Starting phenix.real_space_refine on Tue Jul 29 20:54:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k1h_9906/07_2025/6k1h_9906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k1h_9906/07_2025/6k1h_9906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k1h_9906/07_2025/6k1h_9906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k1h_9906/07_2025/6k1h_9906.map" model { file = "/net/cci-nas-00/data/ceres_data/6k1h_9906/07_2025/6k1h_9906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k1h_9906/07_2025/6k1h_9906.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.84, per 1000 atoms: 0.67 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: 3.16 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.22 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: 3.45 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2814 1.33 - 1.45: 2231 1.45 - 1.57: 6817 1.57 - 1.69: 3 1.69 - 1.81: 135 Bond restraints: 12000 Sorted by residual: bond pdb=" N GLN F 32 " pdb=" CA GLN F 32 " ideal model delta sigma weight residual 1.456 1.514 -0.057 1.27e-02 6.20e+03 2.05e+01 bond pdb=" N GLN C 32 " pdb=" CA GLN C 32 " ideal model delta sigma weight residual 1.456 1.511 -0.054 1.27e-02 6.20e+03 1.83e+01 bond pdb=" N GLN Z 32 " pdb=" CA GLN Z 32 " ideal model delta sigma weight residual 1.456 1.510 -0.054 1.27e-02 6.20e+03 1.83e+01 bond pdb=" CA GLN F 32 " pdb=" C GLN F 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.23e-02 6.61e+03 1.33e+01 bond pdb=" CA GLN C 32 " pdb=" C GLN C 32 " ideal model delta sigma weight residual 1.523 1.479 0.044 1.23e-02 6.61e+03 1.26e+01 ... (remaining 11995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 16055 3.18 - 6.36: 235 6.36 - 9.53: 23 9.53 - 12.71: 6 12.71 - 15.89: 1 Bond angle restraints: 16320 Sorted by residual: angle pdb=" N ARG Y 247 " pdb=" CA ARG Y 247 " pdb=" C ARG Y 247 " ideal model delta sigma weight residual 109.18 125.07 -15.89 1.42e+00 4.96e-01 1.25e+02 angle pdb=" CA GLN C 32 " pdb=" C GLN C 32 " pdb=" O GLN C 32 " ideal model delta sigma weight residual 121.15 112.44 8.71 1.10e+00 8.26e-01 6.27e+01 angle pdb=" CA GLN Z 32 " pdb=" C GLN Z 32 " pdb=" O GLN Z 32 " ideal model delta sigma weight residual 121.15 112.70 8.45 1.10e+00 8.26e-01 5.90e+01 angle pdb=" CA GLN F 32 " pdb=" C GLN F 32 " pdb=" O GLN F 32 " ideal model delta sigma weight residual 121.15 112.79 8.36 1.10e+00 8.26e-01 5.77e+01 angle pdb=" N ARG B 247 " pdb=" CA ARG B 247 " pdb=" C ARG B 247 " ideal model delta sigma weight residual 108.86 118.13 -9.27 1.41e+00 5.03e-01 4.32e+01 ... (remaining 16315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 6560 20.58 - 41.15: 401 41.15 - 61.73: 52 61.73 - 82.31: 28 82.31 - 102.89: 12 Dihedral angle restraints: 7053 sinusoidal: 2676 harmonic: 4377 Sorted by residual: dihedral pdb=" CA ARG C 221 " pdb=" C ARG C 221 " pdb=" N ILE C 222 " pdb=" CA ILE C 222 " ideal model delta harmonic sigma weight residual -180.00 -139.25 -40.75 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ARG Z 221 " pdb=" C ARG Z 221 " pdb=" N ILE Z 222 " pdb=" CA ILE Z 222 " ideal model delta harmonic sigma weight residual -180.00 -139.27 -40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ARG F 221 " pdb=" C ARG F 221 " pdb=" N ILE F 222 " pdb=" CA ILE F 222 " ideal model delta harmonic sigma weight residual -180.00 -139.29 -40.71 0 5.00e+00 4.00e-02 6.63e+01 ... (remaining 7050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1648 0.067 - 0.134: 320 0.134 - 0.200: 15 0.200 - 0.267: 1 0.267 - 0.334: 2 Chirality restraints: 1986 Sorted by residual: chirality pdb=" CA ARG Y 247 " pdb=" N ARG Y 247 " pdb=" C ARG Y 247 " pdb=" CB ARG Y 247 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA ARG E 247 " pdb=" N ARG E 247 " pdb=" C ARG E 247 " pdb=" CB ARG E 247 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ARG B 247 " pdb=" N ARG B 247 " pdb=" C ARG B 247 " pdb=" CB ARG B 247 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1983 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN F 32 " -0.022 2.00e-02 2.50e+03 4.73e-02 2.23e+01 pdb=" C GLN F 32 " 0.082 2.00e-02 2.50e+03 pdb=" O GLN F 32 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY F 33 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 32 " 0.022 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C GLN C 32 " -0.081 2.00e-02 2.50e+03 pdb=" O GLN C 32 " 0.031 2.00e-02 2.50e+03 pdb=" N GLY C 33 