Starting phenix.real_space_refine on Fri Sep 11 21:15:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k1h_9906/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.cif" model { file = "/net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k1h_9906/09_2026/6k1h_9906.map" } 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-2.2.1-6174/lib/python3.11/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: 2.90, per 1000 atoms: 0.25 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: 0.77 Conformation dependent library (CDL) restraints added in 720.8 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: 0.32 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: 1.10 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 - 14.86: 6230 14.86 - 29.71: 550 29.71 - 44.57: 175 44.57 - 59.43: 23 59.43 - 74.28: 9 Dihedral angle restraints: 6987 sinusoidal: 2610 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 6984 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 13.182 74.282 4197 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/Z covalent geometry : bond 0.00665 / 0.31 (12000) covalent geometry : angle 0.97525 / 0.57 (16320) hydrogen bonds : bond 0.24754 / 15.83 ( 582) hydrogen bonds : angle 9.37845 / 6.64 ( 1701) Misc. bond : bond 0.34433 / 17.26 ( 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 : 0.377 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: 0.0834 time to fit residues: 35.1596 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 : 0.352 ------------------------------------------------------------------------------- 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... Z 32 GLN ** 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 ** 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 32 GLN C 71 HIS ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.141147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.115288 restraints weight = 16956.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118410 restraints weight = 9637.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120456 restraints weight = 6787.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.121560 restraints weight = 5465.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122433 restraints weight = 4846.186| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12003 Z= 0.168 Angle : 0.763 10.377 16320 Z= 0.399 Chirality : 0.046 0.171 1986 Planarity : 0.006 0.058 2028 Dihedral : 7.314 57.919 1667 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.50 % Favored : 90.31 % Rotamer: Outliers : 2.04 % Allowed : 11.85 % Favored : 86.11 % 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: -3.81 (0.18), residues: 1548 helix: -1.85 (0.14), residues: 1125 sheet: None (None), residues: 0 loop : -4.06 (0.21), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 150 TYR 0.014 0.002 TYR E 194 PHE 0.022 0.002 PHE C 25 TRP 0.010 0.001 TRP Z 35 HIS 0.005 0.002 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (12000) covalent geometry : angle 0.76347 / 0.40 (16320) hydrogen bonds : bond 0.04926 / 3.23 ( 582) hydrogen bonds : angle 5.57513 / 3.95 ( 1701) Misc. bond : bond 0.00061 / 0.03 ( 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 270 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9136 (mm) cc_final: 0.8920 (mt) REVERT: Y 52 ILE cc_start: 0.8820 (mt) cc_final: 0.8617 (mt) REVERT: Y 149 MET cc_start: 0.7343 (mmt) cc_final: 0.6792 (tmm) REVERT: Y 150 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7114 (tmm160) REVERT: Y 184 ILE cc_start: 0.8642 (mt) cc_final: 0.8355 (mp) REVERT: F 156 LEU cc_start: 0.9213 (mm) cc_final: 0.8967 (mt) REVERT: F 190 LYS cc_start: 0.7869 (mtpt) cc_final: 0.6913 (mttt) REVERT: F 209 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7901 (ttmt) REVERT: E 51 ILE cc_start: 0.9044 (mt) cc_final: 0.8770 (mp) REVERT: E 64 MET cc_start: 0.8543 (pmm) cc_final: 0.8120 (pmm) REVERT: E 149 MET cc_start: 0.7136 (mmt) cc_final: 0.6476 (tmm) REVERT: E 150 ARG cc_start: 0.7610 (mtt180) cc_final: 0.6868 (tmm160) REVERT: E 234 MET cc_start: 0.7948 (mtp) cc_final: 0.7585 (mtm) REVERT: C 143 MET cc_start: 0.8633 (mmt) cc_final: 0.8419 (mmt) REVERT: C 190 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7157 (mttt) REVERT: B 64 MET cc_start: 0.8458 (pmm) cc_final: 0.7631 (pmm) REVERT: B 180 ASN cc_start: 0.8523 (m-40) cc_final: 0.7563 (m-40) outliers start: 25 outliers final: 20 residues processed: 255 average time/residue: 0.0848 time to fit residues: 32.1293 Evaluate side-chains 222 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 247 ARG 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 247 ARG 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: 0.8980 chunk 82 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 105 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Z 71 HIS ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN B 90 GLN ** 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 = 0.3665 r_free = 0.3665 target = 0.141474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115469 restraints weight = 17023.