Starting phenix.real_space_refine on Wed Mar 4 06:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k1h_9906/03_2026/6k1h_9906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k1h_9906/03_2026/6k1h_9906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k1h_9906/03_2026/6k1h_9906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k1h_9906/03_2026/6k1h_9906.map" model { file = "/net/cci-nas-00/data/ceres_data/6k1h_9906/03_2026/6k1h_9906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k1h_9906/03_2026/6k1h_9906.cif" } resolution = 3.52 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= 0.001 sd= 0.015 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 75 5.16 5 C 7704 2.51 5 N 1956 2.21 5 O 2034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11769 Number of models: 1 Model: "" Number of chains: 9 Chain: "Z" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 258} Chain: "Y" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1806 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 238} Chain: "F" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 258} Chain: "E" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1806 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 238} Chain: "C" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2105 Classifications: {'peptide': 273} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 258} Chain: "B" Number of atoms: 1806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1806 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 238} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.83, per 1000 atoms: 0.24 Number of scatterers: 11769 At special positions: 0 Unit cell: (128.448, 123.096, 94.998, 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 75 16.00 O 2034 8.00 N 1956 7.00 C 7704 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 649.7 milliseconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2790 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 71.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'Z' and resid 17 through 29 removed outlier: 3.628A pdb=" N ILE Z 21 " --> pdb=" O THR Z 17 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 57 Proline residue: Z 51 - end of helix removed outlier: 3.875A pdb=" N ARG Z 55 " --> pdb=" O PRO Z 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR Z 57 " --> pdb=" O ILE Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 71 removed outlier: 3.517A pdb=" N ARG Z 69 " --> pdb=" O LYS Z 65 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 98 removed outlier: 3.529A pdb=" N GLU Z 93 " --> pdb=" O THR Z 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU Z 94 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN Z 95 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 127 removed outlier: 4.341A pdb=" N ASN Z 108 " --> pdb=" O ASP Z 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY Z 116 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix removed outlier: 3.702A pdb=" N ASP Z 123 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) Proline residue: Z 124 - end of helix Processing helix chain 'Z' and resid 130 through 138 Processing helix chain 'Z' and resid 151 through 161 removed outlier: 3.537A pdb=" N ASN Z 158 " --> pdb=" O PHE Z 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 174 removed outlier: 3.623A pdb=" N TYR Z 171 " --> pdb=" O TYR Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 178 No H-bonds generated for 'chain 'Z' and resid 176 through 178' Processing helix chain 'Z' and resid 179 through 184 removed outlier: 3.997A pdb=" N MET Z 183 " --> pdb=" O ILE Z 179 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 210 removed outlier: 3.648A pdb=" N SER Z 196 " --> pdb=" O THR Z 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE Z 197 " --> pdb=" O GLU Z 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU Z 200 " --> pdb=" O SER Z 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 242 removed outlier: 3.703A pdb=" N ILE Z 237 " --> pdb=" O THR Z 233 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU Z 241 " --> pdb=" O ILE Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 244 through 258 Processing helix chain 'Z' and resid 259 through 261 No H-bonds generated for 'chain 'Z' and resid 259 through 261' Processing helix chain 'Z' and resid 263 through 266 Processing helix chain 'Z' and resid 267 through 278 removed outlier: 3.514A pdb=" N ILE Z 276 " --> pdb=" O PHE Z 272 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 25 removed outlier: 3.608A pdb=" N VAL Y 9 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE Y 23 " --> pdb=" O GLY Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 44 removed outlier: 3.737A pdb=" N VAL Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL Y 42 " --> pdb=" O LEU Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 61 removed outlier: 4.070A pdb=" N ILE Y 52 " --> pdb=" O THR Y 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 87 removed outlier: 4.383A pdb=" N VAL Y 85 " --> pdb=" O SER Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 117 removed outlier: 4.134A pdb=" N ILE Y 100 " --> pdb=" O ILE Y 96 " (cutoff:3.500A) Proline residue: Y 101 - end of helix removed outlier: 3.616A pdb=" N GLN Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL Y 108 " --> pdb=" O ALA Y 104 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 121 Processing helix chain 'Y' and resid 124 through 129 Processing helix chain 'Y' and resid 133 through 141 removed outlier: 3.780A pdb=" N ILE Y 139 " --> pdb=" O ALA Y 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL Y 141 " --> pdb=" O