Starting phenix.real_space_refine on Wed Feb 4 05:11:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pb1_71450/02_2026/9pb1_71450.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pb1_71450/02_2026/9pb1_71450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pb1_71450/02_2026/9pb1_71450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pb1_71450/02_2026/9pb1_71450.map" model { file = "/net/cci-nas-00/data/ceres_data/9pb1_71450/02_2026/9pb1_71450.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pb1_71450/02_2026/9pb1_71450.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.019 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 5715 2.51 5 N 1523 2.21 5 O 1619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1243 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1306 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1306 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 10, 'TRANS': 156} Chain breaks: 2 Chain: "K" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1331 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1264 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1249 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Chain: "N" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1249 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 8, 'TRANS': 151} Chain breaks: 1 Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8948 At special positions: 0 Unit cell: (108.1, 116.15, 86.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 1619 8.00 N 1523 7.00 C 5715 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: 0.54 Conformation dependent library (CDL) restraints added in 219.4 milliseconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 16 sheets defined 54.8% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'H' and resid 74 through 82 removed outlier: 3.660A pdb=" N GLU H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 110 Processing helix chain 'H' and resid 125 through 138 Processing helix chain 'H' and resid 152 through 161 Processing helix chain 'H' and resid 196 through 214 Processing helix chain 'H' and resid 216 through 226 removed outlier: 3.643A pdb=" N ILE H 220 " --> pdb=" O SER H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 239 Processing helix chain 'I' and resid 75 through 82 removed outlier: 3.554A pdb=" N ARG I 81 " --> pdb=" O SER I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 110 Processing helix chain 'I' and resid 125 through 139 Processing helix chain 'I' and resid 153 through 161 removed outlier: 3.717A pdb=" N LEU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.711A pdb=" N ASN I 207 " --> pdb=" O LYS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 226 Processing helix chain 'I' and resid 231 through 239 Processing helix chain 'J' and resid 74 through 82 removed outlier: 3.822A pdb=" N GLU J 82 " --> pdb=" O ARG J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 110 Processing helix chain 'J' and resid 125 through 139 Processing helix chain 'J' and resid 153 through 161 Processing helix chain 'J' and resid 196 through 214 Processing helix chain 'J' and resid 216 through 225 removed outlier: 3.513A pdb=" N GLU J 225 " --> pdb=" O GLU J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 231 through 238 removed outlier: 3.641A pdb=" N GLU J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 82 removed outlier: 3.619A pdb=" N GLU K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 110 Processing helix chain 'K' and resid 125 through 139 removed outlier: 3.814A pdb=" N ALA K 131 " --> pdb=" O THR K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 161 removed outlier: 3.888A pdb=" N LEU K 157 " --> pdb=" O SER K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 214 Processing helix chain 'K' and resid 216 through 225 removed outlier: 3.599A pdb=" N GLU K 225 " --> pdb=" O GLU K 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 238 Processing helix chain 'L' and resid 72 through 82 removed outlier: 3.511A pdb=" N TYR L 76 " --> pdb=" O ALA L 72 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER L 77 " --> pdb=" O TYR L 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 110 Processing helix chain 'L' and resid 125 through 139 Processing helix chain 'L' and resid 153 through 161 Processing helix chain 'L' and resid 196 through 214 Processing helix chain 'L' and resid 216 through 226 removed outlier: 3.656A pdb=" N ARG L 226 " --> pdb=" O SER L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 239 Processing helix chain 'M' and resid 75 through 82 removed outlier: 3.662A pdb=" N GLU M 82 " --> pdb=" O ARG M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 110 removed outlier: 3.538A pdb=" N LEU M 98 " --> pdb=" O SER M 94 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 139 Processing helix chain 'M' and resid 153 through 161 removed outlier: 3.694A pdb=" N LEU M 157 " --> pdb=" O SER M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.746A pdb=" N ASN M 207 " --> pdb=" O LYS M 203 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS M 212 " --> pdb=" O ILE M 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 216 through 224 Processing helix chain 'M' and resid 231 through 239 Processing helix chain 'N' and resid 75 through 81 removed outlier: 3.593A pdb=" N ARG N 81 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 110 Processing helix chain 'N' and resid 125 through 139 Processing helix chain 'N' and resid 153 through 162 Processing helix chain 'N' and resid 196 through 214 Processing helix chain 'N' and resid 216 through 226 Processing helix chain 'N' and resid 231 through 239 Processing sheet with id=AA1, first strand: chain 'H' and resid 84 through 88 removed outlier: 5.593A pdb=" N SER H 121 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLN H 150 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG H 174 " --> pdb=" O CYS H 147 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY H 149 " --> pdb=" O ARG H 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 84 through 88 removed outlier: 5.593A pdb=" N SER H 121 " --> pdb=" O VAL H 148 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N GLN H 150 " --> pdb=" O SER H 121 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS H 243 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER H 169 " --> pdb=" O LYS H 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 61 through 62 Processing sheet with id=AA4, first strand: chain 'I' and resid 84 through 88 removed outlier: 5.411A pdb=" N SER I 121 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLN I 150 " --> pdb=" O SER I 121 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG I 174 " --> pdb=" O CYS I 147 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY I 149 " --> pdb=" O ARG I 174 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N MET I 176 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA I 151 " --> pdb=" O MET I 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 168 through 169 Processing sheet with id=AA6, first strand: chain 'J' and resid 84 through 88 removed outlier: 5.272A pdb=" N SER J 121 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN J 150 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG J 174 " --> pdb=" O CYS J 147 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY J 149 " --> pdb=" O ARG J 174 