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118653 restraints weight = 9752.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120456 restraints weight = 6877.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.121932 restraints weight = 5618.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122585 restraints weight = 4914.271| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12003 Z= 0.157 Angle : 0.711 10.296 16320 Z= 0.370 Chirality : 0.045 0.170 1986 Planarity : 0.006 0.056 2028 Dihedral : 6.451 47.303 1653 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.43 % Favored : 90.37 % Rotamer: Outliers : 3.10 % Allowed : 13.97 % Favored : 82.92 % 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: -3.20 (0.19), residues: 1548 helix: -1.40 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -3.81 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 150 TYR 0.029 0.002 TYR C 57 PHE 0.022 0.002 PHE E 12 TRP 0.010 0.001 TRP Z 210 HIS 0.004 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (12000) covalent geometry : angle 0.71068 / 0.37 (16320) hydrogen bonds : bond 0.04436 / 2.93 ( 582) hydrogen bonds : angle 5.02208 / 3.56 ( 1701) Misc. bond : bond 0.00119 / 0.06 ( 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 255 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: Z 156 LEU cc_start: 0.9121 (mm) cc_final: 0.8845 (mt) REVERT: Y 28 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8438 (mm110) REVERT: Y 149 MET cc_start: 0.7513 (mmt) cc_final: 0.7050 (tmm) REVERT: Y 150 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7256 (tmm160) REVERT: Y 184 ILE cc_start: 0.8611 (mt) cc_final: 0.8308 (mp) REVERT: F 156 LEU cc_start: 0.9172 (mm) cc_final: 0.8853 (mt) REVERT: F 190 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7095 (mttt) REVERT: F 209 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8043 (ttmt) REVERT: E 149 MET cc_start: 0.7198 (mmt) cc_final: 0.6723 (tmm) REVERT: E 150 ARG cc_start: 0.7554 (mtt180) cc_final: 0.6822 (tmm160) REVERT: E 234 MET cc_start: 0.7893 (mtp) cc_final: 0.7555 (mtm) REVERT: C 143 MET cc_start: 0.8639 (mmt) cc_final: 0.8368 (mmt) REVERT: C 190 LYS cc_start: 0.8108 (mtpt) cc_final: 0.7185 (mttt) REVERT: B 64 MET cc_start: 0.8556 (pmm) cc_final: 0.8007 (pmm) REVERT: B 180 ASN cc_start: 0.8408 (m-40) cc_final: 0.7776 (m-40) REVERT: B 221 ASN cc_start: 0.7927 (p0) cc_final: 0.7381 (p0) outliers start: 38 outliers final: 29 residues processed: 239 average time/residue: 0.0924 time to fit residues: 32.7129 Evaluate side-chains 229 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 157 ILE Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 43 LEU 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 E residue 201 MET 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 139 ILE Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG 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: 1.9990 chunk 37 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 85 optimal weight: 0.0270 chunk 43 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** 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 = 0.3709 r_free = 0.3709 target = 0.145455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119205 restraints weight = 16701.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122467 restraints weight = 9622.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124565 restraints weight = 6794.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125843 restraints weight = 5490.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126203 restraints weight = 4820.283| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12003 Z= 0.133 Angle : 0.672 10.463 16320 Z= 0.348 Chirality : 0.044 0.177 1986 Planarity : 0.005 0.054 2028 Dihedral : 6.128 38.360 1653 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.40 % Favored : 91.41 % Rotamer: Outliers : 3.43 % Allowed : 14.95 % Favored : 81.62 % 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: -2.72 (0.20), residues: 1548 helix: -1.04 (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 0.005 0.001 ARG B 150 TYR 0.013 0.001 TYR F 57 PHE 0.022 0.001 PHE E 12 TRP 0.011 0.001 TRP F 127 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (12000) covalent geometry : angle 0.67185 / 0.35 (16320) hydrogen bonds : bond 0.03812 / 2.53 ( 582) hydrogen bonds : angle 4.74614 / 3.36 ( 1701) Misc. bond : bond 0.00194 / 0.09 ( 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 265 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.403 Fit side-chains REVERT: Z 86 LEU cc_start: 0.7541 (mt) cc_final: 0.7261 (mt) REVERT: Z 156 LEU cc_start: 0.9057 (mm) cc_final: 0.8763 (mt) REVERT: Y 149 MET cc_start: 0.7529 (mmt) cc_final: 0.6881 (tmm) REVERT: Y 184 ILE cc_start: 0.8561 (mt) cc_final: 0.8217 (mp) REVERT: F 190 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7132 (mttt) REVERT: E 149 MET cc_start: 0.7182 (mmt) cc_final: 0.6598 (tmm) REVERT: E 150 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6700 (tmm160) REVERT: E 172 ASN cc_start: 0.7847 (m110) cc_final: 0.7569 (p0) REVERT: E 234 MET cc_start: 0.7851 (mtp) cc_final: 0.7562 (mtm) REVERT: B 64 MET cc_start: 0.8502 (pmm) cc_final: 0.8081 (pmm) REVERT: B 168 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7056 (mm-40) REVERT: B 180 ASN cc_start: 0.8385 (m-40) cc_final: 0.7833 (m-40) outliers start: 42 outliers final: 28 residues processed: 249 average time/residue: 0.0930 time to fit residues: 34.4119 Evaluate side-chains 224 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 129 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 141 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 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 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 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 189 ILE Chi-restraints excluded: chain B residue 247 ARG 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: 5.9990 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 90 GLN ** F 78 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.144255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117912 restraints weight = 16920.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121124 restraints weight = 9759.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123166 restraints weight = 6940.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124259 restraints weight = 5648.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125068 restraints weight = 5040.319| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12003 Z= 0.152 Angle : 0.682 10.252 16320 Z= 0.357 Chirality : 0.044 0.166 1986 Planarity : 0.005 0.053 2028 Dihedral : 5.917 38.386 1653 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.57 % Rotamer: Outliers : 4.25 % Allowed : 16.09 % Favored : 79.66 % 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: -2.55 (0.20), residues: 1548 helix: -0.89 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -3.64 (0.22), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 150 TYR 0.027 0.001 TYR C 57 PHE 0.022 0.002 PHE E 12 TRP 0.010 0.001 TRP F 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (12000) covalent geometry : angle 0.68202 / 0.36 (16320) hydrogen bonds : bond 0.03873 / 2.58 ( 582) hydrogen bonds : angle 4.70851 / 3.35 ( 1701) Misc. bond : bond 0.00505 / 0.26 ( 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 263 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 211 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8207 (m-80) cc_final: 0.7682 (m-10) REVERT: Z 156 LEU cc_start: 0.9082 (mm) cc_final: 0.8799 (mt) REVERT: Y 149 MET cc_start: 0.7610 (mmt) cc_final: 0.6961 (tmm) REVERT: Y 180 ASN cc_start: 0.8208 (m-40) cc_final: 0.7811 (m-40) REVERT: F 190 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7175 (mttt) REVERT: F 209 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8141 (ttmt) REVERT: E 149 MET cc_start: 0.7111 (mmt) cc_final: 0.6635 (tmm) REVERT: E 150 ARG cc_start: 0.7491 (mtt180) cc_final: 0.6811 (tmm160) REVERT: E 234 MET cc_start: 0.7863 (mtp) cc_final: 0.7585 (mtm) REVERT: C 190 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7095 (mttt) REVERT: B 184 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8217 (mp) outliers start: 52 outliers final: 39 residues processed: 242 average time/residue: 0.0884 time to fit residues: 32.4022 Evaluate side-chains 242 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 141 VAL 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 177 ILE 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 159 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 184 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 247 ARG 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: 0.8980 chunk 85 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 17 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** 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 = 0.3701 r_free = 0.3701 target = 0.144801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118575 restraints weight = 16797.