SER Y 137 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.926A pdb=" N VAL Y 151 " --> pdb=" O ALA Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 158 removed outlier: 3.733A pdb=" N VAL Y 158 " --> pdb=" O PRO Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 175 through 186 removed outlier: 3.705A pdb=" N ILE Y 184 " --> pdb=" O ASN Y 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA Y 185 " --> pdb=" O GLY Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 189 through 201 removed outlier: 3.889A pdb=" N GLY Y 193 " --> pdb=" O ILE Y 189 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET Y 200 " --> pdb=" O MET Y 196 " (cutoff:3.500A) Processing helix chain 'Y' and resid 207 through 219 removed outlier: 3.721A pdb=" N ALA Y 217 " --> pdb=" O GLY Y 213 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 241 removed outlier: 3.541A pdb=" N THR Y 232 " --> pdb=" O GLY Y 228 " (cutoff:3.500A) Processing helix chain 'Y' and resid 242 through 246 Processing helix chain 'F' and resid 17 through 29 removed outlier: 3.627A pdb=" N ILE F 21 " --> pdb=" O THR F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 57 Proline residue: F 51 - end of helix removed outlier: 3.875A pdb=" N ARG F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR F 57 " --> pdb=" O ILE F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 71 removed outlier: 3.518A pdb=" N ARG F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 98 removed outlier: 3.529A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 127 removed outlier: 4.340A pdb=" N ASN F 108 " --> pdb=" O ASP F 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 116 " --> pdb=" O VAL F 112 " (cutoff:3.500A) Proline residue: F 117 - end of helix removed outlier: 3.701A pdb=" N ASP F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 130 through 138 Processing helix chain 'F' and resid 151 through 161 removed outlier: 3.537A pdb=" N ASN F 158 " --> pdb=" O PHE F 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.623A pdb=" N TYR F 171 " --> pdb=" O TYR F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 178 No H-bonds generated for 'chain 'F' and resid 176 through 178' Processing helix chain 'F' and resid 179 through 184 removed outlier: 3.997A pdb=" N MET F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 210 removed outlier: 3.648A pdb=" N SER F 196 " --> pdb=" O THR F 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 242 removed outlier: 3.703A pdb=" N ILE F 237 " --> pdb=" O THR F 233 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 241 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 258 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 263 through 266 Processing helix chain 'F' and resid 267 through 278 removed outlier: 3.514A pdb=" N ILE F 276 " --> pdb=" O PHE F 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 25 removed outlier: 3.607A pdb=" N VAL E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU E 10 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 44 removed outlier: 3.736A pdb=" N VAL E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 61 removed outlier: 4.072A pdb=" N ILE E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 4.383A pdb=" N VAL E 85 " --> pdb=" O SER E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 117 removed outlier: 4.134A pdb=" N ILE E 100 " --> pdb=" O ILE E 96 " (cutoff:3.500A) Proline residue: E 101 - end of helix removed outlier: 3.616A pdb=" N GLN E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.780A pdb=" N ILE E 139 " --> pdb=" O ALA E 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 removed outlier: 3.926A pdb=" N VAL E 151 " --> pdb=" O ALA E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 3.733A pdb=" N VAL E 158 " --> pdb=" O PRO E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 175 through 186 removed outlier: 3.704A pdb=" N ILE E 184 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA E 185 " --> pdb=" O GLY E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.889A pdb=" N GLY E 193 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 219 removed outlier: 3.722A pdb=" N ALA E 217 " --> pdb=" O GLY E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 241 removed outlier: 3.541A pdb=" N THR E 232 " --> pdb=" O GLY E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'C' and resid 17 through 29 removed outlier: 3.627A pdb=" N ILE C 21 " --> pdb=" O THR C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 Proline residue: C 51 - end of helix removed outlier: 3.874A pdb=" N ARG C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 57 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 removed outlier: 3.517A pdb=" N ARG C 69 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 98 removed outlier: 3.529A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU C 94 " --> pdb=" O LEU C 90 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 127 removed outlier: 4.340A pdb=" N ASN C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 117 - end of helix removed outlier: 3.702A pdb=" N ASP C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 130 through 138 Processing helix chain 'C' and resid 151 through 161 removed outlier: 3.537A pdb=" N ASN C 158 " --> pdb=" O PHE C 154 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.623A pdb=" N TYR C 171 " --> pdb=" O TYR C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 178 No H-bonds generated for 'chain 'C' and resid 176 through 178' Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.997A pdb=" N MET C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 210 removed outlier: 