mtpp) REVERT: M 209 GLU cc_start: 0.5778 (tt0) cc_final: 0.5528 (tp30) REVERT: M 211 TRP cc_start: 0.7215 (t-100) cc_final: 0.6964 (t-100) REVERT: M 269 GLN cc_start: 0.5889 (mt0) cc_final: 0.5531 (mp10) REVERT: N 131 GLU cc_start: 0.8115 (tt0) cc_final: 0.7772 (tm-30) REVERT: O 38 GLN cc_start: 0.7442 (tp40) cc_final: 0.7152 (tt0) REVERT: O 71 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7262 (t70) REVERT: O 75 TYR cc_start: 0.7513 (m-10) cc_final: 0.6948 (m-80) REVERT: O 78 LYS cc_start: 0.6634 (pttt) cc_final: 0.6118 (mttm) REVERT: O 152 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7985 (pt0) REVERT: O 210 MET cc_start: 0.6552 (mtp) cc_final: 0.6080 (mtt) REVERT: O 214 MET cc_start: 0.5773 (mpp) cc_final: 0.5553 (pmm) REVERT: O 229 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4814 (mtp) REVERT: O 238 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6703 (tm-30) REVERT: O 273 LYS cc_start: 0.7527 (tttp) cc_final: 0.7302 (ttpt) REVERT: O 274 GLU cc_start: 0.7479 (tt0) cc_final: 0.6974 (tt0) REVERT: P 175 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6028 (ttt-90) REVERT: P 182 ARG cc_start: 0.6708 (OUTLIER) cc_final: 0.5839 (mtp180) REVERT: P 229 MET cc_start: 0.3653 (pp-130) cc_final: 0.3425 (pp-130) REVERT: Q 22 GLN cc_start: 0.2535 (OUTLIER) cc_final: 0.2015 (pt0) REVERT: Q 94 ILE cc_start: 0.7134 (pt) cc_final: 0.6869 (pt) REVERT: Q 143 ILE cc_start: 0.6545 (mt) cc_final: 0.6240 (mt) REVERT: Q 229 MET cc_start: 0.2501 (mpt) cc_final: 0.1426 (tpp) outliers start: 56 outliers final: 29 residues processed: 430 average time/residue: 0.9278 time to fit residues: 450.1807 Evaluate side-chains 429 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 385 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 227 LYS Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 328 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 203 optimal weight: 0.5980 chunk 195 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN J 38 GLN J 269 GLN K 206 ASN N 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.198574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.157992 restraints weight = 29789.908| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.32 r_work: 0.3711 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30733 Z= 0.146 Angle : 0.523 7.550 41569 Z= 0.284 Chirality : 0.043 0.286 4668 Planarity : 0.004 0.056 5066 Dihedral : 15.665 173.155 4954 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.91 % Allowed : 13.78 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.14), residues: 3570 helix: 1.54 (0.11), residues: 2198 sheet: 0.27 (0.31), residues: 210 loop : 0.63 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 175 TYR 0.013 0.001 TYR E 115 PHE 0.012 0.001 PHE J 125 TRP 0.013 0.002 TRP J 45 HIS 0.007 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (30733) covalent geometry : angle 0.52346 / 0.28 (41569) hydrogen bonds : bond 0.04384 / 4.22 ( 1619) hydrogen bonds : angle 4.67100 / 4.25 ( 4729) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 400 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8050 (tptt) cc_final: 0.7652 (ttmt) REVERT: D 74 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6025 (ttm170) REVERT: D 95 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7526 (ttm170) REVERT: D 116 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5859 (mpp-170) REVERT: D 184 GLU cc_start: 0.6563 (tp30) cc_final: 0.5692 (tt0) REVERT: D 189 ARG cc_start: 0.6765 (ptp-110) cc_final: 0.6422 (ptp90) REVERT: D 214 MET cc_start: 0.7456 (mtm) cc_final: 0.6994 (mtp) REVERT: E 38 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8152 (tp-100) REVERT: E 