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.121769 restraints weight = 9783.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123551 restraints weight = 6934.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.124999 restraints weight = 5715.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125649 restraints weight = 5024.132| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12003 Z= 0.144 Angle : 0.673 11.744 16320 Z= 0.348 Chirality : 0.043 0.164 1986 Planarity : 0.005 0.053 2028 Dihedral : 5.792 38.117 1653 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.04 % Favored : 90.89 % Rotamer: Outliers : 4.98 % Allowed : 16.09 % Favored : 78.92 % 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: -2.26 (0.21), residues: 1548 helix: -0.70 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -3.43 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 150 TYR 0.015 0.001 TYR C 57 PHE 0.023 0.001 PHE E 12 TRP 0.009 0.001 TRP F 210 HIS 0.006 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (12000) covalent geometry : angle 0.67325 / 0.35 (16320) hydrogen bonds : bond 0.03713 / 2.49 ( 582) hydrogen bonds : angle 4.67443 / 3.33 ( 1701) Misc. bond : bond 0.00411 / 0.21 ( 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 275 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 214 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8318 (m-80) cc_final: 0.7659 (m-10) REVERT: Z 86 LEU cc_start: 0.7626 (mt) cc_final: 0.7342 (mt) REVERT: Z 156 LEU cc_start: 0.9071 (mm) cc_final: 0.8787 (mt) REVERT: Y 149 MET cc_start: 0.7601 (mmt) cc_final: 0.6966 (tmm) REVERT: Y 180 ASN cc_start: 0.8193 (m-40) cc_final: 0.7289 (m-40) REVERT: F 190 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7165 (mttt) REVERT: E 28 GLN cc_start: 0.8706 (mm110) cc_final: 0.8285 (mm110) REVERT: E 149 MET cc_start: 0.7110 (mmt) cc_final: 0.6618 (tmm) REVERT: E 150 ARG cc_start: 0.7405 (mtt180) cc_final: 0.6692 (tmm160) REVERT: E 234 MET cc_start: 0.7850 (mtp) cc_final: 0.7569 (mtm) REVERT: C 190 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7114 (mttt) REVERT: B 20 MET cc_start: 0.7778 (mmm) cc_final: 0.7529 (mmt) REVERT: B 116 ILE cc_start: 0.8593 (tp) cc_final: 0.8381 (tp) REVERT: B 184 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8207 (mp) outliers start: 61 outliers final: 46 residues processed: 254 average time/residue: 0.0854 time to fit residues: 33.1969 Evaluate side-chains 252 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 81 SER Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 143 SER 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 8 ILE Chi-restraints excluded: chain E residue 23 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 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 B residue 8 ILE 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 184 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 247 ARG 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: 3.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 148 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 120 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 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 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 = 0.3719 r_free = 0.3719 target = 0.146181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119915 restraints weight = 16698.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123160 restraints weight = 9681.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125072 restraints weight = 6902.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126444 restraints weight = 5656.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126956 restraints weight = 4989.250| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 12003 Z= 0.139 Angle : 0.658 11.208 16320 Z= 0.341 Chirality : 0.043 0.159 1986 Planarity : 0.005 0.052 2028 Dihedral : 5.650 37.985 1653 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.41 % Allowed : 16.75 % Favored : 78.84 % 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: -2.10 (0.21), residues: 1548 helix: -0.58 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -3.40 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.011 0.001 TYR C 57 PHE 0.023 0.001 PHE E 12 TRP 0.010 0.001 TRP Z 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (12000) covalent geometry : angle 0.65780 / 0.34 (16320) hydrogen bonds : bond 0.03668 / 2.49 ( 582) hydrogen bonds : angle 4.58922 / 3.27 ( 1701) Misc. bond : bond 0.00292 / 0.15 ( 