3.648A pdb=" N SER C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU C 200 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.703A pdb=" N ILE C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 263 through 266 Processing helix chain 'C' and resid 267 through 278 removed outlier: 3.514A pdb=" N ILE C 276 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.608A pdb=" N VAL B 9 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU B 10 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 44 removed outlier: 3.736A pdb=" N VAL B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 61 removed outlier: 4.070A pdb=" N ILE B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 4.383A pdb=" N VAL B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 removed outlier: 4.134A pdb=" N ILE B 100 " --> pdb=" O ILE B 96 " (cutoff:3.500A) Proline residue: B 101 - end of helix removed outlier: 3.616A pdb=" N GLN B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.780A pdb=" N ILE B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.926A pdb=" N VAL B 151 " --> pdb=" O ALA B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.733A pdb=" N VAL B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.705A pdb=" N ILE B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.889A pdb=" N GLY B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 removed outlier: 3.721A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 241 removed outlier: 3.541A pdb=" N THR B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 246 582 hydrogen bonds defined for protein. 1701 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: 1.75 Time building geometry restraints manager: 1.30 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: 2814 1.33 - 1.45: 2231 1.45 - 1.57: 6817 1.57 - 1.69: 3 1.69 - 1.81: 135 Bond restraints: 12000 Sorted by residual: bond pdb=" N GLN F 32 " pdb=" CA GLN F 32 " ideal model delta sigma weight residual 1.456 1.514 -0.057 1.27e-02 6.20e+03 2.05e+01 bond pdb=" N GLN C 32 " pdb=" CA GLN C 32 " ideal model delta sigma weight residual 1.456 1.511 -0.054 1.27e-02 6.20e+03 1.83e+01 bond pdb=" N GLN Z 32 " pdb=" CA GLN Z 32 " ideal model delta sigma weight residual 1.456 1.510 -0.054 1.27e-02 6.20e+03 1.83e+01 bond pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" CA GLN C 32 " pdb=" C GLN C 32 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.23e-02 6.61e+03 1.26e+01 ... (remaining 11995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 16055 3.18 - 6.36: 235 6.36 - 9.53: 23 9.53 - 12.71: 6 12.71 - 15.89: 1 Bond angle restraints: 16320 Sorted by residual: angle pdb=" N ARG Y 247 " pdb=" CA ARG Y 247 " pdb=" C ARG Y 247 " ideal model delta sigma weight residual 109.18 125.07 -15.89 1.42e+00 4.96e-01 1.25e+02 angle pdb=" CA GLN C 32 " pdb=" C GLN C 32 " pdb=" O GLN C 32 " ideal model delta sigma weight residual 121.15 112.44 8.71 1.10e+00 8.26e-01 6.27e+01 angle pdb=" CA GLN Z 32 " pdb=" C GLN Z 32 " pdb=" O GLN Z 32 " ideal model delta sigma weight residual 121.15 112.70 8.45 1.10e+00 8.26e-01 5.90e+01 angle pdb=" CA GLN F 32 " pdb=" C GLN F 32 " pdb=" O GLN F 32 " ideal model delta sigma weight residual 121.15 112.79 8.36 1.10e+00 8.26e-01 5.77e+01 angle pdb=" N ARG B 247 " pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 108.86 118.13 -9.27 1.41e+00 5.03e-01 4.32e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 6560 20.58 - 41.15: 401 41.15 - 61.73: 52 61.73 - 82.31: 28 82.31 - 102.89: 12 Dihedral angle restraints: 7053 sinusoidal: 2676 harmonic: 4377 Sorted by residual: dihedral pdb=" CA ARG C 221 " pdb=" C ARG C 221 " pdb=" N ILE C 222 " pdb=" CA ILE C 222 " ideal model delta harmonic sigma weight residual -180.00 -139.25 -40.75 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ARG Z 221 " pdb=" C ARG Z 221 " pdb=" N ILE Z 222 " pdb=" CA ILE Z 222 " ideal model delta harmonic sigma weight residual -180.00 -139.27 -40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ARG F 221 " pdb=" C ARG F 221 " pdb=" N ILE F 222 " pdb=" CA ILE F 222 " ideal model delta harmonic sigma weight residual -180.00 -139.29 -40.71 0 5.00e+00 4.00e-02 6.63e+01 ... (remaining 7050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1648 0.067 - 0.134: 320 0.134 - 0.200: 15 0.200 - 0.267: 1 0.267 - 0.334: 2 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CA ARG Y 247 " pdb=" N ARG Y 247 " pdb=" C ARG Y 247 " pdb=" CB ARG Y 247 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG E 247 " pdb=" N ARG E 247 " pdb=" C ARG E 247 " pdb=" CB ARG E 247 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ARG B 247 " pdb=" N ARG B 247 " pdb=" C ARG B 247 " pdb=" CB ARG B 247 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1983 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 32 " -0.022 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C GLN F 32 " 0.082 2.00e-02 2.50e+03 pdb=" O GLN F 32 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY F 33 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 32 " 0.022 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C GLN C 32 " -0.081 2.00e-02 2.50e+03 pdb=" O GLN C 32 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY C 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN Z 32 " 0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C GLN Z 32 " -0.080 2.00e-02 2.50e+03 pdb=" O GLN Z 32 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY Z 33 " 0.028 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 108 2.61 - 3.18: 11096 3.18 - 3.75: 17588 3.75 - 4.33: 25714 4.33 - 4.90: 40797 Nonbonded interactions: 95303 Sorted by model distance: nonbonded pdb=" OE1 GLU Z 193 " pdb=" OH TYR Y 245 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLU C 193 " pdb=" OH TYR B 245 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLU F 193 " pdb=" OH TYR E 245 " model vdw 2.032 3.040 nonbonded pdb=" OH TYR Y 238 " pdb=" NE2 GLN B 240 " model vdw 2.126 3.120 nonbonded pdb=" NE2 GLN Y 240 " pdb=" OH TYR E 238 " model vdw 2.126 3.120 ... (remaining 95298 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: 0.03 Found NCS groups: ncs_group { reference = chain 'Z' selection = chain 'F' selection = chain 'C' } ncs_group { reference = chain 'Y' selection = chain 'E' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 11.