Starting phenix.real_space_refine on Fri Oct 23 06:10:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wsd_66197/10_2026/9wsd_66197.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wsd_66197/10_2026/9wsd_66197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wsd_66197/10_2026/9wsd_66197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wsd_66197/10_2026/9wsd_66197.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wsd_66197/10_2026/9wsd_66197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wsd_66197/10_2026/9wsd_66197.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 41 5.16 5 C 5312 2.51 5 N 1486 2.21 5 O 1735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8582 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2103 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 296} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2105 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 290} Chain breaks: 2 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2145 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2117 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 4, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.23 Number of scatterers: 8582 At special positions: 0 Unit cell: (57.24, 60.42, 208.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 8 15.00 O 1735 8.00 N 1486 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 487.9 milliseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 30.2% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 removed outlier: 3.529A pdb=" N VAL A 26 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 removed outlier: 4.096A pdb=" N GLY A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.971A pdb=" N GLY A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 112' Processing helix chain 'A' and resid 112 through 120 removed outlier: 3.599A pdb=" N ALA A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.914A pdb=" N MET A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.615A pdb=" N LYS A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 234 through 245 removed outlier: 3.541A pdb=" N GLU A 238 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N MET A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 244 " --> pdb=" O ALA A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 281 removed outlier: 3.817A pdb=" N PHE A 275 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.841A pdb=" N VAL B 26 " --> pdb=" O GLY B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.919A pdb=" N ARG B 50 " --> pdb=" O GLN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 4.169A pdb=" N GLY B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN B 79 " --> pdb=" O GLU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 108 through 120 removed outlier: 3.643A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) Proline residue: B 114 - end of helix removed outlier: 3.737A pdb=" N ALA B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.783A pdb=" N PHE B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 164 through 168 removed outlier: 4.000A pdb=" N LYS B 167 " --> pdb=" O PRO B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 185 removed outlier: 3.613A pdb=" N ALA B 185 " --> pdb=" O PHE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.894A pdb=" N GLN B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 200 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 removed outlier: 3.919A pdb=" N SER B 218 " --> pdb=" O ARG B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 240 removed outlier: 4.364A pdb=" N GLU B 238 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 removed outlier: 4.085A pdb=" N VAL B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY B 279 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N THR B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.542A pdb=" N GLU C 118 " --> pdb=" O PRO C 114 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 144 removed outlier: 3.520A pdb=" N MET C 143 " --> pdb=" O LYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 150 through 155 removed outlier: 4.381A pdb=" N LYS C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 Processing helix chain 'C' and resid 186 through 191 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 236 through 244 removed outlier: 4.066A pdb=" N MET C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 244 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.697A pdb=" N THR C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.958A pdb=" N ILE C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'D' and resid 73 through 83 removed outlier: 3.707A pdb=" N GLY D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 83 " --> pdb=" O ASN D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.766A pdb=" N ALA D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 123 removed outlier: 3.609A pdb=" N VAL D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 119 " --> pdb=" O VAL D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 139 removed outlier: 3.857A pdb=" N GLU D 138 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY D 139 " --> pdb=" O ASN D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 139' Processing helix chain 'D' and resid 140 through 153 removed outlier: 3.926A pdb=" N GLU D 147 " --> pdb=" O MET D 143 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 178 through 197 removed outlier: 4.652A pdb=" N VAL D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 