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N MET J 176 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA J 151 " --> pdb=" O MET J 176 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 84 through 88 removed outlier: 5.272A pdb=" N SER J 121 " --> pdb=" O VAL J 148 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLN J 150 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N HIS J 168 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR J 145 " --> pdb=" O HIS J 168 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS J 243 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 61 through 62 Processing sheet with id=AA9, first strand: chain 'K' and resid 84 through 88 removed outlier: 6.715A pdb=" N ILE K 115 " --> pdb=" O CYS K 144 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TRP K 146 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET K 117 " --> pdb=" O TRP K 146 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL K 148 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE K 119 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN K 150 " --> pdb=" O ILE K 119 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ARG K 174 " --> pdb=" O CYS K 147 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLY K 149 " --> pdb=" O ARG K 174 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N MET K 176 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA K 151 " --> pdb=" O MET K 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 84 through 88 removed outlier: 6.715A pdb=" N ILE K 115 " --> pdb=" O CYS K 144 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N TRP K 146 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N MET K 117 " --> pdb=" O TRP K 146 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL K 148 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE K 119 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN K 150 " --> pdb=" O ILE K 119 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N HIS K 168 " --> pdb=" O ILE K 143 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR K 145 " --> pdb=" O HIS K 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 84 through 88 removed outlier: 6.337A pdb=" N ILE L 115 " --> pdb=" O CYS L 144 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TRP L 146 " --> pdb=" O ILE L 115 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET L 117 " --> pdb=" O TRP L 146 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL L 148 " --> pdb=" O MET L 117 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE L 119 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN L 150 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG L 174 " --> pdb=" O CYS L 147 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY L 149 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N MET L 176 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA L 151 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 84 through 88 removed outlier: 6.337A pdb=" N ILE L 115 " --> pdb=" O CYS L 144 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N TRP L 146 " --> pdb=" O ILE L 115 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET L 117 " --> pdb=" O TRP L 146 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL L 148 " --> pdb=" O MET L 117 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE L 119 " --> pdb=" O VAL L 148 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN L 150 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 243 " --> pdb=" O ARG L 167 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER L 169 " --> pdb=" O LYS L 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 84 through 88 removed outlier: 6.487A pdb=" N ILE M 115 " --> pdb=" O CYS M 144 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TRP M 146 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET M 117 " --> pdb=" O TRP M 146 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL M 148 " --> pdb=" O MET M 117 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE M 119 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN M 150 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ARG M 174 " --> pdb=" O CYS M 147 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY M 149 " --> pdb=" O ARG M 174 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N MET M 176 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA M 151 " --> pdb=" O MET M 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 84 through 88 removed outlier: 6.487A pdb=" N ILE M 115 " --> pdb=" O CYS M 144 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N TRP M 146 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N MET M 117 " --> pdb=" O TRP M 146 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL M 148 " --> pdb=" O MET M 117 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE M 119 " --> pdb=" O VAL M 148 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLN M 150 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N HIS M 168 " --> pdb=" O ILE M 143 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR M 145 " --> pdb=" O HIS M 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 84 through 88 removed outlier: 5.883A pdb=" N ILE N 115 " --> pdb=" O CYS N 144 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP N 146 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N MET N 117 " --> pdb=" O TRP N 146 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL N 148 " --> pdb=" O MET N 117 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE N 119 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN N 150 " --> pdb=" O ILE N 119 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ARG N 174 " --> pdb=" O CYS N 147 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY N 149 " --> pdb=" O ARG N 174 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N MET N 176 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA N 151 " --> pdb=" O MET N 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 84 through 88 removed outlier: 5.883A pdb=" N ILE N 115 " --> pdb=" O CYS N 144 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TRP N 146 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N MET N 117 " --> pdb=" O TRP N 146 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL N 148 " --> pdb=" O MET N 117 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE N 119 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN N 150 " --> pdb=" O ILE N 119 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N HIS N 168 " --> pdb=" O ILE N 143 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR N 145 " --> pdb=" O HIS N 168 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG N 167 " --> pdb=" O LYS N 243 " (cutoff:3.500A) 516 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.70 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: 2528 1.33 - 1.45: 1307 1.45 - 1.57: 5111 1.57 - 1.69: 0 1.69 - 1.81: 161 Bond restraints: 9107 Sorted by residual: bond pdb=" C SER L 121 " pdb=" N PRO L 122 " ideal model delta sigma weight residual 1.339 1.266 0.073 3.40e-02 8.65e+02 4.62e+00 bond pdb=" CB ASP J 134 " pdb=" CG ASP J 134 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.29e+00 bond pdb=" CB GLU K 234 " pdb=" CG GLU K 234 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" CB ASN M 172 " pdb=" CG ASN M 172 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.20e+00 