140 MET cc_start: 0.9136 (ttm) cc_final: 0.8883 (ttm) REVERT: E 227 LYS cc_start: 0.6972 (ttpp) cc_final: 0.6567 (tptp) REVERT: E 229 MET cc_start: 0.7628 (mmm) cc_final: 0.7370 (mmm) REVERT: E 246 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: F 74 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7530 (ppt-90) REVERT: F 202 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7417 (tp30) REVERT: F 209 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: F 265 LYS cc_start: 0.8158 (mtpm) cc_final: 0.7420 (mtmm) REVERT: G 181 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8132 (mttm) REVERT: G 223 ASN cc_start: 0.7110 (m-40) cc_final: 0.6577 (m-40) REVERT: H 202 GLU cc_start: 0.7349 (tp30) cc_final: 0.7134 (tp30) REVERT: H 261 LYS cc_start: 0.7910 (mptt) cc_final: 0.7416 (mptm) REVERT: I 33 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8444 (mm) REVERT: J 76 ARG cc_start: 0.7157 (ttp-170) cc_final: 0.6580 (ptm-80) REVERT: J 196 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.7594 (m-80) REVERT: J 206 ASN cc_start: 0.8174 (m110) cc_final: 0.7789 (m110) REVERT: K 61 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7640 (mp0) REVERT: K 196 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8669 (t80) REVERT: K 213 GLN cc_start: 0.7565 (mt0) cc_final: 0.7115 (tp40) REVERT: L 37 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7662 (tp40) REVERT: L 175 ARG cc_start: 0.7895 (ttp80) cc_final: 0.7524 (ttm170) REVERT: L 210 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6767 (ttp) REVERT: L 273 LYS cc_start: 0.7437 (pptt) cc_final: 0.6876 (tmmt) REVERT: M 37 GLN cc_start: 0.7308 (tp40) cc_final: 0.6909 (tp40) REVERT: M 184 GLU cc_start: 0.7661 (tt0) cc_final: 0.7193 (pt0) REVERT: M 205 LYS cc_start: 0.7315 (mtpp) cc_final: 0.7088 (mtpp) REVERT: M 211 TRP cc_start: 0.7209 (OUTLIER) cc_final: 0.6967 (t-100) REVERT: M 214 MET cc_start: 0.7744 (pmt) cc_final: 0.7227 (pmm) REVERT: M 271 VAL cc_start: 0.7255 (p) cc_final: 0.6902 (t) REVERT: N 131 GLU cc_start: 0.8068 (tt0) cc_final: 0.7749 (tm-30) REVERT: N 182 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7060 (mtp180) REVERT: O 38 GLN cc_start: 0.7433 (tp40) cc_final: 0.7151 (tt0) REVERT: O 71 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7205 (t70) REVERT: O 75 TYR cc_start: 0.7519 (m-10) cc_final: 0.6885 (m-80) REVERT: O 78 LYS cc_start: 0.6619 (pttt) cc_final: 0.6105 (mttm) REVERT: O 152 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: O 229 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.4896 (mtp) REVERT: O 238 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6738 (tm-30) REVERT: O 273 LYS cc_start: 0.7528 (tttp) cc_final: 0.7309 (ttpt) REVERT: O 274 GLU cc_start: 0.7520 (tt0) cc_final: 0.6765 (tp30) REVERT: P 175 ARG cc_start: 0.6534 (OUTLIER) cc_final: 0.6071 (ttt-90) REVERT: P 182 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.5835 (mtp180) REVERT: Q 22 GLN cc_start: 0.2545 (OUTLIER) cc_final: 0.2022 (pt0) REVERT: Q 94 ILE cc_start: 0.7199 (pt) cc_final: 0.6925 (pt) REVERT: Q 143 ILE cc_start: 0.6574 (mt) cc_final: 0.6266 (mt) REVERT: Q 229 MET cc_start: 0.2511 (mpt) cc_final: 0.1423 (tpp) outliers start: 60 outliers final: 27 residues processed: 433 average time/residue: 0.9094 time to fit residues: 444.3951 Evaluate side-chains 437 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 391 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 182 ARG Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 152 GLU Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 158 optimal weight: 6.9990 chunk 260 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 335 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN ** F 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 206 ASN J 38 GLN J 269 GLN K 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.197598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.157934 restraints weight = 29820.778| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.25 r_work: 0.3696 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30733 Z= 0.166 Angle : 0.548 7.602 41569 Z= 0.296 Chirality : 0.044 0.298 4668 Planarity : 0.005 0.053 5066 Dihedral : 15.733 172.285 4954 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.07 % Allowed : 14.03 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.14), residues: 3570 helix: 1.47 (0.11), residues: 2198 sheet: 0.24 (0.30), residues: 210 loop : 0.57 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 175 TYR 0.013 0.002 TYR E 115 PHE 0.011 0.001 PHE J 125 TRP 0.014 0.002 TRP L 20 HIS 0.008 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (30733) covalent geometry : angle 0.54806 / 0.30 (41569) hydrogen bonds : bond 0.04598 / 4.42 ( 1619) hydrogen bonds : angle 4.71623 / 4.30 ( 4729) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 390 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8115 (tptt) cc_final: 0.7633 (ttmt) REVERT: D 74 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6056 (ttm170) REVERT: D 116 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.5859 (mpp-170) REVERT: D 184 GLU cc_start: 0.6568 (tp30) cc_final: 0.5701 (tt0) REVERT: D 189 ARG cc_start: 0.6841 (ptp-110) cc_final: 0.6484 (ptp90) REVERT: D 214 MET cc_start: 0.7478 (mtm) cc_final: 0.7022 (mtp) REVERT: E 38 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8163 (tp-100) REVERT: E 140 MET cc_start: 0.9152 (ttm) cc_final: 0.8867 (ttm) REVERT: E 227 LYS cc_start: 0.7069 (ttpp) cc_final: 0.6662 (tptp) REVERT: E 229 MET cc_start: 0.7643 (mmm) cc_final: 0.7375 (mmm) REVERT: E 246 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: F 74 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.7538 (ppt-90) REVERT: F 202 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7451 (tp30) REVERT: F 209 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: G 181 LYS cc_start: 0.8442 (mtmt) cc_final: 0.8153 (mttm) REVERT: G 217 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7245 (mttp) REVERT: G 223 ASN cc_start: 0.7119 (m-40) cc_final: 0.6596 (m-40) REVERT: H 202 GLU cc_start: 0.7385 (tp30) cc_final: 0.7177 (tp30) REVERT: H 241 ILE cc_start: 0.8705 (tp) cc_final: 0.8481 (tp) REVERT: H 261 LYS cc_start: 0.7890 (mptt) cc_final: 0.7439 (mptm) REVERT: I 33 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8460 (mm) REVERT: J 76 ARG cc_start: 0.7170 (ttp-170) cc_final: 0.6591 (ptm-80) REVERT: J 196 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.7606 (m-80) REVERT: J 206 ASN cc_start: 0.8198 (m110) cc_final: 0.7831 (m110) REVERT: K 40 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8411 (tttp) REVERT: K 149 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8075 (mp) REVERT: K 196 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8780 (t80) REVERT: K 213 GLN cc_start: 0.7618 (mt0) cc_final: 0.7170 (tp40) REVERT: L 37 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7673 (tp40) REVERT: L 175 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7573 (ttm170) REVERT: L 273 LYS cc_start: 0.7442 (pptt) cc_final: 0.6868 (tmmt) REVERT: M 37 GLN cc_start: 0.7369 (tp40) cc_final: 0.6989 (tp40) REVERT: M 76 ARG cc_start: 0.7275 (ttt180) cc_final: 0.6989 (ptt180) REVERT: M 184 GLU cc_start: 0.7711 (tt0) cc_final: 0.7217 (pt0) REVERT: M 205 LYS cc_start: 0.7366 (mtpp) cc_final: 0.7166 (mtpp) REVERT: M 271 VAL cc_start: 