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 268 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8288 (m-80) cc_final: 0.7579 (m-10) REVERT: Z 86 LEU cc_start: 0.7586 (mt) cc_final: 0.7319 (mt) REVERT: Z 156 LEU cc_start: 0.9090 (mm) cc_final: 0.8807 (mt) REVERT: Y 149 MET cc_start: 0.7570 (mmt) cc_final: 0.6930 (tmm) REVERT: Y 180 ASN cc_start: 0.8171 (m-40) cc_final: 0.6920 (m-40) REVERT: Y 184 ILE cc_start: 0.8497 (mt) cc_final: 0.8138 (mp) REVERT: F 190 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7127 (mttt) REVERT: F 198 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8186 (tp) REVERT: E 28 GLN cc_start: 0.8739 (mm110) cc_final: 0.8385 (mm110) REVERT: E 113 VAL cc_start: 0.8465 (t) cc_final: 0.8263 (t) REVERT: E 150 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6637 (tmm160) REVERT: E 234 MET cc_start: 0.7858 (mtp) cc_final: 0.7537 (mtm) REVERT: B 20 MET cc_start: 0.7608 (mmm) cc_final: 0.7084 (mmt) REVERT: B 24 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7637 (mm) REVERT: B 116 ILE cc_start: 0.8663 (tp) cc_final: 0.8431 (tp) REVERT: B 166 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: B 184 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8123 (mp) outliers start: 54 outliers final: 41 residues processed: 249 average time/residue: 0.0861 time to fit residues: 32.2277 Evaluate side-chains 248 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 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 23 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 143 SER 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 198 LEU Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 237 ILE 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 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 159 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR 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 Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 120 optimal weight: 0.0040 chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 0.0170 chunk 110 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.4230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN C 32 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121945 restraints weight = 16537.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.125186 restraints weight = 9588.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126995 restraints weight = 6836.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.128485 restraints weight = 5627.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128938 restraints weight = 4940.440| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12003 Z= 0.130 Angle : 0.661 12.966 16320 Z= 0.341 Chirality : 0.042 0.167 1986 Planarity : 0.005 0.051 2028 Dihedral : 5.508 37.613 1652 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.25 % Allowed : 17.24 % Favored : 78.51 % 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: -1.88 (0.21), residues: 1548 helix: -0.39 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -3.39 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 202 TYR 0.038 0.001 TYR F 57 PHE 0.024 0.001 PHE E 12 TRP 0.015 0.001 TRP Z 210 HIS 0.006 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (12000) covalent geometry : angle 0.66144 / 0.34 (16320) hydrogen bonds : bond 0.03508 / 2.34 ( 582) hydrogen bonds : angle 4.52961 / 3.21 ( 1701) Misc. bond : bond 0.00239 / 0.12 ( 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 277 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8174 (m-80) cc_final: 0.7477 (m-10) REVERT: Z 86 LEU cc_start: 0.7531 (mt) cc_final: 0.7318 (mt) REVERT: Z 156 LEU cc_start: 0.9074 (mm) cc_final: 0.8802 (mt) REVERT: Z 177 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7240 (tp) REVERT: Y 149 MET cc_start: 0.7506 (mmt) cc_final: 0.7018 (tmm) REVERT: Y 180 ASN cc_start: 0.8284 (m-40) cc_final: 0.7487 (m-40) REVERT: F 143 MET cc_start: 0.8606 (mmt) cc_final: 0.8303 (mmm) REVERT: F 156 LEU cc_start: 0.8733 (mm) cc_final: 0.8341 (mt) REVERT: F 190 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7155 (mttt) REVERT: F 198 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8234 (tp) REVERT: E 28 GLN cc_start: 0.8726 (mm110) cc_final: 0.8439 (mm110) REVERT: E 113 VAL cc_start: 0.8463 (t) cc_final: 0.8199 (t) REVERT: E 116 ILE cc_start: 0.8570 (tp) cc_final: 0.8223 (tp) REVERT: E 150 ARG cc_start: 0.7253 (mtt180) cc_final: 0.6519 (tmm160) REVERT: E 234 MET cc_start: 0.7850 (mtp) cc_final: 0.7555 (mtm) REVERT: C 66 GLN cc_start: 0.6190 (tt0) cc_final: 0.5839 (tp40) REVERT: B 116 ILE cc_start: 0.8666 (tp) cc_final: 0.8347 (tp) REVERT: B 166 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7369 (tp30) REVERT: B 184 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8077 (mp) outliers start: 52 outliers final: 39 residues processed: 257 average time/residue: 0.0825 time to fit residues: 32.3998 Evaluate side-chains 253 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 23 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 143 SER 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 50 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 219 VAL 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 90 GLN Chi-restraints excluded: chain E residue 141 VAL 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 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 8 ILE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 SER 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 247 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 36 optimal weight: 0.0020 chunk 33 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 131 optimal weight: 0.0670 chunk 117 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 overall best weight: 0.5528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 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 = 0.3725 r_free = 0.3725 target = 0.146876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120502 restraints weight = 16453.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123692 restraints weight = 9655.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125733 restraints weight = 6926.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126836 restraints weight = 5663.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.127740 restraints weight = 5049.804| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12003 Z= 0.134 Angle : 0.664 10.483 16320 Z= 0.345 Chirality : 0.043 0.146 1986 Planarity : 0.005 0.051 2028 Dihedral : 5.437 37.411 1652 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 3.51 % Allowed : 18.79 % Favored : 77.70 % 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: -1.78 (0.21), residues: 1548 helix: -0.33 (0.16), residues: 1122 sheet: None (None), residues: 0 loop : -3.37 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 150 TYR 0.030 0.001 TYR F 57 PHE 0.025 0.001 PHE C 25 TRP 0.013 0.001 TRP Z 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (12000) covalent geometry : angle 0.66356 / 0.34 (16320) hydrogen bonds : bond 0.03487 / 2.32 ( 582) hydrogen bonds : angle 4.51226 / 3.21 ( 1701) Misc. bond : bond 0.00226 / 0.11 ( 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 252 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 86 LEU cc_start: 0.7576 (mt) cc_final: 0.7349 (mt) REVERT: Z 156 LEU cc_start: 0.8993 (mm) cc_final: 0.8708 (mt) REVERT: Z 177 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7224 (tp) REVERT: Z 266 TRP cc_start: 0.7838 (m100) cc_final: 0.7353 (m-10) REVERT: Y 116 ILE cc_start: 0.8513 (tp) cc_final: 0.8286 (tp) REVERT: Y 149 MET cc_start: 0.7490 (mmt) cc_final: 0.6980 (tmm) REVERT: Y 180 ASN cc_start: 0.8219 (m-40) cc_final: 0.7469 (m-40) REVERT: F 143 MET cc_start: 0.8576 (mmt) cc_final: 0.8278 (mmm) REVERT: F 156 LEU cc_start: 0.8732 (mm) cc_final: 0.8343 (mt) REVERT: F 190 LYS cc_start: 0.7920 (mtpt) cc_final: 0.7142 (mttt) REVERT: E 116 ILE cc_start: 0.8530 (tp) cc_final: 0.8246 (tp) REVERT: E 234 MET cc_start: 0.7854 (mtp) cc_final: 0.7584 (mtm) REVERT: C 66 GLN cc_start: 0.6124 (tt0) cc_final: 0.5780 (tp40) REVERT: B 116 ILE cc_start: 0.8645 (tp) cc_final: 0.8327 (tp) REVERT: B 166 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: B 184 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8097 (mp) outliers start: 43 outliers final: 35 residues processed: 238 average time/residue: 0.0855 time to fit residues: 30.8633 Evaluate side-chains 235 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 94 GLU 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 23 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 143 SER 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 196 SER Chi-restraints excluded: chain F residue 219 VAL 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 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 8 ILE 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 Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 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 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 = 0.3721 r_free = 0.3721 target = 0.146584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.119993 restraints weight = 16654.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.123230 restraints weight = 9730.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.125055 restraints weight = 6964.