bond pdb=" CB ASP L 134 " pdb=" CG ASP L 134 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.20e+00 ... (remaining 9102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11753 2.33 - 4.67: 478 4.67 - 7.00: 60 7.00 - 9.33: 10 9.33 - 11.67: 3 Bond angle restraints: 12304 Sorted by residual: angle pdb=" N LYS J 203 " pdb=" CA LYS J 203 " pdb=" CB LYS J 203 " ideal model delta sigma weight residual 110.12 115.35 -5.23 1.47e+00 4.63e-01 1.27e+01 angle pdb=" CA MET N 136 " pdb=" CB MET N 136 " pdb=" CG MET N 136 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LEU L 170 " pdb=" CB LEU L 170 " pdb=" CG LEU L 170 " ideal model delta sigma weight residual 116.30 104.63 11.67 3.50e+00 8.16e-02 1.11e+01 angle pdb=" N PRO I 171 " pdb=" CA PRO I 171 " pdb=" C PRO I 171 " ideal model delta sigma weight residual 113.81 118.63 -4.82 1.45e+00 4.76e-01 1.10e+01 angle pdb=" CB MET N 136 " pdb=" CG MET N 136 " pdb=" SD MET N 136 " ideal model delta sigma weight residual 112.70 122.42 -9.72 3.00e+00 1.11e-01 1.05e+01 ... (remaining 12299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 5117 17.81 - 35.62: 397 35.62 - 53.42: 77 53.42 - 71.23: 20 71.23 - 89.04: 13 Dihedral angle restraints: 5624 sinusoidal: 2272 harmonic: 3352 Sorted by residual: dihedral pdb=" CA LEU N 170 " pdb=" C LEU N 170 " pdb=" N PRO N 171 " pdb=" CA PRO N 171 " ideal model delta harmonic sigma weight residual -180.00 -152.16 -27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA CYS H 86 " pdb=" C CYS H 86 " pdb=" N VAL H 87 " pdb=" CA VAL H 87 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA CYS J 86 " pdb=" C CYS J 86 " pdb=" N VAL J 87 " pdb=" CA VAL J 87 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 5621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 779 0.046 - 0.091: 460 0.091 - 0.137: 139 0.137 - 0.182: 40 0.182 - 0.228: 8 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA ARG L 71 " pdb=" N ARG L 71 " pdb=" C ARG L 71 " pdb=" CB ARG L 71 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LYS N 214 " pdb=" N LYS N 214 " pdb=" C LYS N 214 " pdb=" CB LYS N 214 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA PRO I 171 " pdb=" N PRO I 171 " pdb=" C PRO I 171 " pdb=" CB PRO I 171 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1423 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA L 72 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C ALA L 72 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA L 72 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR L 73 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 133 " -0.022 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR J 133 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR J 133 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR J 133 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR J 133 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR J 133 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR J 133 " -0.032 2.00e-02 2.50e+03 pdb=" OH TYR J 133 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 174 " -0.249 9.50e-02 1.11e+02 1.12e-01 9.23e+00 pdb=" NE ARG L 174 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG L 174 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG L 174 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG L 174 " -0.002 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1286 2.75 - 3.28: 9125 3.28 - 3.82: 14425 3.82 - 4.36: 17530 4.36 - 4.90: 30029 Nonbonded interactions: 72395 Sorted by model distance: nonbonded pdb=" OH TYR H 73 " pdb=" NH2 ARG H 81 " model vdw 2.207 3.120 nonbonded pdb=" N SER J 231 " pdb=" OE2 GLU J 234 " model vdw 2.213 3.120 nonbonded pdb=" N GLU H 197 " pdb=" OE1 GLU H 197 " model vdw 2.224 3.120 nonbonded pdb=" NH2 ARG I 167 " pdb=" O GLY I 239 " model vdw 2.232 3.120 nonbonded pdb=" ND1 HIS N 178 " pdb=" O MET N 224 " model vdw 2.237 3.120 ... (remaining 72390 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 'H' and (resid 74 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 109 or (resid 110 and (name N or n \ ame CA or name C or name O or name CB )) or resid 111 through 227 or (resid 228 \ and (name N or name CA or name C or name O or name CB )) or resid 229 through 24 \ 6)) selection = (chain 'I' and (resid 74 through 96 or (resid 97 and (name N or name CA or name \ C or name O or name CB )) or resid 98 through 109 or (resid 110 and (name N or n \ ame CA or name C or name O or name CB )) or resid 111 through 227 or (resid 228 \ and (name N or name CA or name C or name O or name CB )) or resid 229 through 24 \ 6)) selection = (chain 'J' and (resid 74 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 227 o \ r (resid 228 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 29 through 246)) selection = (chain 'K' and (resid 74 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 227 or (resid 228 and \ (name N or name CA or name C or name O or name CB )) or resid 229 through 246)) \ selection = (chain 'L' and (resid 74 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 246)) \ selection = (chain 'M' and (resid 74 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 227 o \ r (resid 228 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 29 through 246)) selection = (chain 'N' and (resid 74 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 96 or (resid 97 and (name N or nam \ e CA or name C or name O or name CB )) or resid 98 through 109 or (resid 110 and \ (name N or name CA or name C or name O or name CB )) or resid 111 through 227 o \ r (resid 228 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 29 through 246)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.073 9107 Z= 0.483 Angle : 1.062 11.667 12304 Z= 0.564 Chirality : 0.062 0.228 1426 Planarity : 0.008 0.112 1544 Dihedral : 14.322 89.037 3456 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.50 % Allowed : 7.96 % Favored : 91.53 % 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: -1.37 (0.22), residues: 1113 helix: -0.61 (0.19), residues: 611 sheet: -0.46 (0.44), residues: 121 loop : -1.31 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG L 174 TYR 0.046 0.006 TYR M 229 PHE 0.025 0.004 PHE I 105 TRP 0.047 0.005 TRP L 146 HIS 0.016 0.003 HIS L 168 Details of bonding type rmsd covalent geometry : bond 0.01140 ( 9107) covalent geometry : angle 1.06228 (12304) hydrogen bonds : bond 0.22093 ( 474) hydrogen bonds : angle 7.76793 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 445 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 73 TYR cc_start: 0.7158 (m-80) cc_final: 0.6811 (m-10) REVERT: H 134 ASP cc_start: 0.7382 (m-30) cc_final: 0.6467 (m-30) REVERT: H 138 TYR cc_start: 0.5296 (m-80) cc_final: 0.4811 (m-80) REVERT: H 228 ARG cc_start: 0.8477 (ptp-110) cc_final: 0.8184 (ptm-80) REVERT: H 233 MET cc_start: 0.8050 (mmm) cc_final: 0.7739 (tpp) REVERT: H 234 GLU cc_start: 0.7610 (mp0) cc_final: 0.7408 (tp30) REVERT: I 88 MET cc_start: 0.7494 (mtp) cc_final: 0.7159 (mtt) REVERT: I 98 LEU cc_start: 0.9299 (tp) cc_final: 0.8838 (tp) REVERT: I 102 GLN cc_start: 0.9108 (mt0) cc_final: 0.8262 (mt0) REVERT: I 141 ASN cc_start: 0.7860 (m-40) cc_final: 0.7562 (m-40) REVERT: I 146 TRP cc_start: 0.8734 (m100) cc_final: 0.8125 (m100) REVERT: I 167 ARG cc_start: 0.8471 (mtm180) cc_final: 0.8194 (mtm-85) REVERT: I 172 ASN cc_start: 0.8289 (m-40) cc_final: 