0.7299 (p) cc_final: 0.6975 (t) REVERT: N 131 GLU cc_start: 0.8093 (tt0) cc_final: 0.7787 (tm-30) REVERT: N 214 MET cc_start: 0.5794 (mpp) cc_final: 0.5582 (ptp) REVERT: N 229 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.2795 (mmt) REVERT: O 38 GLN cc_start: 0.7444 (tp40) cc_final: 0.7172 (tt0) REVERT: O 71 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7234 (t70) REVERT: O 75 TYR cc_start: 0.7528 (m-10) cc_final: 0.6949 (m-80) REVERT: O 210 MET cc_start: 0.6552 (mtp) cc_final: 0.6047 (mtt) REVERT: O 214 MET cc_start: 0.6641 (OUTLIER) cc_final: 0.6419 (pmt) REVERT: O 229 MET cc_start: 0.5612 (OUTLIER) cc_final: 0.4996 (mtp) REVERT: O 238 GLU cc_start: 0.7424 (tm-30) cc_final: 0.6775 (tm-30) REVERT: O 273 LYS cc_start: 0.7515 (tttp) cc_final: 0.6929 (mtmt) REVERT: O 274 GLU cc_start: 0.7527 (tt0) cc_final: 0.6788 (tp30) REVERT: P 175 ARG cc_start: 0.6601 (OUTLIER) cc_final: 0.6138 (ttt-90) REVERT: P 182 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.5831 (mtp180) REVERT: Q 22 GLN cc_start: 0.2636 (OUTLIER) cc_final: 0.2073 (pt0) REVERT: Q 94 ILE cc_start: 0.7229 (pt) cc_final: 0.6953 (pt) REVERT: Q 111 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6407 (mt-10) REVERT: Q 143 ILE cc_start: 0.6627 (mt) cc_final: 0.6315 (mt) REVERT: Q 214 MET cc_start: 0.2638 (OUTLIER) cc_final: 0.2209 (ttm) REVERT: Q 229 MET cc_start: 0.2408 (mpt) cc_final: 0.1356 (tpp) outliers start: 65 outliers final: 28 residues processed: 426 average time/residue: 0.9580 time to fit residues: 460.0993 Evaluate side-chains 425 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 377 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 40 LYS Chi-restraints excluded: chain K residue 149 LEU Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain O residue 37 GLN Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 214 MET Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 206 optimal weight: 0.7980 chunk 282 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 293 optimal weight: 6.9990 chunk 259 optimal weight: 0.0020 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 overall best weight: 1.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.199519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157219 restraints weight = 29805.316| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.46 r_work: 0.3758 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 30733 Z= 0.117 Angle : 0.496 7.279 41569 Z= 0.271 Chirality : 0.042 0.310 4668 Planarity : 0.004 0.053 5066 Dihedral : 15.569 173.146 4954 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.72 % Allowed : 14.45 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.14), residues: 3570 helix: 1.63 (0.11), residues: 2198 sheet: 0.37 (0.31), residues: 210 loop : 0.63 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 175 TYR 0.013 0.001 TYR E 115 PHE 0.010 0.001 PHE M 204 TRP 0.016 0.002 TRP L 20 HIS 0.005 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (30733) covalent geometry : angle 0.49641 / 0.27 (41569) hydrogen bonds : bond 0.03984 / 3.84 ( 1619) hydrogen bonds : angle 4.64209 / 4.22 ( 4729) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 400 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8075 (tptt) cc_final: 0.7651 (ttmt) REVERT: D 74 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6077 (ttm170) REVERT: D 116 ARG cc_start: 0.6644 (OUTLIER) cc_final: 0.5782 (mpp-170) REVERT: D 184 GLU cc_start: 0.6588 (tp30) cc_final: 0.5725 (tt0) REVERT: D 189 ARG cc_start: 0.6826 (ptp-110) cc_final: 0.6314 (ptp90) REVERT: D 214 MET cc_start: 0.7528 (mtm) cc_final: 0.7096 (mtp) REVERT: E 38 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8169 (tp-100) REVERT: E 140 MET cc_start: 0.9127 (ttm) cc_final: 0.8882 (ttm) REVERT: E 227 LYS cc_start: 0.7183 (ttpp) cc_final: 0.6777 (tptp) REVERT: E 229 MET cc_start: 0.7642 (mmm) cc_final: 0.7425 (mmm) REVERT: F 202 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7499 (tp30) REVERT: F 209 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7284 (tm-30) REVERT: G 181 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8155 (mttm) REVERT: G 223 ASN cc_start: 0.7138 (m-40) cc_final: 0.6632 (m-40) REVERT: H 202 GLU cc_start: 0.7405 (tp30) cc_final: 0.7200 (tp30) REVERT: H 261 LYS cc_start: 0.7899 (mptt) cc_final: 0.7461 (mptm) REVERT: I 33 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8425 (mm) REVERT: J 76 ARG cc_start: 0.7186 (ttp-170) cc_final: 0.6648 (ptm-80) REVERT: J 78 LYS cc_start: 0.7459 (mmmm) cc_final: 0.7142 (mmmt) REVERT: J 163 ASP cc_start: 0.8327 (m-30) cc_final: 0.8049 (m-30) REVERT: J 196 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: J 206 ASN cc_start: 0.8222 (m110) cc_final: 0.7846 (m110) REVERT: K 61 GLU cc_start: 0.8626 (mt-10) cc_final: 0.7722 (mp0) REVERT: K 196 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8642 (t80) REVERT: K 213 GLN cc_start: 0.7691 (mt0) cc_final: 0.7267 (tp40) REVERT: L 37 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7714 (tp40) REVERT: L 175 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7600 (ttm170) REVERT: L 210 MET cc_start: 0.7179 (ttp) cc_final: 0.6790 (ttp) REVERT: L 238 GLU cc_start: 0.7656 (mt-10) cc_final: 0.6651 (tm-30) REVERT: L 273 LYS cc_start: 0.7457 (pptt) cc_final: 0.6923 (tmmt) REVERT: M 37 GLN cc_start: 0.7358 (tp40) cc_final: 0.6992 (tp40) REVERT: M 184 GLU cc_start: 0.7780 (tt0) cc_final: 0.7332 (pt0) REVERT: M 205 LYS cc_start: 0.7315 (mtpp) cc_final: 0.7114 (mtpp) REVERT: M 211 TRP cc_start: 0.7289 (OUTLIER) cc_final: 0.7005 (t-100) REVERT: N 131 GLU cc_start: 0.8097 (tt0) cc_final: 0.7787 (tm-30) REVERT: N 214 MET cc_start: 0.5879 (mpp) cc_final: 0.5495 (ptp) REVERT: N 229 MET cc_start: 0.3558 (OUTLIER) cc_final: 0.2759 (mmt) REVERT: O 38 GLN cc_start: 0.7441 (tp40) cc_final: 0.7147 (tt0) REVERT: O 71 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7263 (t70) REVERT: O 75 TYR cc_start: 0.7514 (m-10) cc_final: 0.6992 (m-80) REVERT: O 210 MET cc_start: 0.6590 (mtp) cc_final: 0.6108 (mtt) REVERT: O 229 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.4921 (mtp) REVERT: O 238 GLU cc_start: 0.7429 (tm-30) cc_final: 0.6688 (tm-30) REVERT: O 273 LYS cc_start: 0.7527 (tttp) cc_final: 0.6971 (mtmt) REVERT: O 274 GLU cc_start: 0.7526 (tt0) cc_final: 0.6801 (tp30) REVERT: P 175 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.6158 (ttt-90) REVERT: P 182 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5806 (mtp180) REVERT: Q 22 GLN cc_start: 0.2507 (OUTLIER) cc_final: 0.2018 (pt0) REVERT: Q 94 ILE cc_start: 0.7261 (pt) cc_final: 0.6972 (pt) REVERT: Q 143 ILE cc_start: 0.6699 (mt) cc_final: 0.6393 (mt) REVERT: Q 214 MET cc_start: 0.2762 (OUTLIER) cc_final: 0.2337 (ttm) REVERT: Q 229 MET cc_start: 0.2534 (mpt) cc_final: 0.1452 (tpp) outliers start: 54 outliers final: 26 residues processed: 428 average time/residue: 0.9040 time to fit residues: 437.5508 Evaluate side-chains 422 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 381 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 229 MET Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 175 ARG Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 193 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 245 optimal weight: 0.9990 chunk 187 optimal weight: 0.0370 chunk 42 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 239 