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.009 0.345 12003 Z= 0.628 Angle : 0.975 15.892 16320 Z= 0.575 Chirality : 0.050 0.334 1986 Planarity : 0.007 0.061 2028 Dihedral : 15.198 102.886 4263 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 13.31 % Favored : 86.50 % Rotamer: Outliers : 0.90 % Allowed : 0.49 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -4.44 (0.18), residues: 1548 helix: -2.52 (0.14), residues: 1101 sheet: None (None), residues: 0 loop : -3.61 (0.24), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 54 TYR 0.011 0.001 TYR C 171 PHE 0.017 0.002 PHE B 222 TRP 0.019 0.002 TRP B 138 HIS 0.005 0.001 HIS Z 71 Details of bonding type rmsd covalent geometry : bond 0.00665 (12000) covalent geometry : angle 0.97525 (16320) hydrogen bonds : bond 0.24754 ( 582) hydrogen bonds : angle 9.37845 ( 1701) Misc. bond : bond 0.34433 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 272 time to evaluate : 0.410 Fit side-chains REVERT: Z 129 THR cc_start: 0.8711 (p) cc_final: 0.8485 (p) REVERT: Y 52 ILE cc_start: 0.8815 (mt) cc_final: 0.8593 (mt) REVERT: Y 149 MET cc_start: 0.7222 (mmt) cc_final: 0.6972 (tmm) REVERT: F 71 HIS cc_start: 0.6698 (m-70) cc_final: 0.6460 (m-70) REVERT: F 156 LEU cc_start: 0.9442 (mm) cc_final: 0.9195 (mt) REVERT: F 190 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7298 (mttt) REVERT: E 16 CYS cc_start: 0.7870 (t) cc_final: 0.7573 (t) REVERT: E 149 MET cc_start: 0.6964 (mmt) cc_final: 0.6698 (tmm) REVERT: E 234 MET cc_start: 0.7998 (mtp) cc_final: 0.7594 (mtm) REVERT: C 14 LYS cc_start: 0.7204 (mmmt) cc_final: 0.6976 (mmmt) REVERT: C 71 HIS cc_start: 0.7069 (m-70) cc_final: 0.6788 (m-70) REVERT: C 143 MET cc_start: 0.8604 (mmt) cc_final: 0.8360 (mmt) REVERT: C 159 LEU cc_start: 0.8801 (mt) cc_final: 0.8447 (mt) REVERT: C 190 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7238 (mttt) REVERT: B 180 ASN cc_start: 0.8669 (m-40) cc_final: 0.7931 (m-40) outliers start: 11 outliers final: 8 residues processed: 282 average time/residue: 0.0940 time to fit residues: 39.2233 Evaluate side-chains 222 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 214 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain Y residue 248 VAL Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 ASN ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 240 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN B 172 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114559 restraints weight = 16988.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117745 restraints weight = 9665.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119764 restraints weight = 6800.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120814 restraints weight = 5498.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121702 restraints weight = 4892.429| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12003 Z= 0.170 Angle : 0.771 10.330 16320 Z= 0.401 Chirality : 0.046 0.173 1986 Planarity : 0.006 0.059 2028 Dihedral : 8.789 57.791 1733 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.82 % Favored : 89.99 % Rotamer: Outliers : 2.53 % Allowed : 11.11 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -3.77 (0.18), residues: 1548 helix: -1.85 (0.14), residues: 1122 sheet: None (None), residues: 0 loop : -3.97 (0.22), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 247 TYR 0.013 0.001 TYR E 194 PHE 0.023 0.002 PHE C 25 TRP 0.010 0.001 TRP Z 35 HIS 0.005 0.002 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00378 (12000) covalent geometry : angle 0.77087 (16320) hydrogen bonds : bond 0.05180 ( 582) hydrogen bonds : angle 5.61704 ( 1701) Misc. bond : bond 0.00009 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 238 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: Y 52 ILE cc_start: 0.8827 (mt) cc_final: 0.8613 (mt) REVERT: Y 149 MET cc_start: 0.7333 (mmt) cc_final: 0.6806 (tmm) REVERT: Y 150 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7130 (tmm160) REVERT: Y 180 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: Y 184 ILE cc_start: 0.8658 (mt) cc_final: 0.8379 (mp) REVERT: F 156 LEU cc_start: 0.9212 (mm) cc_final: 0.8969 (mt) REVERT: F 190 LYS cc_start: 0.7889 (mtpt) cc_final: 0.6956 (mttt) REVERT: F 209 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7910 (ttmt) REVERT: E 51 ILE cc_start: 0.9067 (mt) cc_final: 0.8799 (mp) REVERT: E 149 MET cc_start: 0.7130 (mmt) cc_final: 0.6495 (tmm) REVERT: E 150 ARG cc_start: 0.7614 (mtt180) cc_final: 0.6888 (tmm160) REVERT: E 234 MET cc_start: 0.7947 (mtp) cc_final: 0.7598 (mtm) REVERT: C 143 MET cc_start: 0.8629 (mmt) cc_final: 0.8417 (mmt) REVERT: C 190 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7186 (mttt) REVERT: B 64 MET cc_start: 0.8443 (pmm) cc_final: 0.7585 (pmm) REVERT: B 180 ASN cc_start: 0.8544 (m-40) cc_final: 0.7565 (m-40) outliers start: 31 outliers final: 20 residues processed: 253 average time/residue: 0.0939 time to fit residues: 35.3532 Evaluate side-chains 226 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain Y residue 248 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 44 optimal weight: 0.0030 chunk 82 optimal weight: 0.0170 chunk 56 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 93 optimal weight: 0.0470 chunk 102 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.3126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 HIS Y 90 GLN F 71 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118888 restraints weight = 16875.