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN Z 32 " 0.022 2.00e-02 2.50e+03 4.60e-02 2.12e+01 pdb=" C GLN Z 32 " -0.080 2.00e-02 2.50e+03 pdb=" O GLN Z 32 " 0.030 2.00e-02 2.50e+03 pdb=" N GLY Z 33 " 0.028 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 108 2.61 - 3.18: 11096 3.18 - 3.75: 17588 3.75 - 4.33: 25714 4.33 - 4.90: 40797 Nonbonded interactions: 95303 Sorted by model distance: nonbonded pdb=" OE1 GLU Z 193 " pdb=" OH TYR Y 245 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLU C 193 " pdb=" OH TYR B 245 " model vdw 2.032 3.040 nonbonded pdb=" OE1 GLU F 193 " pdb=" OH TYR E 245 " model vdw 2.032 3.040 nonbonded pdb=" OH TYR Y 238 " pdb=" NE2 GLN B 240 " model vdw 2.126 3.120 nonbonded pdb=" NE2 GLN Y 240 " pdb=" OH TYR E 238 " model vdw 2.126 3.120 ... (remaining 95298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'Y' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Z' } 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: 0.390 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.830 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.345 12003 Z= 0.628 Angle : 0.975 15.892 16320 Z= 0.575 Chirality : 0.050 0.334 1986 Planarity : 0.007 0.061 2028 Dihedral : 15.198 102.886 4263 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 20.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP B 138 HIS 0.005 0.001 HIS Z 71 PHE 0.017 0.002 PHE B 222 TYR 0.011 0.001 TYR C 171 ARG 0.009 0.001 ARG F 54 Details of bonding type rmsd hydrogen bonds : bond 0.24754 ( 582) hydrogen bonds : angle 9.37845 ( 1701) covalent geometry : bond 0.00665 (12000) covalent geometry : angle 0.97525 (16320) Misc. bond : bond 0.34433 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 272 time to evaluate : 1.273 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: 0.2201 time to fit residues: 91.3208 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 : 1.186 ------------------------------------------------------------------------------- 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 129 optimal weight: 5.9990 chunk 115 optimal weight: 0.0670 chunk 64 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 98 ASN ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 240 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.137561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111648 restraints weight = 16965.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114689 restraints weight = 9797.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.116656 restraints weight = 6947.316| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12003 Z= 0.211 Angle : 0.799 10.267 16320 Z= 0.417 Chirality : 0.047 0.180 1986 Planarity : 0.007 0.063 2028 Dihedral : 8.923 55.598 1733 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.40 % Favored : 89.41 % Rotamer: Outliers : 2.61 % Allowed : 11.36 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.18), residues: 1548 helix: -1.96 (0.14), residues: 1125 sheet: None (None), residues: 0 loop : -3.96 (0.22), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Z 35 HIS 0.006 0.002 HIS C 230 PHE 0.023 0.002 PHE C 25 TYR 0.016 0.001 TYR E 194 ARG 0.004 0.001 ARG C 54 Details of bonding type rmsd hydrogen bonds : bond 0.05382 ( 582) hydrogen bonds : angle 5.69295 ( 1701) covalent geometry : bond 0.00503 (12000) covalent geometry : angle 0.79933 (16320) Misc. bond : bond 0.00011 ( 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 264 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: Y 52 ILE cc_start: 0.8834 (mt) cc_final: 0.8632 (mt) REVERT: Y 149 MET cc_start: 0.7381 (mmt) cc_final: 0.7007 (tmm) REVERT: Y 180 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8229 (m-40) REVERT: Y 184 ILE cc_start: 0.8651 (mt) cc_final: 0.8358 (mp) REVERT: F 57 TYR cc_start: 0.8119 (m-80) cc_final: 0.7919 (m-10) REVERT: F 156 LEU cc_start: 0.9253 (mm) cc_final: 0.9026 (mt) REVERT: F 190 LYS cc_start: 0.7881 (mtpt) cc_final: 0.6977 (mttt) REVERT: F 209 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7935 (ttmt) REVERT: E 51 ILE cc_start: 0.9055 (mt) cc_final: 0.8778 (mp) REVERT: E 149 MET cc_start: 0.7157 (mmt) cc_final: 0.6636 (tmm) REVERT: E 150 ARG cc_start: 0.7374 (mtt180) cc_final: 0.6971 (tmm160) REVERT: E 170 MET cc_start: 0.6811 (tpt) cc_final: 0.6540 (tpt) REVERT: E 234 MET cc_start: 0.7973 (mtp) cc_final: 0.7631 (mtm) REVERT: C 143 MET cc_start: 0.8652 (mmt) cc_final: 