0.8086 (m110) REVERT: J 148 VAL cc_start: 0.9027 (t) cc_final: 0.8822 (m) REVERT: J 206 TYR cc_start: 0.7789 (m-10) cc_final: 0.7491 (m-10) REVERT: L 78 ARG cc_start: 0.9081 (tpt170) cc_final: 0.8769 (tpt170) REVERT: L 81 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7948 (ttt180) REVERT: L 245 LEU cc_start: 0.8220 (mm) cc_final: 0.7180 (tt) REVERT: M 120 ASN cc_start: 0.8334 (t0) cc_final: 0.8095 (t0) REVERT: M 202 LYS cc_start: 0.8599 (tttt) cc_final: 0.8332 (mmtt) REVERT: M 203 LYS cc_start: 0.8852 (mptt) cc_final: 0.8442 (mmtm) REVERT: M 220 ILE cc_start: 0.9095 (mm) cc_final: 0.8836 (mm) REVERT: N 74 ASP cc_start: 0.6370 (m-30) cc_final: 0.6053 (m-30) REVERT: N 78 ARG cc_start: 0.6620 (mmt-90) cc_final: 0.5610 (ptp-170) REVERT: N 81 ARG cc_start: 0.8081 (ptt90) cc_final: 0.7738 (ttm170) REVERT: N 133 TYR cc_start: 0.8998 (t80) cc_final: 0.8649 (t80) REVERT: N 176 MET cc_start: 0.7538 (ttm) cc_final: 0.7327 (ttt) REVERT: N 202 LYS cc_start: 0.7981 (tttt) cc_final: 0.7698 (tttt) REVERT: N 243 LYS cc_start: 0.7861 (mttt) cc_final: 0.7623 (mtmt) outliers start: 5 outliers final: 0 residues processed: 448 average time/residue: 0.0970 time to fit residues: 58.2847 Evaluate side-chains 299 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 178 HIS I 141 ASN K 102 GLN K 111 ASN K 204 GLN L 168 HIS L 207 ASN M 204 GLN N 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109224 restraints weight = 16442.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.112424 restraints weight = 8794.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.114606 restraints weight = 5713.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116066 restraints weight = 4179.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.117117 restraints weight = 3309.350| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 9107 Z= 0.158 Angle : 0.683 8.720 12304 Z= 0.351 Chirality : 0.046 0.157 1426 Planarity : 0.005 0.062 1544 Dihedral : 5.158 21.917 1233 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.03 % Allowed : 16.53 % Favored : 79.44 % 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: -0.16 (0.23), residues: 1113 helix: 0.41 (0.19), residues: 630 sheet: 0.15 (0.49), residues: 93 loop : -0.87 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 81 TYR 0.017 0.002 TYR L 76 PHE 0.024 0.002 PHE I 105 TRP 0.030 0.003 TRP N 146 HIS 0.006 0.001 HIS H 178 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9107) covalent geometry : angle 0.68319 (12304) hydrogen bonds : bond 0.04381 ( 474) hydrogen bonds : angle 4.86999 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 355 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 215 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8330 (mm-40) REVERT: H 228 ARG cc_start: 0.8571 (ptp-110) cc_final: 0.8119 (ptm-80) REVERT: H 234 GLU cc_start: 0.7896 (mp0) cc_final: 0.7297 (mp0) REVERT: I 98 LEU cc_start: 0.9146 (tp) cc_final: 0.8791 (mt) REVERT: I 102 GLN cc_start: 0.9165 (mt0) cc_final: 0.8217 (mp10) REVERT: I 234 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7369 (tm-30) REVERT: J 107 GLN cc_start: 0.8234 (tp40) cc_final: 0.7423 (tt0) REVERT: J 116 HIS cc_start: 0.8035 (m-70) cc_final: 0.7556 (m-70) REVERT: J 137 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7029 (mp10) REVERT: J 148 VAL cc_start: 0.9057 (t) cc_final: 0.8721 (m) REVERT: K 202 LYS cc_start: 0.7373 (ttpp) cc_final: 0.7105 (mtmm) REVERT: K 218 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7685 (mm-40) REVERT: L 81 ARG cc_start: 0.8476 (mmm-85) cc_final: 0.8079 (ttt180) REVERT: L 202 LYS cc_start: 0.8146 (tttt) cc_final: 0.7772 (tttt) REVERT: L 245 LEU cc_start: 0.8192 (mm) cc_final: 0.7366 (tt) REVERT: M 148 VAL cc_start: 0.9059 (t) cc_final: 0.8804 (p) REVERT: M 231 SER cc_start: 0.9086 (p) cc_final: 0.8672 (m) REVERT: N 74 ASP cc_start: 0.6127 (m-30) cc_final: 0.5617 (m-30) REVERT: N 78 ARG cc_start: 0.6712 (mmt-90) cc_final: 0.5013 (ptp-170) REVERT: N 105 PHE cc_start: 0.7663 (t80) cc_final: 0.7387 (t80) REVERT: N 118 TYR cc_start: 0.8744 (m-80) cc_final: 0.8516 (m-10) REVERT: N 154 MET cc_start: 0.8166 (tpp) cc_final: 0.7812 (tpp) REVERT: N 237 GLU cc_start: 0.7549 (pp20) cc_final: 0.6923 (pp20) REVERT: N 243 LYS cc_start: 0.7954 (mttt) cc_final: 0.7723 (mtmt) outliers start: 40 outliers final: 21 residues processed: 378 average time/residue: 0.0981 time to fit residues: 48.8692 Evaluate side-chains 329 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 150 GLN Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 224 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 111 ASN H 207 ASN I 120 ASN J 179 GLN J 212 HIS K 102 GLN K 111 ASN K 204 GLN L 168 HIS ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 GLN N 102 GLN N 204 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.122775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107539 restraints weight = 16420.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.110721 restraints weight = 8850.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112902 restraints weight = 5793.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114360 restraints weight = 4258.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.115394 restraints weight = 3386.349| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9107 Z= 0.162 Angle : 0.641 8.407 12304 Z= 0.325 Chirality : 0.045 0.164 1426 Planarity : 0.005 0.065 1544 Dihedral : 4.783 20.866 1233 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.64 % Allowed : 17.24 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.24), residues: 1113 helix: 0.81 (0.20), residues: 632 sheet: 0.01 (0.51), residues: 91 loop : -0.60 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 81 TYR 0.013 0.001 TYR L 76 PHE 0.018 0.002 PHE I 105 TRP 0.037 0.003 TRP N 146 HIS 0.004 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9107) covalent geometry : angle 0.64056 (12304) hydrogen bonds : bond 0.03992 ( 474) hydrogen bonds : angle 4.66252 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 327 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: H 113 LYS cc_start: 0.9030 (mttp) cc_final: 0.8712 (mtpt) REVERT: H 179 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7682 (tm-30) REVERT: H 215 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8325 (mm-40) REVERT: H 221 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6287 (mm-30) REVERT: I 98 LEU cc_start: 0.9089 (tp) cc_final: 0.8795 (mt) REVERT: I 102 GLN cc_start: 0.9213 (mt0) cc_final: 0.8212 (mp10) REVERT: I 172 ASN cc_start: 0.8228 (m-40) cc_final: 0.7922 (m110) REVERT: I 234 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7508 (tm-30) REVERT: J 107 GLN cc_start: 0.8231 (tp40) cc_final: 0.7468 (tt0) REVERT: J 116 HIS cc_start: 0.7876 (m-70) cc_final: 0.7325 (m-70) REVERT: J 137 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7061 (mp10) REVERT: J 148 VAL cc_start: 0.8956 (t) cc_final: 0.8642 (m) REVERT: K 105 PHE cc_start: 0.8720 (t80) cc_final: 0.8517 (t80) REVERT: K 113 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7834 (ttmm) REVERT: K 228 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7318 (ttp80) REVERT: L 78 ARG cc_start: 0.8908 (tpt170) cc_final: 0.8529 (tpt170) REVERT: L 81 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8134 (ttt180) REVERT: L 245 LEU cc_start: 0.8342 (mm) cc_final: 0.7397 (tt) REVERT: M 203 LYS cc_start: 0.8858 (mptt) cc_final: 0.8621 (mttp) REVERT: M 231 SER cc_start: 0.9123 (p) cc_final: 0.8729 (m) REVERT: N 74 ASP cc_start: 0.6095 (m-30) cc_final: 0.5654 (m-30) REVERT: N 78 ARG cc_start: 0.6065 (mmt-90) cc_final: 0.5184 (ptp-170) REVERT: N 105 PHE cc_start: 0.7676 (t80) cc_final: 0.7345 (t80) REVERT: N 118 TYR cc_start: 0.8815 (m-80) cc_final: 0.8459 (m-10) REVERT: N 154 MET cc_start: 0.8211 (tpp) cc_final: 0.7864 (tpp) REVERT: N 168 HIS cc_start: 0.7874 (m170) cc_final: 0.7599 (m90) REVERT: N 237 GLU cc_start: 0.7708 (pp20) cc_final: 0.7116 (pp20) outliers start: 46 outliers final: 30 residues processed: 350 average time/residue: 0.0891 time to fit residues: 41.3670 Evaluate side-chains 338 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 307 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 179 GLN Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 166 MET Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 71 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 179 GLN I 247 HIS K 102 GLN K 204 GLN M 204 GLN N 204 GLN N 212 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106087 restraints weight = 16718.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109205 restraints weight = 9110.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111369 restraints weight = 6050.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.112873 restraints weight = 4480.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113910 restraints weight = 3562.764| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9107 Z= 0.183 Angle : 0.660 8.479 12304 Z= 0.333 Chirality : 0.045 0.158 1426 Planarity : 0.005 0.062 1544 Dihedral : 4.722 19.979 1233 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.95 % Allowed : 17.14 % Favored : 76.92 % 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: 0.47 (0.24), residues: 1113 helix: 1.02 (0.20), residues: 630 sheet: 0.01 (0.50), residues: 95 loop : -0.67 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 228 TYR 0.018 0.002 TYR M 206 PHE 0.028 0.002 PHE M 105 TRP 0.024 0.002 TRP N 146 HIS 0.009 0.001 HIS I 247 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 9107) covalent geometry : angle 0.66027 (12304) hydrogen bonds : bond 0.03841 ( 474) hydrogen bonds : angle 4.60839 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 321 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: H 113 LYS cc_start: 0.9010 (mttp) cc_final: 0.8709 (mtpt) REVERT: H 138 TYR cc_start: 0.5572 (m-10) cc_final: 0.5104 (m-80) REVERT: H 215 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8264 (mm-40) REVERT: I 98 LEU cc_start: 0.9132 (tp) cc_final: 0.8807 (mt) REVERT: I 102 GLN cc_start: 0.9215 (mt0) cc_final: 0.8208 (mp10) REVERT: I 172 ASN cc_start: 0.8245 (m-40) cc_final: 0.7888 (m110) REVERT: J 107 GLN cc_start: 0.8193 (tp40) cc_final: 0.7451 (tt0) REVERT: J 116 HIS cc_start: 0.7891 (m-70) cc_final: 0.7546 (m-70) REVERT: J 137 GLN cc_start: 0.7495 (mm-40) cc_final: 0.7096 (mp10) REVERT: J 148 VAL cc_start: 0.9085 (t) cc_final: 0.8631 (m) REVERT: K 73 TYR cc_start: 0.7578 (m-80) cc_final: 0.7161 (m-80) REVERT: K 105 PHE cc_start: 0.8715 (t80) cc_final: 0.8513 (t80) REVERT: K 113 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7894 (ttmm) REVERT: K 228 ARG cc_start: 0.7743 (ttp-170) cc_final: 0.7179 (ttp80) REVERT: L 81 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8175 (ttt180) REVERT: L 202 LYS cc_start: 0.8319 (tttt) cc_final: 0.7887 (tttt) REVERT: L 245 LEU cc_start: 0.8353 (mm) cc_final: 0.7384 (tt) REVERT: M 203 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8596 (mttp) REVERT: M 206 TYR cc_start: 0.7308 (m-10) cc_final: 0.6909 (m-10) REVERT: M 231 SER cc_start: 0.9121 (p) cc_final: 0.8743 (m) REVERT: N 74 ASP cc_start: 0.6168 (m-30) cc_final: 0.5712 (m-30) REVERT: N 78 ARG cc_start: 0.6211 (mmt-90) cc_final: 0.5289 (ptm160) REVERT: N 88 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7601 (mtp) REVERT: N 105 PHE cc_start: 0.7639 (t80) cc_final: 0.7354 (t80) REVERT: N 118 TYR cc_start: 0.8930 (m-80) cc_final: 0.8495 (m-10) REVERT: N 177 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7850 (mt) REVERT: N 197 GLU cc_start: 0.7278 (pm20) cc_final: 0.6518 (pm20) REVERT: N 237 GLU cc_start: 0.7818 (pp20) cc_final: 0.7241 (pp20) outliers start: 59 outliers final: 45 residues processed: 353 average time/residue: 0.0951 time to fit residues: 44.8914 Evaluate side-chains 350 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 301 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 179 GLN Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 203 LYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 177 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 246 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 102 GLN M 204 GLN N 102 GLN N 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104505 restraints weight = 16706.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107637 restraints weight = 9182.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109760 restraints weight = 6064.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111172 restraints weight = 4485.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112203 restraints weight = 3593.951| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9107 Z= 0.204 Angle : 0.693 8.567 12304 Z= 0.347 Chirality : 0.046 0.164 1426 Planarity : 0.005 0.061 1544 Dihedral : 4.724 19.269 1233 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 6.35 % Allowed : 18.04 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1113 helix: 0.98 (0.20), residues: 630 sheet: -0.16 (0.51), residues: 95 loop : -0.67 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 226 TYR 0.022 0.002 TYR M 206 PHE 0.024 0.002 PHE I 105 TRP 0.044 0.003 TRP N 146 HIS 0.004 0.001 HIS M 168 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9107) covalent geometry : angle 0.69295 (12304) hydrogen bonds : bond 0.03862 ( 474) hydrogen bonds : angle 4.64927 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 319 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: H 113 LYS cc_start: 0.8995 (mttp) cc_final: 0.8701 (mtpt) REVERT: H 138 TYR cc_start: 0.5757 (m-10) cc_final: 0.5332 (m-80) REVERT: H 214 LYS cc_start: 0.8352 (mmmt) cc_final: 0.7992 (mtpt) REVERT: H 215 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8265 (mm-40) REVERT: I 98 LEU cc_start: 0.9130 (tp) cc_final: 0.8779 (mt) REVERT: I 102 GLN cc_start: 0.9238 (mt0) cc_final: 0.8143 (mp10) REVERT: I 172 ASN cc_start: 0.8267 (m-40) cc_final: 0.7930 (m110) REVERT: J 116 HIS cc_start: 0.7891 (m-70) cc_final: 0.7557 (m-70) REVERT: J 137 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7179 (mp10) REVERT: J 148 VAL cc_start: 0.9043 (t) cc_final: 0.8655 (m) REVERT: J 206 TYR cc_start: 0.7734 (m-80) cc_final: 0.7371 (m-80) REVERT: K 73 TYR cc_start: 0.7470 (m-80) cc_final: 0.7114 (m-80) REVERT: K 105 PHE cc_start: 0.8755 (t80) cc_final: 0.8555 (t80) REVERT: K 113 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7901 (ttmm) REVERT: K 228 ARG cc_start: 0.7682 (ttp-170) cc_final: 0.7219 (ttp80) REVERT: L 81 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8134 (ttt180) REVERT: L 202 LYS cc_start: 0.8300 (tttt) cc_final: 0.8004 (tttt) REVERT: L 245 LEU cc_start: 0.8254 (mm) cc_final: 0.7298 (tt) REVERT: M 203 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8630 (mttp) REVERT: M 231 SER cc_start: 0.9129 (p) cc_final: 0.8771 (m) REVERT: N 78 ARG cc_start: 0.6389 (mmt-90) cc_final: 0.5318 (ptp-170) REVERT: N 105 PHE cc_start: 0.7639 (t80) cc_final: 0.7339 (t80) REVERT: N 118 TYR cc_start: 0.8985 (m-80) cc_final: 0.8721 (m-10) REVERT: N 197 GLU cc_start: 0.7237 (pm20) cc_final: 0.6590 (pm20) REVERT: N 224 MET cc_start: 0.7115 (tpt) cc_final: 0.6882 (tpt) outliers start: 63 outliers final: 48 residues processed: 352 average time/residue: 0.0939 time to fit residues: 43.9089 Evaluate side-chains 348 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 298 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 127 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 203 LYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 233 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 166 MET Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 212 HIS K 102 GLN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 GLN N 168 HIS N 204 GLN N 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105625 restraints weight = 16558.