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.122228 restraints weight = 9602.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124038 restraints weight = 6736.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125556 restraints weight = 5506.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126222 restraints weight = 4814.678| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12003 Z= 0.140 Angle : 0.688 10.373 16320 Z= 0.362 Chirality : 0.044 0.170 1986 Planarity : 0.006 0.054 2028 Dihedral : 6.233 49.498 1716 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.98 % Favored : 90.83 % Rotamer: Outliers : 2.78 % Allowed : 13.73 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % 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: -3.09 (0.19), residues: 1548 helix: -1.30 (0.15), residues: 1104 sheet: None (None), residues: 0 loop : -3.76 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Z 131 TYR 0.029 0.002 TYR C 57 PHE 0.021 0.002 PHE E 12 TRP 0.009 0.001 TRP F 210 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00303 (12000) covalent geometry : angle 0.68834 (16320) hydrogen bonds : bond 0.04226 ( 582) hydrogen bonds : angle 5.00915 ( 1701) Misc. bond : bond 0.00467 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.484 Fit side-chains REVERT: Z 156 LEU cc_start: 0.9114 (mm) cc_final: 0.8835 (mt) REVERT: Y 28 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8449 (mm110) REVERT: Y 52 ILE cc_start: 0.8780 (mt) cc_final: 0.8561 (mt) REVERT: Y 64 MET cc_start: 0.8323 (pmm) cc_final: 0.8030 (pmm) REVERT: Y 149 MET cc_start: 0.7535 (mmt) cc_final: 0.6875 (tmm) REVERT: Y 150 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7077 (tmm160) REVERT: Y 180 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7992 (m-40) REVERT: Y 184 ILE cc_start: 0.8595 (mt) cc_final: 0.8303 (mp) REVERT: F 156 LEU cc_start: 0.9168 (mm) cc_final: 0.8850 (mt) REVERT: F 190 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7061 (mttt) REVERT: F 209 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8152 (ttmt) REVERT: E 64 MET cc_start: 0.8593 (pmm) cc_final: 0.8274 (pmm) REVERT: E 149 MET cc_start: 0.7089 (mmt) cc_final: 0.6506 (tmm) REVERT: E 150 ARG cc_start: 0.7471 (mtt180) cc_final: 0.6782 (tmm160) REVERT: E 234 MET cc_start: 0.7873 (mtp) cc_final: 0.7551 (mtm) REVERT: C 74 PHE cc_start: 0.6918 (m-10) cc_final: 0.6642 (m-10) REVERT: C 143 MET cc_start: 0.8599 (mmt) cc_final: 0.8348 (mmt) REVERT: B 64 MET cc_start: 0.8458 (pmm) cc_final: 0.7844 (pmm) REVERT: B 180 ASN cc_start: 0.8404 (m-40) cc_final: 0.7814 (m-40) REVERT: B 221 ASN cc_start: 0.7876 (p0) cc_final: 0.7283 (p0) outliers start: 34 outliers final: 22 residues processed: 250 average time/residue: 0.0907 time to fit residues: 33.9140 Evaluate side-chains 225 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117944 restraints weight = 16824.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121177 restraints weight = 9732.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123250 restraints weight = 6896.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124348 restraints weight = 5585.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125260 restraints weight = 4963.751| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12003 Z= 0.145 Angle : 0.677 10.761 16320 Z= 0.354 Chirality : 0.044 0.170 1986 Planarity : 0.005 0.054 2028 Dihedral : 6.011 42.395 1715 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.59 % Favored : 91.21 % Rotamer: Outliers : 3.27 % Allowed : 14.54 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.20), residues: 1548 helix: -1.13 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -3.69 (0.23), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 54 TYR 0.011 0.001 TYR C 57 PHE 0.021 0.001 PHE E 12 TRP 0.010 0.001 TRP F 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00336 (12000) covalent geometry : angle 0.67714 (16320) hydrogen bonds : bond 0.04023 ( 582) hydrogen bonds : angle 4.84674 ( 1701) Misc. bond : bond 0.00355 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9067 (mm) cc_final: 0.8775 (mt) REVERT: Y 28 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8479 (mm110) REVERT: Y 149 MET cc_start: 0.7545 (mmt) cc_final: 0.6921 (tmm) REVERT: Y 150 ARG cc_start: 0.7435 (mtt180) cc_final: 0.7206 (tmm160) REVERT: Y 180 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: Y 184 ILE cc_start: 0.8590 (mt) cc_final: 0.8271 (mp) REVERT: F 156 LEU cc_start: 0.9149 (mm) cc_final: 0.8848 (mt) REVERT: F 190 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7067 (mttt) REVERT: E 149 MET cc_start: 0.7186 (mmt) cc_final: 0.6606 (tmm) REVERT: E 150 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6812 (tmm160) REVERT: E 172 ASN cc_start: 0.7824 (m110) cc_final: 0.7514 (p0) REVERT: E 234 MET cc_start: 0.7856 (mtp) cc_final: 0.7534 (mtm) REVERT: C 190 LYS cc_start: 0.7831 (mtpt) cc_final: 0.7085 (mttt) REVERT: B 64 MET cc_start: 0.8505 (pmm) cc_final: 0.7937 (pmm) REVERT: B 168 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7056 (mm-40) outliers start: 40 outliers final: 31 residues processed: 241 average time/residue: 0.0958 time to fit residues: 34.0099 Evaluate side-chains 230 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 135 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 137 optimal weight: 0.0030 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.142725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116335 restraints weight = 16956.