0.8427 (mmt) REVERT: C 190 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7265 (mttt) REVERT: B 64 MET cc_start: 0.8507 (pmm) cc_final: 0.7595 (pmm) REVERT: B 180 ASN cc_start: 0.8633 (m-40) cc_final: 0.8036 (m-40) outliers start: 32 outliers final: 25 residues processed: 248 average time/residue: 0.2375 time to fit residues: 86.6023 Evaluate side-chains 235 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 180 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 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain Y residue 248 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 220 THR Chi-restraints excluded: chain C residue 32 GLN 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 224 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 83 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 71 HIS ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 HIS ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3660 r_free = 0.3660 target = 0.141099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.115043 restraints weight = 16984.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.118233 restraints weight = 9758.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.120175 restraints weight = 6881.095| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1989 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= 0.161 Angle : 0.705 10.321 16320 Z= 0.372 Chirality : 0.045 0.174 1986 Planarity : 0.006 0.059 2028 Dihedral : 6.561 47.986 1723 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.56 % Favored : 90.25 % Rotamer: Outliers : 3.51 % Allowed : 13.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.19), residues: 1548 helix: -1.46 (0.15), residues: 1122 sheet: None (None), residues: 0 loop : -3.88 (0.23), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 210 HIS 0.005 0.001 HIS C 71 PHE 0.022 0.002 PHE E 12 TYR 0.011 0.001 TYR C 171 ARG 0.004 0.001 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 582) hydrogen bonds : angle 5.07700 ( 1701) covalent geometry : bond 0.00374 (12000) covalent geometry : angle 0.70545 (16320) Misc. bond : bond 0.00311 ( 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 266 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 1.679 Fit side-chains REVERT: Y 149 MET cc_start: 0.7547 (mmt) cc_final: 0.6955 (tmm) REVERT: Y 150 ARG cc_start: 0.7650 (mtt180) cc_final: 0.7111 (tmm160) REVERT: Y 180 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8110 (m-40) REVERT: Y 184 ILE cc_start: 0.8590 (mt) cc_final: 0.8296 (mp) REVERT: F 36 ASN cc_start: 0.8360 (m-40) cc_final: 0.7976 (m-40) REVERT: F 156 LEU cc_start: 0.9186 (mm) cc_final: 0.8879 (mt) REVERT: F 190 LYS cc_start: 0.7824 (mtpt) cc_final: 0.6898 (mttt) REVERT: F 209 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8053 (ttmt) REVERT: E 64 MET cc_start: 0.8755 (pmm) cc_final: 0.8424 (pmm) REVERT: E 149 MET cc_start: 0.7126 (mmt) cc_final: 0.6727 (tmm) REVERT: E 150 ARG cc_start: 0.7594 (mtt180) cc_final: 0.6873 (tmm160) REVERT: E 234 MET cc_start: 0.7935 (mtp) cc_final: 0.7615 (mtm) REVERT: C 14 LYS cc_start: 0.7426 (mmmt) cc_final: 0.6118 (mmmt) REVERT: C 143 MET cc_start: 0.8665 (mmt) cc_final: 0.8346 (mmt) REVERT: C 190 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7251 (mttt) REVERT: B 64 MET cc_start: 0.8535 (pmm) cc_final: 0.7905 (pmm) REVERT: B 180 ASN cc_start: 0.8592 (m-40) cc_final: 0.7980 (m-40) REVERT: B 221 ASN cc_start: 0.8017 (p0) cc_final: 0.7405 (p0) outliers start: 43 outliers final: 31 residues processed: 245 average time/residue: 0.3080 time to fit residues: 109.5285 Evaluate side-chains 235 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 61 ASN 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 180 ASN Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 139 ILE 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 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 110 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.143259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116702 restraints weight = 16785.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119868 restraints weight = 9773.