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.108766 restraints weight = 9022.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110917 restraints weight = 5924.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112380 restraints weight = 4355.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.113326 restraints weight = 3462.171| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9107 Z= 0.185 Angle : 0.680 10.838 12304 Z= 0.341 Chirality : 0.045 0.149 1426 Planarity : 0.005 0.059 1544 Dihedral : 4.679 18.348 1233 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 6.35 % Allowed : 19.35 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1113 helix: 1.09 (0.20), residues: 630 sheet: -0.28 (0.49), residues: 101 loop : -0.64 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 228 TYR 0.023 0.001 TYR M 206 PHE 0.012 0.002 PHE L 105 TRP 0.034 0.002 TRP N 146 HIS 0.004 0.001 HIS N 168 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 9107) covalent geometry : angle 0.67973 (12304) hydrogen bonds : bond 0.03704 ( 474) hydrogen bonds : angle 4.59972 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 320 time to evaluate : 0.277 Fit side-chains REVERT: H 113 LYS cc_start: 0.8967 (mttp) cc_final: 0.8695 (mtpt) REVERT: H 138 TYR cc_start: 0.5666 (m-10) cc_final: 0.5266 (m-80) REVERT: H 167 ARG cc_start: 0.8583 (mtm180) cc_final: 0.8248 (mtm-85) REVERT: H 215 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8238 (mm-40) REVERT: H 242 ASP cc_start: 0.6127 (m-30) cc_final: 0.5798 (m-30) REVERT: I 98 LEU cc_start: 0.9125 (tp) cc_final: 0.8830 (mt) REVERT: I 102 GLN cc_start: 0.9229 (mt0) cc_final: 0.8176 (mp10) REVERT: I 154 MET cc_start: 0.8487 (mmm) cc_final: 0.8224 (mmm) REVERT: I 172 ASN cc_start: 0.8176 (m-40) cc_final: 0.7868 (m110) REVERT: I 206 TYR cc_start: 0.8350 (m-80) cc_final: 0.8014 (m-80) REVERT: J 92 ASP cc_start: 0.7685 (t70) cc_final: 0.7453 (t70) REVERT: J 116 HIS cc_start: 0.7836 (m-70) cc_final: 0.7539 (m-70) REVERT: J 137 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7157 (mp10) REVERT: J 148 VAL cc_start: 0.9042 (t) cc_final: 0.8691 (m) REVERT: J 196 GLU cc_start: 0.8286 (tp30) cc_final: 0.7483 (tp30) REVERT: K 73 TYR cc_start: 0.7462 (m-80) cc_final: 0.7174 (m-80) REVERT: K 113 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7832 (ttmm) REVERT: K 228 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7289 (ttp80) REVERT: L 81 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8106 (ttt180) REVERT: L 202 LYS cc_start: 0.8343 (tttt) cc_final: 0.8110 (tttt) REVERT: L 245 LEU cc_start: 0.8103 (mm) cc_final: 0.7216 (tt) REVERT: M 203 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8634 (mttp) REVERT: M 221 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7872 (mm-30) REVERT: M 231 SER cc_start: 0.9093 (p) cc_final: 0.8726 (m) REVERT: N 78 ARG cc_start: 0.6291 (mmt-90) cc_final: 0.5215 (ptp-170) REVERT: N 88 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7551 (mtp) REVERT: N 118 TYR cc_start: 0.9000 (m-80) cc_final: 0.8731 (m-10) REVERT: N 197 GLU cc_start: 0.7142 (pm20) cc_final: 0.6614 (pm20) REVERT: N 237 GLU cc_start: 0.7877 (pp20) cc_final: 0.7411 (pp20) outliers start: 63 outliers final: 49 residues processed: 357 average time/residue: 0.0891 time to fit residues: 42.3109 Evaluate side-chains 354 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain L residue 227 ASP Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 203 LYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain M residue 233 MET Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 220 ILE Chi-restraints excluded: chain N residue 228 ARG Chi-restraints excluded: chain N residue 246 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 103 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 ASN J 212 HIS M 120 ASN M 204 GLN N 102 GLN N 204 GLN N 212 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.121912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106857 restraints weight = 16624.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110004 restraints weight = 8966.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112132 restraints weight = 5830.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113616 restraints weight = 4273.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.114621 restraints weight = 3369.084| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9107 Z= 0.155 Angle : 0.689 9.898 12304 Z= 0.342 Chirality : 0.045 0.145 1426 Planarity : 0.005 0.059 1544 Dihedral : 4.603 17.765 1233 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.04 % Allowed : 21.77 % Favored : 73.19 % 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: 0.54 (0.25), residues: 1113 helix: 1.12 (0.20), residues: 630 sheet: -0.30 (0.52), residues: 89 loop : -0.62 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 226 TYR 0.022 0.001 TYR M 206 PHE 0.025 0.002 PHE K 105 TRP 0.024 0.002 TRP N 146 HIS 0.004 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9107) covalent geometry : angle 0.68870 (12304) hydrogen bonds : bond 0.03574 ( 474) hydrogen bonds : angle 4.50430 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 318 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: H 113 LYS cc_start: 0.8967 (mttp) cc_final: 0.8679 (mtpt) REVERT: H 138 TYR cc_start: 0.5575 (m-10) cc_final: 0.5097 (m-80) REVERT: H 214 LYS cc_start: 0.8318 (mmmt) cc_final: 0.8011 (mtpt) REVERT: I 172 ASN cc_start: 0.8103 (m-40) cc_final: 0.7837 (m110) REVERT: I 224 MET cc_start: 0.8526 (mmm) cc_final: 0.8242 (mmm) REVERT: I 228 ARG cc_start: 0.7844 (tmt170) cc_final: 0.7342 (tmt170) REVERT: J 92 ASP cc_start: 0.7687 (t70) cc_final: 0.7446 (t70) REVERT: J 107 GLN cc_start: 0.8240 (tp40) cc_final: 0.7521 (tt0) REVERT: J 116 HIS cc_start: 0.7825 (m-70) cc_final: 0.7359 (m-70) REVERT: J 137 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7096 (mp10) REVERT: J 148 VAL cc_start: 0.9031 (t) cc_final: 0.8649 (m) REVERT: J 206 TYR cc_start: 0.7560 (m-80) cc_final: 0.7317 (m-80) REVERT: K 73 TYR cc_start: 0.7353 (m-80) cc_final: 0.7062 (m-80) REVERT: K 113 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7771 (ttmm) REVERT: K 228 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7276 (ttp80) REVERT: L 81 