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119467 restraints weight = 9893.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121433 restraints weight = 7078.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122730 restraints weight = 5801.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123341 restraints weight = 5123.510| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 12003 Z= 0.173 Angle : 0.688 10.196 16320 Z= 0.362 Chirality : 0.045 0.170 1986 Planarity : 0.005 0.056 2028 Dihedral : 5.927 38.823 1715 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.63 % Favored : 90.18 % Rotamer: Outliers : 4.41 % Allowed : 15.60 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.20), residues: 1548 helix: -1.06 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -3.65 (0.24), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 247 TYR 0.010 0.001 TYR E 194 PHE 0.029 0.002 PHE B 219 TRP 0.012 0.001 TRP F 210 HIS 0.004 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00418 (12000) covalent geometry : angle 0.68777 (16320) hydrogen bonds : bond 0.04054 ( 582) hydrogen bonds : angle 4.78832 ( 1701) Misc. bond : bond 0.00703 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9093 (mm) cc_final: 0.8807 (mt) REVERT: Y 149 MET cc_start: 0.7562 (mmt) cc_final: 0.7030 (tmm) REVERT: Y 150 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7258 (tmm160) REVERT: F 190 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7206 (mttt) REVERT: F 266 TRP cc_start: 0.7893 (m100) cc_final: 0.7362 (m-10) REVERT: E 149 MET cc_start: 0.7137 (mmt) cc_final: 0.6663 (tmm) REVERT: E 150 ARG cc_start: 0.7616 (mtt180) cc_final: 0.6969 (tmm160) REVERT: E 234 MET cc_start: 0.7903 (mtp) cc_final: 0.7582 (mtm) REVERT: C 190 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7176 (mttt) REVERT: B 64 MET cc_start: 0.8552 (pmm) cc_final: 0.8084 (pmm) outliers start: 54 outliers final: 41 residues processed: 235 average time/residue: 0.0910 time to fit residues: 31.9622 Evaluate side-chains 238 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 196 MET Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.0980 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118202 restraints weight = 16746.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121398 restraints weight = 9758.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123424 restraints weight = 6924.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124493 restraints weight = 5644.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125429 restraints weight = 5025.615| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12003 Z= 0.141 Angle : 0.659 10.299 16320 Z= 0.346 Chirality : 0.043 0.168 1986 Planarity : 0.005 0.055 2028 Dihedral : 5.779 39.059 1715 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.59 % Favored : 91.21 % Rotamer: Outliers : 4.82 % Allowed : 15.36 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.21), residues: 1548 helix: -0.85 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -3.49 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.031 0.001 TYR C 57 PHE 0.023 0.001 PHE B 12 TRP 0.011 0.001 TRP C 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00330 (12000) covalent geometry : angle 0.65899 (16320) hydrogen bonds : bond 0.03787 ( 582) hydrogen bonds : angle 4.68414 ( 1701) Misc. bond : bond 0.00367 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8266 (m-80) cc_final: 0.7765 (m-10) REVERT: Z 156 LEU cc_start: 0.9070 (mm) cc_final: 0.8784 (mt) REVERT: Y 149 MET cc_start: 0.7509 (mmt) cc_final: 0.6999 (tmm) REVERT: Y 150 ARG cc_start: 0.7431 (mtt180) cc_final: 0.7079 (tmm160) REVERT: F 190 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7201 (mttt) REVERT: E 149 MET cc_start: 0.7103 (mmt) cc_final: 0.6627 (tmm) REVERT: E 150 ARG cc_start: 0.7477 (mtt180) cc_final: 0.6752 (tmm160) REVERT: E 234 MET cc_start: 0.7854 (mtp) cc_final: 0.7570 (mtm) REVERT: C 190 LYS cc_start: 0.7835 (mtpt) cc_final: 0.7125 (mttt) REVERT: B 20 MET cc_start: 0.7749 (mmm) cc_final: 0.7503 (mmt) REVERT: B 98 LEU cc_start: 0.9338 (tt) cc_final: 0.9127 (tt) REVERT: B 184 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8200 (mp) outliers start: 59 outliers final: 46 residues processed: 249 average time/residue: 0.0933 time to fit residues: 35.1576 Evaluate side-chains 244 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 84 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 86 optimal weight: 0.1980 chunk 120 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119524 restraints weight = 16682.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122739 restraints weight = 9701.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124521 restraints weight = 6923.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126006 restraints weight = 5718.