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121944 restraints weight = 6986.766| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12003 Z= 0.145 Angle : 0.680 10.607 16320 Z= 0.356 Chirality : 0.044 0.176 1986 Planarity : 0.005 0.057 2028 Dihedral : 6.265 49.151 1722 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.79 % Favored : 91.02 % Rotamer: Outliers : 3.84 % Allowed : 16.01 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.60 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.20), residues: 1548 helix: -1.18 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -3.73 (0.23), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 210 HIS 0.004 0.001 HIS B 140 PHE 0.023 0.002 PHE Y 12 TYR 0.010 0.001 TYR E 194 ARG 0.005 0.001 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 582) hydrogen bonds : angle 4.85579 ( 1701) covalent geometry : bond 0.00332 (12000) covalent geometry : angle 0.67982 (16320) Misc. bond : bond 0.00347 ( 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 269 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 3.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 28 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8475 (mm110) REVERT: Y 149 MET cc_start: 0.7625 (mmt) cc_final: 0.6879 (tmm) REVERT: Y 150 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7220 (tmm160) REVERT: Y 180 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.7965 (m-40) REVERT: Y 184 ILE cc_start: 0.8587 (mt) cc_final: 0.8269 (mp) REVERT: F 156 LEU cc_start: 0.9185 (mm) cc_final: 0.8899 (mt) REVERT: F 190 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7201 (mttt) REVERT: E 149 MET cc_start: 0.7118 (mmt) cc_final: 0.6727 (tmm) REVERT: E 150 ARG cc_start: 0.7541 (mtt180) cc_final: 0.6802 (tmm160) REVERT: E 172 ASN cc_start: 0.7956 (m110) cc_final: 0.7675 (p0) REVERT: E 234 MET cc_start: 0.7918 (mtp) cc_final: 0.7633 (mtm) REVERT: C 143 MET cc_start: 0.8632 (mmt) cc_final: 0.8405 (mmt) REVERT: C 190 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7222 (mttt) REVERT: B 64 MET cc_start: 0.8542 (pmm) cc_final: 0.8025 (pmm) REVERT: B 168 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7125 (mm-40) outliers start: 47 outliers final: 32 residues processed: 248 average time/residue: 0.3259 time to fit residues: 121.4698 Evaluate side-chains 231 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 2.234 ------------------------------------------------------------------------------- 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 196 SER 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 180 ASN Chi-restraints excluded: chain Y residue 247 ARG Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 196 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 GLN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3669 r_free = 0.3669 target = 0.142107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.115788 restraints weight = 16761.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118951 restraints weight = 9774.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.120841 restraints weight = 6946.348| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2462 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= 0.157 Angle : 0.671 10.225 16320 Z= 0.353 Chirality : 0.044 0.171 1986 Planarity : 0.005 0.057 2028 Dihedral : 6.094 48.080 1722 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.50 % Favored : 90.31 % Rotamer: Outliers : 4.74 % Allowed : 16.01 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.20), residues: 1548 helix: -1.04 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -3.68 (0.23), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 210 HIS 0.005 0.001 HIS B 140 PHE 0.023 0.002 PHE E 12 TYR 0.009 0.001 TYR C 171 ARG 0.003 0.000 ARG Z 69 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 582) hydrogen bonds : angle 4.78689 ( 1701) covalent geometry : bond 0.00376 (12000) covalent geometry : angle 0.67123 (16320) Misc. bond : bond 0.00252 ( 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 266 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 1.462 Fit side-chains revert: symmetry clash REVERT: Y 149 MET cc_start: 0.7605 (mmt) cc_final: 0.6962 (tmm) REVERT: Y 150 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7241 (tmm160) REVERT: Y 180 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.7933 (m-40) REVERT: Y 184 ILE cc_start: 0.8540 (mt) cc_final: 0.8182 (mp) REVERT: F 190 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7214 (mttt) REVERT: E 149 MET cc_start: 0.7071 (mmt) cc_final: 0.6676 (tmm) REVERT: E 150 ARG cc_start: 0.7606 (mtt180) cc_final: 0.6962 (tmm160) REVERT: E 234 MET cc_start: 0.7847 (mtp) cc_final: 0.7568 (mtm) REVERT: C 190 LYS cc_start: 0.7962 (mtpt) cc_final: 0.7246 (mttt) outliers start: 58 outliers final: 47 residues processed: 247 average time/residue: 0.2219 time to fit residues: 81.1628 Evaluate side-chains 244 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 177 ILE Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 16 CYS Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 191 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 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 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 32 GLN 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 196 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU 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 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 77 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 172 ASN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 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 = 0.3682 r_free = 0.3682 target = 0.143215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.116762 restraints weight = 16964.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119943 restraints weight = 9810.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121979 restraints weight = 6970.881| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12003 Z= 0.145 Angle : 0.655 10.275 16320 Z= 0.344 Chirality : 0.043 0.167 1986 Planarity : 0.005 0.056 2028 Dihedral : 5.972 48.147 1722 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.98 % Favored : 90.83 % Rotamer: Outliers : 4.98 % Allowed : 16.34 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.20), residues: 1548 helix: -0.89 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -3.61 (0.23), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 210 HIS 0.006 0.001 HIS B 140 PHE 0.023 0.001 PHE E 12 TYR 0.012 0.001 TYR C 57 ARG 0.003 0.000 ARG Z 70 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 582) hydrogen bonds : angle 4.73269 ( 1701) covalent geometry : bond 0.00344 (12000) covalent geometry : angle 0.65508 (16320) Misc. bond : bond 0.00144 ( 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 269 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8336 (m-80) cc_final: 0.7709 (m-10) REVERT: Y 149 MET cc_start: 0.7599 (mmt) cc_final: 0.6918 (tmm) REVERT: Y 150 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7064 (tmm160) REVERT: Y 180 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.7892 (m-40) REVERT: Y 184 ILE cc_start: 0.8539 (mt) cc_final: 0.8176 (mp) REVERT: F 190 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7212 (mttt) REVERT: E 149 MET cc_start: 0.7092 (mmt) cc_final: 0.6584 (tmm) REVERT: E 150 ARG cc_start: 0.7531 (mtt180) cc_final: 0.6743 (tmm160) REVERT: E 172 ASN cc_start: 0.7915 (m110) cc_final: 0.7705 (p0) REVERT: E 234 MET cc_start: 0.7856 (mtp) cc_final: 0.7574 (mtm) REVERT: C 190 LYS cc_start: 0.7936 (mtpt) cc_final: 0.7225 (mttt) REVERT: B 20 MET cc_start: 0.7695 (mmm) cc_final: 0.7403 (mmt) REVERT: B 116 ILE cc_start: 0.8638 (tp) cc_final: 0.8405 (tp) outliers start: 61 outliers final: 50 residues processed: 246 average time/residue: 0.2056 time to fit residues: 75.6945 Evaluate side-chains 250 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 61 ASN Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 196 SER 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 24 LEU Chi-restraints excluded: chain Y residue 141 VAL Chi-restraints excluded: chain Y residue 143 SER Chi-restraints excluded: chain Y residue 180 ASN Chi-restraints excluded: chain Y residue 191 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 86 LEU 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 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 32 GLN 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 196 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 90 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.3686 r_free = 0.3686 target = 0.143682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116977 restraints weight = 16862.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120183 restraints weight = 9797.