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.197838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.154159 restraints weight = 29624.625| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.59 r_work: 0.3699 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30733 Z= 0.160 Angle : 0.551 8.930 41569 Z= 0.296 Chirality : 0.044 0.323 4668 Planarity : 0.005 0.053 5066 Dihedral : 15.700 173.490 4954 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.56 % Allowed : 14.96 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.14), residues: 3570 helix: 1.53 (0.11), residues: 2198 sheet: 0.29 (0.31), residues: 210 loop : 0.55 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 175 TYR 0.013 0.002 TYR E 115 PHE 0.016 0.001 PHE M 204 TRP 0.016 0.002 TRP L 20 HIS 0.007 0.001 HIS L 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (30733) covalent geometry : angle 0.55055 / 0.30 (41569) hydrogen bonds : bond 0.04502 / 4.32 ( 1619) hydrogen bonds : angle 4.69881 / 4.28 ( 4729) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7140 Ramachandran restraints generated. 3570 Oldfield, 0 Emsley, 3570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: D 40 LYS cc_start: 0.8085 (tptt) cc_final: 0.7657 (ttmt) REVERT: D 74 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6062 (ttm170) REVERT: D 116 ARG cc_start: 0.6650 (OUTLIER) cc_final: 0.5752 (mpp-170) REVERT: D 184 GLU cc_start: 0.6588 (tp30) cc_final: 0.5710 (tt0) REVERT: D 214 MET cc_start: 0.7524 (mtm) cc_final: 0.7067 (mtp) REVERT: E 38 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8185 (tp-100) REVERT: E 140 MET cc_start: 0.9145 (ttm) cc_final: 0.8865 (ttm) REVERT: E 227 LYS cc_start: 0.7218 (ttpp) cc_final: 0.6825 (tptp) REVERT: E 270 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6564 (mp0) REVERT: F 74 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7604 (ppt-90) REVERT: F 202 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7501 (tp30) REVERT: F 209 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7276 (tm-30) REVERT: G 181 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8180 (mttm) REVERT: G 217 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7291 (mttp) REVERT: G 223 ASN cc_start: 0.7135 (m-40) cc_final: 0.6574 (m-40) REVERT: H 202 GLU cc_start: 0.7424 (tp30) cc_final: 0.7223 (tp30) REVERT: H 261 LYS cc_start: 0.7888 (mptt) cc_final: 0.7431 (mptm) REVERT: I 33 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8459 (mm) REVERT: J 76 ARG cc_start: 0.7202 (ttp-170) cc_final: 0.6656 (ptm-80) REVERT: J 78 LYS cc_start: 0.7470 (mmmm) cc_final: 0.7145 (mmmt) REVERT: J 163 ASP cc_start: 0.8380 (m-30) cc_final: 0.8141 (m-30) REVERT: J 196 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7587 (m-80) REVERT: J 206 ASN cc_start: 0.8195 (m110) cc_final: 0.7839 (m110) REVERT: K 196 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8774 (t80) REVERT: L 37 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7720 (tp40) REVERT: L 175 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7619 (ttm170) REVERT: L 238 GLU cc_start: 0.7693 (mt-10) cc_final: 0.6702 (tm-30) REVERT: L 273 LYS cc_start: 0.7454 (pptt) cc_final: 0.6873 (tmmt) REVERT: M 37 GLN cc_start: 0.7421 (tp40) cc_final: 0.7030 (tp40) REVERT: M 184 GLU cc_start: 0.7771 (tt0) cc_final: 0.7269 (pt0) REVERT: M 205 LYS cc_start: 0.7368 (mtpp) cc_final: 0.7161 (mtpp) REVERT: M 211 TRP cc_start: 0.7291 (OUTLIER) cc_final: 0.7005 (t-100) REVERT: N 131 GLU cc_start: 0.8153 (tt0) cc_final: 0.7850 (tm-30) REVERT: N 214 MET cc_start: 0.5811 (mpp) cc_final: 0.5606 (ptp) REVERT: N 246 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6279 (tp30) REVERT: O 38 