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126489 restraints weight = 5033.984| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12003 Z= 0.135 Angle : 0.640 10.325 16320 Z= 0.337 Chirality : 0.043 0.159 1986 Planarity : 0.005 0.053 2028 Dihedral : 5.584 38.620 1715 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.25 % Allowed : 16.50 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.21), residues: 1548 helix: -0.69 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Z 221 TYR 0.025 0.001 TYR C 57 PHE 0.025 0.001 PHE E 12 TRP 0.011 0.001 TRP C 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00317 (12000) covalent geometry : angle 0.63981 (16320) hydrogen bonds : bond 0.03585 ( 582) hydrogen bonds : angle 4.59212 ( 1701) Misc. bond : bond 0.00279 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 217 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8279 (m-80) cc_final: 0.7625 (m-10) REVERT: Z 156 LEU cc_start: 0.9054 (mm) cc_final: 0.8771 (mt) REVERT: Z 177 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7331 (tp) REVERT: Y 149 MET cc_start: 0.7448 (mmt) cc_final: 0.6941 (tmm) REVERT: Y 150 ARG cc_start: 0.7326 (mtt180) cc_final: 0.7039 (tmm160) REVERT: Y 180 ASN cc_start: 0.8172 (m-40) cc_final: 0.7306 (m-40) REVERT: F 190 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7213 (mttt) REVERT: E 28 GLN cc_start: 0.8741 (mm110) cc_final: 0.8296 (mm110) REVERT: E 150 ARG cc_start: 0.7346 (mtt180) cc_final: 0.6679 (tmm160) REVERT: E 234 MET cc_start: 0.7839 (mtp) cc_final: 0.7597 (mtm) REVERT: C 190 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7127 (mttt) REVERT: B 20 MET cc_start: 0.7575 (mmm) cc_final: 0.7063 (mmt) REVERT: B 24 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7629 (mm) REVERT: B 116 ILE cc_start: 0.8619 (tp) cc_final: 0.8403 (tp) REVERT: B 166 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7244 (tp30) REVERT: B 184 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8164 (mp) outliers start: 52 outliers final: 37 residues processed: 252 average time/residue: 0.0931 time to fit residues: 34.8134 Evaluate side-chains 246 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 120 optimal weight: 0.0270 chunk 50 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 4 optimal weight: 0.0870 chunk 110 optimal weight: 0.0770 chunk 90 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.148314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.122021 restraints weight = 16500.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125351 restraints weight = 9579.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127444 restraints weight = 6791.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.128784 restraints weight = 5520.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.129420 restraints weight = 4852.503| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12003 Z= 0.126 Angle : 0.640 10.494 16320 Z= 0.336 Chirality : 0.042 0.165 1986 Planarity : 0.005 0.051 2028 Dihedral : 5.398 37.813 1714 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.59 % Allowed : 17.08 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -1.94 (0.21), residues: 1548 helix: -0.47 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 221 TYR 0.017 0.001 TYR C 57 PHE 0.024 0.001 PHE B 12 TRP 0.012 0.001 TRP C 127 HIS 0.005 0.001 HIS Y 140 Details of bonding type rmsd covalent geometry : bond 0.00288 (12000) covalent geometry : angle 0.64036 (16320) hydrogen bonds : bond 0.03384 ( 582) hydrogen bonds : angle 4.53924 ( 1701) Misc. bond : bond 0.00218 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8125 (m-80) cc_final: 0.7445 (m-10) REVERT: Z 86 LEU cc_start: 0.7353 (mt) cc_final: 0.7117 (mt) REVERT: Z 156 LEU cc_start: 0.9034 (mm) cc_final: 0.8759 (mt) REVERT: Y 149 MET cc_start: 0.7507 (mmt) cc_final: 0.6742 (tmm) REVERT: Y 150 ARG cc_start: 0.7064 (mtt180) cc_final: 0.6625 (tmm160) REVERT: Y 180 ASN cc_start: 0.8257 (m-40) cc_final: 0.7441 (m-40) REVERT: F 57 TYR cc_start: 0.7752 (m-10) cc_final: 0.7430 (m-10) REVERT: F 143 MET cc_start: 0.8528 (mmt) cc_final: 0.8226 (mmm) REVERT: F 190 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7150 (mttt) REVERT: E 116 ILE cc_start: 0.8567 (tp) cc_final: 0.8240 (tp) REVERT: E 150 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6533 (tmm160) REVERT: E 234 MET cc_start: 0.7816 (mtp) cc_final: 0.7569 (mtm) REVERT: B 24 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7741 (mm) REVERT: B 116 ILE cc_start: 0.8622 (tp) cc_final: 0.8318 (tp) REVERT: B 166 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7243 (tp30) REVERT: B 184 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8098 (mp) outliers start: 44 outliers final: 30 residues processed: 254 average time/residue: 0.0931 time to fit residues: 35.7841 Evaluate side-chains 243 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 56 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 GLN ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.146813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120347 restraints weight = 16449.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123559 restraints weight = 9709.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125615 restraints weight = 6980.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.126694 restraints weight = 5696.