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.126542 restraints weight = 5733.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127082 restraints weight = 5037.043| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3404 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= 0.137 Angle : 0.668 10.648 16320 Z= 0.346 Chirality : 0.043 0.142 1986 Planarity : 0.005 0.051 2028 Dihedral : 5.414 37.395 1652 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.59 % Allowed : 18.63 % Favored : 77.78 % 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: -1.65 (0.21), residues: 1548 helix: -0.24 (0.16), residues: 1122 sheet: None (None), residues: 0 loop : -3.30 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.027 0.001 TYR F 57 PHE 0.024 0.001 PHE E 12 TRP 0.015 0.001 TRP Z 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (12000) covalent geometry : angle 0.66827 / 0.35 (16320) hydrogen bonds : bond 0.03475 / 2.31 ( 582) hydrogen bonds : angle 4.50812 / 3.20 ( 1701) Misc. bond : bond 0.00222 / 0.11 ( 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 246 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Z 86 LEU cc_start: 0.7596 (mt) cc_final: 0.7362 (mt) REVERT: Z 156 LEU cc_start: 0.8978 (mm) cc_final: 0.8676 (mt) REVERT: Z 177 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7193 (tp) REVERT: Z 266 TRP cc_start: 0.7870 (m100) cc_final: 0.7349 (m-10) REVERT: Y 116 ILE cc_start: 0.8512 (tp) cc_final: 0.8288 (tp) REVERT: Y 149 MET cc_start: 0.7446 (mmt) cc_final: 0.7059 (tmm) REVERT: Y 180 ASN cc_start: 0.8223 (m-40) cc_final: 0.7461 (m-40) REVERT: F 143 MET cc_start: 0.8596 (mmt) cc_final: 0.8279 (mmm) REVERT: F 156 LEU cc_start: 0.8710 (mm) cc_final: 0.8317 (mt) REVERT: F 190 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7134 (mttt) REVERT: E 116 ILE cc_start: 0.8548 (tp) cc_final: 0.8246 (tp) REVERT: E 234 MET cc_start: 0.7871 (mtp) cc_final: 0.7592 (mtm) REVERT: C 66 GLN cc_start: 0.6153 (tt0) cc_final: 0.5829 (tp40) REVERT: B 28 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8445 (mm-40) REVERT: B 116 ILE cc_start: 0.8645 (tp) cc_final: 0.8326 (tp) REVERT: B 166 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: B 184 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8083 (mp) outliers start: 44 outliers final: 40 residues processed: 231 average time/residue: 0.0876 time to fit residues: 30.9185 Evaluate side-chains 236 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 94 GLU 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 23 ILE Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 143 SER 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 50 VAL Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 219 VAL 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 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 147 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 141 VAL Chi-restraints excluded: chain B residue 143 SER 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 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 14 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 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 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 = 0.3701 r_free = 0.3701 target = 0.144846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118103 restraints weight = 16778.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121325 restraints weight = 9844.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123349 restraints weight = 7046.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124667 restraints weight = 5765.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125248 restraints weight = 5085.678| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12003 Z= 0.149 Angle : 0.675 10.444 16320 Z= 0.351 Chirality : 0.043 0.143 1986 Planarity : 0.005 0.052 2028 Dihedral : 5.424 37.647 1652 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 3.84 % Allowed : 18.87 % Favored : 77.29 % 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: -1.62 (0.21), residues: 1548 helix: -0.23 (0.16), residues: 1122 sheet: None (None), residues: 0 loop : -3.27 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 55 TYR 0.025 0.001 TYR F 57 PHE 0.030 0.002 PHE Z 25 TRP 0.018 0.001 TRP Z 210 HIS 0.005 0.001 HIS B 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12000) covalent geometry : angle 0.67537 / 0.35 (16320) hydrogen bonds : bond 0.03622 / 2.41 ( 582) hydrogen bonds : angle 4.53615 / 3.23 ( 1701) Misc. bond : bond 0.00252 / 0.13 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1868.24 seconds wall clock time: 33 minutes 8.93 seconds (1988.93 seconds total)