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.122276 restraints weight = 7008.414| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12003 Z= 0.149 Angle : 0.662 10.255 16320 Z= 0.347 Chirality : 0.043 0.163 1986 Planarity : 0.005 0.055 2028 Dihedral : 5.854 49.035 1722 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.17 % Favored : 90.76 % Rotamer: Outliers : 4.58 % Allowed : 17.16 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.21), residues: 1548 helix: -0.80 (0.16), residues: 1125 sheet: None (None), residues: 0 loop : -3.46 (0.25), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 210 HIS 0.005 0.001 HIS B 140 PHE 0.024 0.001 PHE E 12 TYR 0.008 0.001 TYR C 57 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 582) hydrogen bonds : angle 4.68733 ( 1701) covalent geometry : bond 0.00357 (12000) covalent geometry : angle 0.66171 (16320) Misc. bond : bond 0.00125 ( 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 279 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8303 (m-80) cc_final: 0.7632 (m-10) REVERT: Y 149 MET cc_start: 0.7575 (mmt) cc_final: 0.6865 (tmm) REVERT: Y 150 ARG cc_start: 0.7549 (mtt180) cc_final: 0.7050 (tmm160) REVERT: Y 160 LEU cc_start: 0.8344 (mm) cc_final: 0.7971 (mt) REVERT: Y 180 ASN cc_start: 0.8322 (m-40) cc_final: 0.7912 (m-40) REVERT: Y 184 ILE cc_start: 0.8528 (mt) cc_final: 0.8166 (mp) REVERT: F 190 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7204 (mttt) REVERT: F 198 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8249 (tp) REVERT: E 150 ARG cc_start: 0.7490 (mtt180) cc_final: 0.6685 (tmm160) REVERT: E 172 ASN cc_start: 0.7914 (m110) cc_final: 0.7703 (p0) REVERT: E 234 MET cc_start: 0.7855 (mtp) cc_final: 0.7550 (mtm) REVERT: C 66 GLN cc_start: 0.6119 (tt0) cc_final: 0.5863 (tp40) REVERT: C 190 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7114 (mttt) REVERT: C 221 ARG cc_start: 0.3653 (OUTLIER) cc_final: 0.2705 (ttm170) REVERT: B 20 MET cc_start: 0.7493 (mmm) cc_final: 0.7006 (mmt) REVERT: B 24 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7754 (mm) REVERT: B 116 ILE cc_start: 0.8629 (tp) cc_final: 0.8397 (tp) outliers start: 56 outliers final: 47 residues processed: 263 average time/residue: 0.2421 time to fit residues: 92.8049 Evaluate side-chains 256 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 196 SER 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 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 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 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 32 GLN 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 196 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU 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 93 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 102 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 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 = 0.3699 r_free = 0.3699 target = 0.144865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118477 restraints weight = 16632.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121698 restraints weight = 9652.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123718 restraints weight = 6878.841| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12003 Z= 0.139 Angle : 0.652 10.432 16320 Z= 0.342 Chirality : 0.043 0.169 1986 Planarity : 0.005 0.055 2028 Dihedral : 5.752 49.275 1721 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.58 % Allowed : 16.99 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.21), residues: 1548 helix: -0.67 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 210 HIS 0.006 0.001 HIS B 140 PHE 0.025 0.001 PHE E 12 TYR 0.008 0.001 TYR C 57 ARG 0.009 0.000 ARG F 221 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 582) hydrogen bonds : angle 4.63376 ( 1701) covalent geometry : bond 0.00330 (12000) covalent geometry : angle 0.65199 (16320) Misc. bond : bond 0.00111 ( 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 266 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 210 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 57 TYR cc_start: 0.8329 (m-80) cc_final: 0.7613 (m-10) REVERT: Y 149 MET cc_start: 0.7507 (mmt) cc_final: 0.6840 (tmm) REVERT: Y 150 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6866 (tmm160) REVERT: Y 160 LEU cc_start: 0.8340 (mm) cc_final: 0.8006 (mt) REVERT: Y 180 ASN cc_start: 0.8363 (m-40) cc_final: 0.7675 (m-40) REVERT: Y 184 ILE cc_start: 0.8507 (mt) cc_final: 0.8133 (mp) REVERT: F 190 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7203 (mttt) REVERT: F 198 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8282 (tp) REVERT: E 28 