192 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 removed outlier: 3.780A pdb=" N ARG D 214 " --> pdb=" O PHE D 210 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 245 removed outlier: 3.565A pdb=" N ILE D 244 " --> pdb=" O ALA D 240 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 5.640A pdb=" N VAL A 98 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL A 130 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE A 100 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N THR A 132 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N THR A 127 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE A 161 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA A 129 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 163 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 131 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 222 through 227 removed outlier: 3.683A pdb=" N ARG A 307 " --> pdb=" O THR A 265 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 265 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 260 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N GLY A 295 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 262 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER A 297 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 264 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 40 removed outlier: 6.549A pdb=" N VAL B 15 " --> pdb=" O PHE B 40 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 99 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA B 101 " --> pdb=" O ILE B 16 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 130 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 100 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N THR B 132 " --> pdb=" O ILE B 100 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA B 102 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 159 " --> pdb=" O THR B 127 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.515A pdb=" N GLY B 226 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 310 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 230 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU B 306 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B 260 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N GLY B 295 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N VAL B 262 " --> pdb=" O GLY B 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 15 through 16 removed outlier: 5.926A pdb=" N VAL C 98 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 130 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE C 100 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR C 132 " --> pdb=" O ILE C 100 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA C 102 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS C 133 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 222 through 223 removed outlier: 4.842A pdb=" N TYR C 222 " --> pdb=" O GLY C 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 226 through 230 removed outlier: 4.069A pdb=" N ALA C 230 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU C 306 " --> pdb=" O ALA C 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 263 through 266 removed outlier: 4.318A pdb=" N ALA C 266 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.795A pdb=" N ILE D 13 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N PHE D 40 " --> pdb=" O ILE D 13 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL D 15 " --> pdb=" O PHE D 40 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 99 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL D 98 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 130 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ILE D 100 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR D 132 " --> pdb=" O ILE D 100 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ALA D 102 " --> pdb=" O THR D 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 225 through 230 removed outlier: 3.705A pdb=" N VAL D 308 " --> pdb=" O GLY D 228 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG D 307 " --> pdb=" O THR D 265 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 265 " --> pdb=" O ARG D 307 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR D 309 " --> pdb=" O ASN D 263 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY D 295 " --> pdb=" O VAL D 262 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 444 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2998 1.35 - 1.47: 1652 1.47 - 1.58: 3915 1.58 - 1.70: 12 1.70 - 1.82: 82 Bond restraints: 8659 Sorted by residual: bond pdb=" CA ILE A 125 " pdb=" C ILE A 125 " ideal model delta sigma weight residual 1.523 1.543 -0.020 1.27e-02 6.20e+03 2.52e+00 bond pdb=" CB VAL C 311 " pdb=" CG1 VAL C 311 " ideal model delta sigma weight residual 1.521 1.573 -0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" CB ASP B 253 " pdb=" CG ASP B 253 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.27e+00 bond pdb=" N MET C 220 " pdb=" CA MET C 220 " ideal model delta sigma weight residual 1.462 1.485 -0.023 1.54e-02 4.22e+03 2.23e+00 bond pdb=" CA VAL C 311 " pdb=" CB VAL C 311 " ideal model delta sigma weight residual 1.540 1.560 -0.020 1.36e-02 5.41e+03 2.09e+00 ... (remaining 8654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 11502 3.15 - 6.30: 196 6.30 - 9.45: 44 9.45 - 12.61: 7 12.61 - 15.76: 5 Bond angle restraints: 11754 Sorted by residual: angle pdb=" C