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127637 restraints weight = 5079.642| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12003 Z= 0.138 Angle : 0.647 10.493 16320 Z= 0.342 Chirality : 0.043 0.147 1986 Planarity : 0.005 0.052 2028 Dihedral : 5.321 38.327 1714 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 3.59 % Allowed : 17.73 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.79 (0.21), residues: 1548 helix: -0.36 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -3.35 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 221 TYR 0.012 0.001 TYR C 57 PHE 0.024 0.001 PHE C 25 TRP 0.010 0.001 TRP C 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00332 (12000) covalent geometry : angle 0.64713 (16320) hydrogen bonds : bond 0.03526 ( 582) hydrogen bonds : angle 4.53652 ( 1701) Misc. bond : bond 0.00218 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8164 (m-80) cc_final: 0.7498 (m-10) REVERT: Z 86 LEU cc_start: 0.7431 (mt) cc_final: 0.7157 (mt) REVERT: Y 149 MET cc_start: 0.7486 (mmt) cc_final: 0.6683 (tmm) REVERT: Y 150 ARG cc_start: 0.7073 (mtt180) cc_final: 0.6611 (tmm160) REVERT: Y 180 ASN cc_start: 0.8247 (m-40) cc_final: 0.7415 (m-40) REVERT: F 143 MET cc_start: 0.8505 (mmt) cc_final: 0.8197 (mmm) REVERT: F 156 LEU cc_start: 0.8740 (mm) cc_final: 0.8354 (mt) REVERT: F 190 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7153 (mttt) REVERT: E 116 ILE cc_start: 0.8589 (tp) cc_final: 0.8253 (tp) REVERT: E 149 MET cc_start: 0.7022 (mmt) cc_final: 0.6642 (mmt) REVERT: E 150 ARG cc_start: 0.7516 (mtt180) cc_final: 0.6372 (tmm160) REVERT: E 234 MET cc_start: 0.7845 (mtp) cc_final: 0.7591 (mtm) REVERT: C 235 GLN cc_start: 0.8574 (tp40) cc_final: 0.8109 (tp40) REVERT: B 24 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7647 (mm) REVERT: B 116 ILE cc_start: 0.8673 (tp) cc_final: 0.8344 (tp) REVERT: B 166 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: B 184 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8099 (mp) outliers start: 44 outliers final: 36 residues processed: 243 average time/residue: 0.0882 time to fit residues: 32.5540 Evaluate side-chains 239 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 0.0970 chunk 41 optimal weight: 0.0470 chunk 113 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.148068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.121727 restraints weight = 16514.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.124926 restraints weight = 9624.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127122 restraints weight = 6866.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.128262 restraints weight = 5556.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128972 restraints weight = 4923.350| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12003 Z= 0.133 Angle : 0.677 14.772 16320 Z= 0.349 Chirality : 0.043 0.143 1986 Planarity : 0.005 0.051 2028 Dihedral : 5.284 37.797 1714 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.51 % Allowed : 17.81 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.64 (0.21), residues: 1548 helix: -0.24 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -3.42 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 221 TYR 0.009 0.001 TYR F 57 PHE 0.024 0.001 PHE B 12 TRP 0.010 0.001 TRP E 138 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00314 (12000) covalent geometry : angle 0.67716 (16320) hydrogen bonds : bond 0.03454 ( 582) hydrogen bonds : angle 4.53716 ( 1701) Misc. bond : bond 0.00205 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 86 LEU cc_start: 0.7357 (mt) cc_final: 0.7133 (mt) REVERT: Y 116 ILE cc_start: 0.8509 (tp) cc_final: 0.8239 (tp) REVERT: Y 149 MET cc_start: 0.7352 (mmt) cc_final: 0.6603 (tmm) REVERT: Y 150 ARG cc_start: 0.7260 (mtt180) cc_final: 0.6418 (tmm160) REVERT: Y 180 ASN cc_start: 0.8188 (m-40) cc_final: 0.7443 (m-40) REVERT: F 143 MET cc_start: 0.8499 (mmt) cc_final: 0.8257 (mmm) REVERT: F 156 LEU cc_start: 0.8712 (mm) cc_final: 0.8340 (mt) REVERT: F 190 LYS cc_start: 0.7961 (mtpt) cc_final: 0.7184 (mttt) REVERT: F 198 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8296 (tp) REVERT: E 116 ILE cc_start: 0.8540 (tp) cc_final: 0.8254 (tp) REVERT: E 149 MET cc_start: 0.6980 (mmt) cc_final: 0.6604 (mmt) REVERT: E 234 MET cc_start: 0.7833 (mtp) cc_final: 0.7564 (mtm) REVERT: C 66 GLN cc_start: 0.6108 (tt0) cc_final: 0.5780 (tp40) REVERT: B 28 GLN cc_start: 0.8644 (mm-40) cc_final: 0.8416 (mm-40) REVERT: B 116 ILE cc_start: 0.8619 (tp) cc_final: 0.8306 (tp) REVERT: B 166 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7157 (tp30) REVERT: B 184 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8092 (mp) outliers start: 43 outliers final: 35 residues processed: 238 average time/residue: 0.0894 time to fit residues: 32.1044 Evaluate side-chains 240 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 191 VAL Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 74 PHE Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.121469 restraints weight = 16586.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124701 restraints weight = 9670.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126811 restraints weight = 6888.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.128140 restraints weight = 5588.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128540 restraints weight = 4909.226| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12003 Z= 0.136 Angle : 0.674 14.470 16320 Z= 0.348 Chirality : 0.043 0.141 1986 Planarity : 0.005 0.051 2028 Dihedral : 5.241 37.738 1714 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.27 % Allowed : 18.46 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.52 (0.22), residues: 1548 helix: -0.14 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -3.42 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 221 TYR 0.011 0.001 TYR Z 57 PHE 0.024 0.001 PHE E 12 TRP 0.010 0.001 TRP Z 127 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00322 (12000) covalent geometry : angle 0.67367 (16320) hydrogen bonds : bond 0.03505 ( 582) hydrogen bonds : angle 4.49055 ( 1701) Misc. bond : bond 0.00203 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1884.31 seconds wall clock time: 33 minutes 22.76 seconds (2002.76 seconds total)