GLN cc_start: 0.8798 (mm110) cc_final: 0.8598 (mm-40) REVERT: E 113 VAL cc_start: 0.8467 (t) cc_final: 0.8244 (t) REVERT: E 150 ARG cc_start: 0.7437 (mtt180) cc_final: 0.6671 (tmm160) REVERT: E 180 ASN cc_start: 0.8411 (m-40) cc_final: 0.7686 (m-40) REVERT: E 234 MET cc_start: 0.7854 (mtp) cc_final: 0.7561 (mtm) REVERT: C 66 GLN cc_start: 0.6248 (tt0) cc_final: 0.5940 (tp40) REVERT: C 190 LYS cc_start: 0.7923 (mtpt) cc_final: 0.7166 (mttt) REVERT: B 24 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7765 (mm) REVERT: B 116 ILE cc_start: 0.8657 (tp) cc_final: 0.8444 (tp) outliers start: 56 outliers final: 46 residues processed: 248 average time/residue: 0.2104 time to fit residues: 77.6904 Evaluate side-chains 253 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 196 SER 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 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 86 LEU Chi-restraints excluded: chain F residue 121 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 174 SER Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN 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 32 GLN 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 196 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain B residue 8 ILE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 247 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 19 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 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 = 0.145020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118721 restraints weight = 16615.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121936 restraints weight = 9667.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.123687 restraints weight = 6899.465| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12003 Z= 0.140 Angle : 0.664 10.469 16320 Z= 0.346 Chirality : 0.043 0.186 1986 Planarity : 0.005 0.054 2028 Dihedral : 5.654 49.345 1721 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.33 % Allowed : 17.57 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.21), residues: 1548 helix: -0.55 (0.16), residues: 1128 sheet: None (None), residues: 0 loop : -3.37 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 210 HIS 0.006 0.001 HIS B 140 PHE 0.025 0.001 PHE E 12 TYR 0.008 0.001 TYR C 171 ARG 0.009 0.001 ARG C 221 Details of bonding type rmsd hydrogen bonds : bond 0.03615 ( 582) hydrogen bonds : angle 4.59422 ( 1701) covalent geometry : bond 0.00330 (12000) covalent geometry : angle 0.66396 (16320) Misc. bond : bond 0.00104 ( 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 260 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Y 149 MET cc_start: 0.7504 (mmt) cc_final: 0.6810 (tmm) REVERT: Y 150 ARG cc_start: 0.7337 (mtt180) cc_final: 0.6833 (tmm160) REVERT: Y 160 LEU cc_start: 0.8379 (mm) cc_final: 0.8094 (mt) REVERT: Y 180 ASN cc_start: 0.8330 (m-40) cc_final: 0.7647 (m-40) REVERT: Y 184 ILE cc_start: 0.8468 (mt) cc_final: 0.8095 (mp) REVERT: F 190 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7178 (mttt) REVERT: E 28 GLN cc_start: 0.8767 (mm110) cc_final: 0.8558 (mm-40) REVERT: E 52 ILE cc_start: 0.8404 (mt) cc_final: 0.8173 (mp) REVERT: E 113 VAL cc_start: 0.8472 (t) cc_final: 0.8239 (t) REVERT: E 150 ARG cc_start: 0.7354 (mtt180) cc_final: 0.6613 (tmm160) REVERT: E 180 ASN cc_start: 0.8369 (m-40) cc_final: 0.7660 (m-40) REVERT: E 234 MET cc_start: 0.7853 (mtp) cc_final: 0.7590 (mtm) REVERT: C 66 GLN cc_start: 0.6255 (tt0) cc_final: 0.5941 (tp40) REVERT: B 116 ILE cc_start: 0.8651 (tp) cc_final: 0.8344 (tp) outliers start: 53 outliers final: 48 residues processed: 242 average time/residue: 0.2258 time to fit residues: 82.8656 Evaluate side-chains 243 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 196 SER 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 50 VAL Chi-restraints excluded: chain F residue 86 LEU 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 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 GLN 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 196 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 160 LEU 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 32 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 148 optimal weight: 0.4980 chunk 104 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 86 optimal weight: 0.0070 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 32 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120257 restraints weight = 16491.