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8129 (ttt180) REVERT: L 82 GLU cc_start: 0.8234 (mt-10) cc_final: 0.8015 (mt-10) REVERT: L 86 CYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7998 (p) REVERT: L 100 ILE cc_start: 0.8941 (pt) cc_final: 0.8410 (mt) REVERT: L 199 MET cc_start: 0.8027 (mpp) cc_final: 0.7810 (ppp) REVERT: L 202 LYS cc_start: 0.8270 (tttt) cc_final: 0.7893 (tttt) REVERT: L 245 LEU cc_start: 0.8124 (mm) cc_final: 0.7218 (tt) REVERT: M 200 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7247 (mtmm) REVERT: M 231 SER cc_start: 0.9102 (p) cc_final: 0.8737 (m) REVERT: N 78 ARG cc_start: 0.6320 (mmt-90) cc_final: 0.5711 (tpp-160) REVERT: N 88 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7502 (mtp) REVERT: N 105 PHE cc_start: 0.7648 (t80) cc_final: 0.7444 (t80) REVERT: N 118 TYR cc_start: 0.9006 (m-80) cc_final: 0.8736 (m-10) REVERT: N 179 GLN cc_start: 0.7292 (mm110) cc_final: 0.6404 (pp30) REVERT: N 197 GLU cc_start: 0.7164 (pm20) cc_final: 0.6646 (pm20) REVERT: N 237 GLU cc_start: 0.7848 (pp20) cc_final: 0.7422 (pp20) outliers start: 50 outliers final: 41 residues processed: 347 average time/residue: 0.0976 time to fit residues: 44.7336 Evaluate side-chains 345 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 301 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 94 SER Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 176 MET Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 198 ILE Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 86 CYS Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 127 THR Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 205 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 4 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 ASN J 212 HIS M 204 GLN N 204 GLN N 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.116427 restraints weight = 16284.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119994 restraints weight = 8310.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122394 restraints weight = 5220.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123942 restraints weight = 3727.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.125083 restraints weight = 2901.460| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9107 Z= 0.131 Angle : 0.690 11.480 12304 Z= 0.340 Chirality : 0.044 0.140 1426 Planarity : 0.005 0.059 1544 Dihedral : 4.469 18.824 1233 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.23 % Allowed : 22.18 % Favored : 73.59 % 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: 0.70 (0.25), residues: 1113 helix: 1.21 (0.21), residues: 630 sheet: -0.23 (0.50), residues: 100 loop : -0.49 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 228 TYR 0.033 0.001 TYR I 206 PHE 0.028 0.002 PHE K 105 TRP 0.022 0.002 TRP N 146 HIS 0.003 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9107) covalent geometry : angle 0.69016 (12304) hydrogen bonds : bond 0.03432 ( 474) hydrogen bonds : angle 4.39564 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 327 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 107 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8366 (tp40) REVERT: H 113 LYS cc_start: 0.8970 (mttp) cc_final: 0.8682 (mtpt) REVERT: H 138 TYR cc_start: 0.5297 (m-10) cc_final: 0.4798 (m-80) REVERT: H 214 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7983 (mtpt) REVERT: I 146 TRP cc_start: 0.8511 (m100) cc_final: 0.7654 (m-90) REVERT: I 172 ASN cc_start: 0.7944 (m-40) cc_final: 0.7710 (m110) REVERT: I 206 TYR cc_start: 0.8100 (m-80) cc_final: 0.7827 (m-80) REVERT: I 228 ARG cc_start: 0.7781 (tmt170) cc_final: 0.7241 (tmt170) REVERT: J 80 LEU cc_start: 0.8730 (tt) cc_final: 0.8423 (tt) REVERT: J 107 GLN cc_start: 0.8222 (tp40) cc_final: 0.7553 (tt0) REVERT: J 116 HIS cc_start: 0.7735 (m-70) cc_final: 0.7373 (m-70) REVERT: J 137 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7009 (mp10) REVERT: J 148 VAL cc_start: 0.9021 (t) cc_final: 0.8676 (m) REVERT: J 206 TYR cc_start: 0.7580 (m-80) cc_final: 0.7350 (m-80) REVERT: K 73 TYR cc_start: 0.7279 (m-80) cc_final: 0.7029 (m-80) REVERT: K 113 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7782 (ttmm) REVERT: K 228 ARG cc_start: 0.7813 (ttp-170) cc_final: 0.7406 (ttp80) REVERT: L 78 ARG cc_start: 0.8869 (tpt170) cc_final: 0.8627 (tpt170) REVERT: L 81 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8172 (ttt180) REVERT: L 100 ILE cc_start: 0.8981 (pt) cc_final: 0.8417 (mt) REVERT: L 199 MET cc_start: 0.7985 (mpp) cc_final: 0.7783 (ppp) REVERT: L 202 LYS cc_start: 0.8215 (tttt) cc_final: 0.7868 (tttt) REVERT: L 245 LEU cc_start: 0.8104 (mm) cc_final: 0.7217 (tt) REVERT: M 87 VAL cc_start: 0.8616 (t) cc_final: 0.8413 (p) REVERT: M 203 LYS cc_start: 0.8529 (mptp) cc_final: 0.8212 (mmtm) REVERT: M 231 SER cc_start: 0.9113 (p) cc_final: 0.8733 (m) REVERT: N 78 ARG cc_start: 0.6229 (mmt-90) cc_final: 0.5612 (tpp-160) REVERT: N 88 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7540 (mtp) REVERT: N 118 TYR cc_start: 0.8992 (m-80) cc_final: 0.8611 (m-10) REVERT: N 179 GLN cc_start: 0.7425 (mm110) cc_final: 0.6492 (pp30) REVERT: N 197 GLU cc_start: 0.7102 (pm20) cc_final: 0.6621 (pm20) REVERT: N 203 LYS cc_start: 0.8474 (tptp) cc_final: 0.8051 (ttpt) REVERT: N 237 GLU cc_start: 0.7846 (pp20) cc_final: 0.7636 (pp20) outliers start: 42 outliers final: 35 residues processed: 353 average time/residue: 0.0967 time to fit residues: 45.3347 Evaluate side-chains 345 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 307 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 205 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN J 212 HIS ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 GLN N 178 HIS N 204 GLN N 212 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112775 restraints weight = 16337.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116258 restraints weight = 8408.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118610 restraints weight = 5322.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120183 restraints weight = 3828.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121253 restraints weight = 2988.814| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9107 Z= 0.220 Angle : 0.757 12.283 12304 Z= 0.377 Chirality : 0.047 0.231 1426 Planarity : 0.005 0.058 1544 Dihedral : 4.690 19.884 1233 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.23 % Allowed : 23.49 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1113 helix: 0.98 (0.20), residues: 628 sheet: -0.35 (0.50), residues: 105 loop : -0.58 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 226 TYR 0.030 0.002 TYR I 206 PHE 0.030 0.003 PHE N 105 TRP 0.028 0.002 TRP N 146 HIS 0.005 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00526 ( 9107) covalent geometry : angle 0.75744 (12304) hydrogen bonds : bond 0.03814 ( 474) hydrogen bonds : angle 4.57975 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 113 LYS cc_start: 0.8920 (mttp) cc_final: 0.8657 (mtpt) REVERT: H 138 TYR cc_start: 0.5485 (m-10) cc_final: 0.5101 (m-80) REVERT: H 214 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8078 (mtpt) REVERT: I 146 TRP cc_start: 0.8578 (m100) cc_final: 0.7734 (m-90) REVERT: J 116 HIS cc_start: 0.7845 (m-70) cc_final: 0.7387 (m-70) REVERT: J 137 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7172 (mp10) REVERT: J 148 VAL cc_start: 