GLY A 175 " pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 121.97 132.24 -10.27 1.80e+00 3.09e-01 3.25e+01 angle pdb=" N ARG A 50 " pdb=" CA ARG A 50 " pdb=" C ARG A 50 " ideal model delta sigma weight residual 113.38 107.10 6.28 1.17e+00 7.31e-01 2.88e+01 angle pdb=" C GLY B 175 " pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 121.97 131.41 -9.44 1.80e+00 3.09e-01 2.75e+01 angle pdb=" C MET C 29 " pdb=" N VAL C 30 " pdb=" CA VAL C 30 " ideal model delta sigma weight residual 121.97 130.57 -8.60 1.80e+00 3.09e-01 2.28e+01 angle pdb=" C GLY D 175 " pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 121.97 130.44 -8.47 1.80e+00 3.09e-01 2.21e+01 ... (remaining 11749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 4673 16.56 - 33.12: 350 33.12 - 49.68: 90 49.68 - 66.24: 7 66.24 - 82.81: 4 Dihedral angle restraints: 5124 sinusoidal: 1822 harmonic: 3302 Sorted by residual: dihedral pdb=" CA ASP A 253 " pdb=" C ASP A 253 " pdb=" N LEU A 254 " pdb=" CA LEU A 254 " ideal model delta harmonic sigma weight residual -180.00 -162.68 -17.32 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ILE D 176 " pdb=" C ILE D 176 " pdb=" N SER D 177 " pdb=" CA SER D 177 " ideal model delta harmonic sigma weight residual 180.00 163.25 16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA LEU D 205 " pdb=" C LEU D 205 " pdb=" N MET D 206 " pdb=" CA MET D 206 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 1225 0.086 - 0.172: 190 0.172 - 0.258: 11 0.258 - 0.344: 6 0.344 - 0.430: 2 Chirality restraints: 1434 Sorted by residual: chirality pdb=" CB ILE D 163 " pdb=" CA ILE D 163 " pdb=" CG1 ILE D 163 " pdb=" CG2 ILE D 163 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB ILE C 161 " pdb=" CA ILE C 161 " pdb=" CG1 ILE C 161 " pdb=" CG2 ILE C 161 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB THR C 132 " pdb=" CA THR C 132 " pdb=" OG1 THR C 132 " pdb=" CG2 THR C 132 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1431 not shown) Planarity restraints: 1540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET D 217 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C MET D 217 " -0.041 2.00e-02 2.50e+03 pdb=" O MET D 217 " 0.015 2.00e-02 2.50e+03 pdb=" N SER D 218 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 137 " 0.011 2.00e-02 2.50e+03 1.58e-02 4.35e+00 pdb=" CG PHE D 137 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE D 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE D 137 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE D 137 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 137 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE D 137 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 137 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C PHE D 137 " 0.036 2.00e-02 2.50e+03 pdb=" O PHE D 137 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU D 138 " -0.012 2.00e-02 2.50e+03 ... (remaining 1537 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2539 2.82 - 3.34: 7166 3.34 - 3.86: 13661 3.86 - 4.38: 14719 4.38 - 4.90: 25564 Nonbonded interactions: 63649 Sorted by model distance: nonbonded pdb=" O GLY A 61 " pdb=" OG1 THR A 65 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR B 132 " pdb=" OD1 ASN B 165 " model vdw 2.311 3.040 nonbonded pdb=" O ARG D 214 " pdb=" OG SER D 218 " model vdw 2.318 3.040 nonbonded pdb=" O ASP A 273 " pdb=" OG1 THR A 277 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR C 44 " pdb=" OG1 THR C 108 " model vdw 2.328 3.040 ... (remaining 63644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 30 or resid 38 through 40 or resid 42 through 4 \ 9 or (resid 50 and (name N or name CA or name C or name O or name CB )) or resid \ 51 through 58 or resid 60 through 61 or (resid 64 and (name N or name CA or nam \ e C or name O or name CB )) or resid 65 or (resid 66 and (name N or name CA or n \ ame C or name O or name CB )) or resid 67 through 82 or (resid 83 through 84 and \ (name N or name CA or name C or name O or name CB )) or resid 85 through 121 or \ (resid 122 through 123 and (name N or name CA or name C or name O or name CB )) \ or resid 124 through 135 or (resid 136 through 137 and (name N or name CA or na \ me C or name O or name CB )) or resid 138 through 175 or (resid 176 and (name N \ or name CA or name C or name O or name CB )) or resid 177 through 179 or (resid \ 180 through 181 and (name N or name CA or name C or name O or name CB )) or resi \ d 182 through 223 or (resid 224 and (name N or name CA or name C or name O or na \ me CB )) or resid 225 through 233 or (resid 234 and (name N or name CA or name C \ or name O or name CB )) or resid 235 through 237 or (resid 238 through 240 and \ (name N or name CA or name C or name O or name CB )) or resid 241 or (resid 242 \ through 243 and (name N or name CA or name C or name O or name CB )) or resid 24 \ 4 through 254 or (resid 255 and (name N or name CA or name C or name O or name C \ B )) or resid 256 through 282 or (resid 283 through 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 315 or resid 401)) selection = (chain 'B' and (resid 11 through 53 or resid 55 through 58 or resid 60 through 6 \ 1 or (resid 64 and (name N or name CA or name C or name O or name CB )) or resid \ 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or res \ id 67 through 88 or (resid 89 through 91 and (name N or name CA or name C or nam \ e O or name CB )) or resid 92 through 117 or (resid 118 and (name N or name CA o \ r name C or