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123379 restraints weight = 9532.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125398 restraints weight = 6822.456| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12003 Z= 0.132 Angle : 0.656 11.168 16320 Z= 0.341 Chirality : 0.043 0.159 1986 Planarity : 0.005 0.054 2028 Dihedral : 5.584 49.304 1721 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 4.41 % Allowed : 17.65 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1548 helix: -0.41 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -3.38 (0.25), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 127 HIS 0.006 0.001 HIS B 140 PHE 0.024 0.001 PHE B 12 TYR 0.011 0.001 TYR Z 57 ARG 0.007 0.001 ARG C 221 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 582) hydrogen bonds : angle 4.54625 ( 1701) covalent geometry : bond 0.00309 (12000) covalent geometry : angle 0.65597 (16320) Misc. bond : bond 0.00091 ( 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 271 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Z 86 LEU cc_start: 0.7456 (mt) cc_final: 0.7188 (mt) REVERT: Y 149 MET cc_start: 0.7477 (mmt) cc_final: 0.6637 (tmm) REVERT: Y 150 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6746 (tmm160) REVERT: Y 160 LEU cc_start: 0.8332 (mm) cc_final: 0.8076 (mt) REVERT: Y 180 ASN cc_start: 0.8285 (m-40) cc_final: 0.7694 (m-40) REVERT: F 143 MET cc_start: 0.8550 (mmt) cc_final: 0.8247 (mmm) REVERT: F 190 LYS cc_start: 0.7995 (mtpt) cc_final: 0.7182 (mttt) REVERT: F 198 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8323 (tp) REVERT: E 113 VAL cc_start: 0.8451 (t) cc_final: 0.8182 (t) REVERT: E 116 ILE cc_start: 0.8591 (tp) cc_final: 0.8258 (tp) REVERT: E 150 ARG cc_start: 0.7568 (mtt180) cc_final: 0.6412 (tmm160) REVERT: E 180 ASN cc_start: 0.8321 (m-40) cc_final: 0.7633 (m-40) REVERT: E 234 MET cc_start: 0.7829 (mtp) cc_final: 0.7542 (mtm) REVERT: C 66 GLN cc_start: 0.6460 (tt0) cc_final: 0.6111 (tp40) REVERT: B 116 ILE cc_start: 0.8683 (tp) cc_final: 0.8355 (tp) REVERT: B 184 ILE cc_start: 0.8479 (mt) cc_final: 0.8208 (mp) outliers start: 54 outliers final: 49 residues processed: 250 average time/residue: 0.2165 time to fit residues: 79.7617 Evaluate side-chains 255 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 205 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 94 GLU Chi-restraints excluded: chain Z residue 121 VAL Chi-restraints excluded: chain Z residue 147 LEU Chi-restraints excluded: chain Z residue 196 SER 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 50 VAL Chi-restraints excluded: chain F residue 86 LEU 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 183 MET Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 32 GLN 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 196 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 16 CYS 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 247 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 74 optimal weight: 0.8980 chunk 136 optimal weight: 0.0970 chunk 134 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN ** C 32 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.119783 restraints weight = 16547.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122977 restraints weight = 9683.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125039 restraints weight = 6944.583| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12003 Z= 0.142 Angle : 0.688 11.002 16320 Z= 0.358 Chirality : 0.044 0.156 1986 Planarity : 0.005 0.059 2028 Dihedral : 5.565 49.450 1721 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 4.41 % Allowed : 18.38 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.60 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.21), residues: 1548 helix: -0.36 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -3.37 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 210 HIS 0.005 0.001 HIS B 140 PHE 0.028 0.001 PHE B 219 TYR 0.023 0.001 TYR Z 57 ARG 0.007 0.001 ARG C 221 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 582) hydrogen bonds : angle 4.55206 ( 1701) covalent geometry : bond 0.00335 (12000) covalent geometry : angle 0.68754 (16320) Misc. bond : bond 0.00626 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.82 seconds wall clock time: 75 minutes 6.43 seconds (4506.43 seconds total)