0.9099 (t) cc_final: 0.8708 (m) REVERT: J 206 TYR cc_start: 0.7654 (m-80) cc_final: 0.7394 (m-80) REVERT: K 73 TYR cc_start: 0.7252 (m-80) cc_final: 0.6988 (m-80) REVERT: K 113 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7766 (ttmm) REVERT: K 228 ARG cc_start: 0.7838 (ttp-170) cc_final: 0.7444 (ttp80) REVERT: L 78 ARG cc_start: 0.8954 (tpt170) cc_final: 0.8656 (tpt170) REVERT: L 81 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.8167 (ttt180) REVERT: L 202 LYS cc_start: 0.8252 (tttt) cc_final: 0.7916 (tttt) REVERT: L 245 LEU cc_start: 0.8157 (mm) cc_final: 0.7271 (tt) REVERT: M 200 LYS cc_start: 0.8029 (mttp) cc_final: 0.7730 (mtmm) REVERT: M 203 LYS cc_start: 0.8545 (mptp) cc_final: 0.8285 (mmtm) REVERT: M 231 SER cc_start: 0.9116 (p) cc_final: 0.8750 (m) REVERT: N 78 ARG cc_start: 0.6347 (mmt-90) cc_final: 0.5515 (tpp-160) REVERT: N 88 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7543 (mtp) REVERT: N 118 TYR cc_start: 0.9040 (m-80) cc_final: 0.8807 (m-10) REVERT: N 179 GLN cc_start: 0.7621 (mm110) cc_final: 0.6603 (pp30) REVERT: N 197 GLU cc_start: 0.7101 (pm20) cc_final: 0.6677 (pm20) REVERT: N 220 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7855 (tp) outliers start: 42 outliers final: 36 residues processed: 338 average time/residue: 0.0911 time to fit residues: 40.8848 Evaluate side-chains 348 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 309 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 77 SER Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 198 ILE Chi-restraints excluded: chain I residue 233 MET Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 98 LEU Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 0.0470 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 172 ASN I 172 ASN J 212 HIS M 120 ASN M 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117282 restraints weight = 16119.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120874 restraints weight = 8164.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123261 restraints weight = 5092.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124847 restraints weight = 3610.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.125973 restraints weight = 2786.056| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9107 Z= 0.135 Angle : 0.737 12.334 12304 Z= 0.362 Chirality : 0.044 0.146 1426 Planarity : 0.005 0.057 1544 Dihedral : 4.550 24.215 1233 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.43 % Allowed : 24.19 % Favored : 72.38 % 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: 0.61 (0.25), residues: 1113 helix: 1.14 (0.21), residues: 630 sheet: -0.28 (0.51), residues: 99 loop : -0.51 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 226 TYR 0.014 0.001 TYR I 138 PHE 0.034 0.002 PHE K 105 TRP 0.023 0.002 TRP N 146 HIS 0.003 0.001 HIS H 212 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9107) covalent geometry : angle 0.73748 (12304) hydrogen bonds : bond 0.03473 ( 474) hydrogen bonds : angle 4.36306 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 LYS cc_start: 0.8923 (mttp) cc_final: 0.8620 (mtpt) REVERT: H 138 TYR cc_start: 0.5262 (m-10) cc_final: 0.4902 (m-80) REVERT: H 141 ASN cc_start: 0.8493 (m-40) cc_final: 0.8281 (m-40) REVERT: I 206 TYR cc_start: 0.8220 (m-80) cc_final: 0.7989 (m-80) REVERT: J 107 GLN cc_start: 0.8202 (tp40) cc_final: 0.7559 (tt0) REVERT: J 116 HIS cc_start: 0.7651 (m-70) cc_final: 0.7345 (m-70) REVERT: J 137 GLN cc_start: 0.7470 (mm-40) cc_final: 0.7025 (mp10) REVERT: J 148 VAL cc_start: 0.9083 (t) cc_final: 0.8735 (m) REVERT: J 206 TYR cc_start: 0.7566 (m-80) cc_final: 0.7328 (m-80) REVERT: K 73 TYR cc_start: 0.7159 (m-80) cc_final: 0.6927 (m-80) REVERT: K 113 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7721 (ttmm) REVERT: K 226 ARG cc_start: 0.7749 (mmm160) cc_final: 0.7352 (tpt-90) REVERT: K 228 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.7391 (ttp80) REVERT: L 78 ARG cc_start: 0.8919 (tpt170) cc_final: 0.8526 (tpt170) REVERT: L 81 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8151 (ttt180) REVERT: L 100 ILE cc_start: 0.8925 (pt) cc_final: 0.8367 (mt) REVERT: L 202 LYS cc_start: 0.8227 (tttt) cc_final: 0.7715 (tttt) REVERT: L 245 LEU cc_start: 0.8102 (mm) cc_final: 0.7205 (tt) REVERT: M 203 LYS cc_start: 0.8549 (mptp) cc_final: 0.8248 (mmtm) REVERT: M 231 SER cc_start: 0.9105 (p) cc_final: 0.8735 (m) REVERT: N 78 ARG cc_start: 0.6292 (mmt-90) cc_final: 0.5690 (tpp-160) REVERT: N 88 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7533 (mtp) REVERT: N 118 TYR cc_start: 0.8969 (m-80) cc_final: 0.8657 (m-10) REVERT: N 179 GLN cc_start: 0.7424 (mm110) cc_final: 0.6564 (pp30) REVERT: N 197 GLU cc_start: 0.6978 (pm20) cc_final: 0.6556 (pm20) REVERT: N 203 LYS cc_start: 0.8521 (tptp) cc_final: 0.8124 (ttpt) REVERT: N 234 GLU cc_start: 0.6274 (pm20) cc_final: 0.6038 (pm20) outliers start: 34 outliers final: 30 residues processed: 342 average time/residue: 0.0967 time to fit residues: 43.7527 Evaluate side-chains 339 residues out of total 997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 307 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 TYR Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 176 MET Chi-restraints excluded: chain I residue 229 TYR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 97 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain K residue 108 SER Chi-restraints excluded: chain K residue 113 LYS Chi-restraints excluded: chain K residue 166 MET Chi-restraints excluded: chain K residue 212 HIS Chi-restraints excluded: chain K residue 241 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 134 ASP Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 157 LEU Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 225 GLU Chi-restraints excluded: chain M residue 144 CYS Chi-restraints excluded: chain M residue 224 MET Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 153 SER Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 168 HIS ** H 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 HIS L 215 GLN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111944 restraints weight = 16343.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115265 restraints weight = 8388.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.117577 restraints weight = 5411.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119140 restraints weight = 3892.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120139 restraints weight = 3035.663| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 9107 Z= 0.249 Angle : 0.802 12.713 12304 Z= 0.401 Chirality : 0.048 0.212 1426 Planarity : 0.005 0.055 1544 Dihedral : 4.787 24.334 1233 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.83 % Allowed : 24.19 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1113 helix: 0.89 (0.20), residues: 628 sheet: -0.49 (0.48), residues: 112 loop : -0.58 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 226 TYR 0.019 0.002 TYR M 206 PHE 0.030 0.003 PHE N 105 TRP 0.033 0.003 TRP N 146 HIS 0.005 0.001 HIS M 168 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 9107) covalent geometry : angle 0.80239 (12304) hydrogen bonds : bond 0.03986 ( 474) hydrogen bonds : angle 4.64492 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1375.05 seconds wall clock time: 24 minutes 36.25 seconds (1476.25 seconds total)