GLN cc_start: 0.7467 (tp40) cc_final: 0.7161 (tt0) REVERT: O 71 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7709 (t70) REVERT: O 210 MET cc_start: 0.6483 (mtp) cc_final: 0.5943 (mtt) REVERT: O 229 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.4972 (mtp) REVERT: O 238 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6637 (tm-30) REVERT: O 273 LYS cc_start: 0.7538 (tttp) cc_final: 0.6946 (mtmt) REVERT: O 274 GLU cc_start: 0.7514 (tt0) cc_final: 0.6764 (tp30) REVERT: P 182 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.5844 (mtp180) REVERT: Q 22 GLN cc_start: 0.2544 (OUTLIER) cc_final: 0.1911 (pt0) REVERT: Q 94 ILE cc_start: 0.7244 (pt) cc_final: 0.6962 (pt) REVERT: Q 143 ILE cc_start: 0.6629 (mt) cc_final: 0.6317 (mt) REVERT: Q 214 MET cc_start: 0.2717 (OUTLIER) cc_final: 0.2295 (ttm) REVERT: Q 229 MET cc_start: 0.2404 (mpt) cc_final: 0.1358 (tpp) outliers start: 49 outliers final: 26 residues processed: 413 average time/residue: 0.8941 time to fit residues: 416.8633 Evaluate side-chains 416 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 375 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 74 ARG Chi-restraints excluded: chain D residue 116 ARG Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 196 PHE Chi-restraints excluded: chain G residue 217 LYS Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 71 ASP Chi-restraints excluded: chain I residue 78 LYS Chi-restraints excluded: chain I residue 118 THR Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 273 LYS Chi-restraints excluded: chain K residue 196 PHE Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 260 LEU Chi-restraints excluded: chain K residue 273 LYS Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain M residue 180 ILE Chi-restraints excluded: chain M residue 211 TRP Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 182 ARG Chi-restraints excluded: chain P residue 188 GLU Chi-restraints excluded: chain P residue 209 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 59 VAL Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 214 MET Chi-restraints excluded: chain Q residue 218 LEU Chi-restraints excluded: chain Q residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 236 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 54 optimal weight: 0.0670 chunk 216 optimal weight: 4.9990 chunk 245 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 269 GLN F 213 GLN F 269 GLN G 206 ASN J 38 GLN J 269 GLN K 206 ASN ** L 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.197134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.154660 restraints weight = 29943.468| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 1.42 r_work: 0.3747 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30733 Z= 0.138 Angle : 0.523 8.848 41569 Z= 0.283 Chirality : 0.043 0.339 4668 Planarity : 0.004 0.054 5066 Dihedral : 15.636 177.268 4954 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.56 % Allowed : 15.08 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.14), residues: 3570 helix: 1.58 (0.11), residues: 2198 sheet: 0.34 (0.31), residues: 210 loop : 0.56 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG O 191 TYR 0.013 0.001 TYR E 115 PHE 0.015 0.001 PHE M 204 TRP 0.016 0.002 TRP H 20 HIS 0.005 0.001 HIS I 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (30733) covalent geometry : angle 0.52322 / 0.28 (41569) hydrogen bonds : bond 0.04214 / 4.06 ( 1619) hydrogen bonds : angle 4.66987 / 4.25 ( 4729) =============================================================================== Job complete usr+sys time: 16781.96 seconds wall clock time: 285 minutes 9.77 seconds (17109.77 seconds total)