name O or name CB )) or resid 119 through 121 or (resid 122 through \ 123 and (name N or name CA or name C or name O or name CB )) or resid 124 throug \ h 136 or (resid 137 and (name N or name CA or name C or name O or name CB )) or \ resid 138 through 139 or (resid 140 through 141 and (name N or name CA or name C \ or name O or name CB )) or resid 142 through 154 or (resid 155 and (name N or n \ ame CA or name C or name O or name CB )) or resid 156 through 166 or (resid 167 \ and (name N or name CA or name C or name O or name CB )) or resid 168 through 16 \ 9 or (resid 170 through 171 and (name N or name CA or name C or name O or name C \ B )) or resid 173 or (resid 174 and (name N or name CA or name C or name O or na \ me CB )) or resid 175 or (resid 176 and (name N or name CA or name C or name O o \ r name CB )) or resid 177 through 179 or (resid 180 through 181 and (name N or n \ ame CA or name C or name O or name CB )) or resid 182 through 186 or (resid 187 \ and (name N or name CA or name C or name O or name CB )) or resid 188 through 18 \ 9 or (resid 190 and (name N or name CA or name C or name O or name CB )) or resi \ d 191 through 218 or (resid 219 through 220 and (name N or name CA or name C or \ name O or name CB )) or resid 221 through 223 or (resid 224 and (name N or name \ CA or name C or name O or name CB )) or resid 225 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB )) or resid 235 through 237 or \ (resid 238 through 240 and (name N or name CA or name C or name O or name CB )) \ or resid 241 or (resid 242 through 243 and (name N or name CA or name C or name \ O or name CB )) or resid 244 through 246 or (resid 247 and (name N or name CA o \ r name C or name O or name CB )) or resid 248 through 250 or (resid 251 and (nam \ e N or name CA or name C or name O or name CB )) or resid 252 or (resid 253 and \ (name N or name CA or name C or name O or name CB )) or resid 254 or (resid 255 \ and (name N or name CA or name C or name O or name CB )) or resid 256 through 27 \ 9 or (resid 280 through 281 and (name N or name CA or name C or name O or name C \ B )) or resid 282 through 284 or (resid 285 through 286 and (name N or name CA o \ r name C or name O or name CB )) or resid 287 through 315 or resid 401)) selection = (chain 'C' and (resid 11 through 30 or resid 38 through 40 or resid 42 through 4 \ 9 or (resid 50 and (name N or name CA or name C or name O or name CB )) or resid \ 51 through 53 or resid 55 through 58 or resid 60 through 63 or (resid 64 and (n \ ame N or name CA or name C or name O or name CB )) or resid 65 through 82 or (re \ sid 83 through 84 and (name N or name CA or name C or name O or name CB )) or re \ sid 85 through 117 or (resid 118 and (name N or name CA or name C or name O or n \ ame CB )) or resid 119 through 121 or (resid 122 through 123 and (name N or name \ CA or name C or name O or name CB )) or resid 124 through 135 or (resid 136 thr \ ough 137 and (name N or name CA or name C or name O or name CB )) or resid 138 t \ hrough 139 or (resid 140 through 141 and (name N or name CA or name C or name O \ or name CB )) or resid 142 through 154 or (resid 155 and (name N or name CA or n \ ame C or name O or name CB )) or resid 156 through 166 or (resid 167 and (name N \ or name CA or name C or name O or name CB )) or resid 168 through 169 or (resid \ 170 through 171 and (name N or name CA or name C or name O or name CB )) or res \ id 173 through 179 or (resid 180 through 181 and (name N or name CA or name C or \ name O or name CB )) or resid 182 through 186 or (resid 187 and (name N or name \ CA or name C or name O or name CB )) or resid 188 through 189 or (resid 190 and \ (name N or name CA or name C or name O or name CB )) or resid 191 through 218 o \ r (resid 219 through 220 and (name N or name CA or name C or name O or name CB ) \ ) or resid 221 through 232 or (resid 233 through 234 and (name N or name CA or n \ ame C or name O or name CB )) or resid 235 through 237 or (resid 238 through 240 \ and (name N or name CA or name C or name O or name CB )) or resid 241 through 2 \ 46 or (resid 247 and (name N or name CA or name C or name O or name CB )) or res \ id 248 through 250 or (resid 251 and (name N or name CA or name C or name O or n \ ame CB )) or resid 252 or (resid 253 and (name N or name CA or name C or name O \ or name CB )) or resid 254 or (resid 255 and (name N or name CA or name C or nam \ e O or name CB )) or resid 256 through 279 or (resid 280 through 281 and (name N \ or name CA or name C or name O or name CB )) or resid 282 or (resid 283 through \ 286 and (name N or name CA or name C or name O or name CB )) or resid 287 throu \ gh 315 or resid 401)) selection = (chain 'D' and (resid 11 through 30 or resid 38 through 40 or resid 42 through 4 \ 9 or (resid 50 and (name N or name CA or name C or name O or name CB )) or resid \ 51 through 53 or resid 55 through 61 or resid 64 through 83 or (resid 84 and (n \ ame N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 thro \ ugh 87 and (name N or name CA or name C or name O or name CB )) or resid 88 thro \ ugh 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) o \ r resid 119 through 135 or (resid 136 through 137 and (name N or name CA or name \ C or name O or name CB )) or resid 138 through 139 or (resid 140 through 141 an \ d (name N or name CA or name C or name O or name CB )) or resid 142 through 154 \ or (resid 155 and (name N or name CA or name C or name O or name CB )) or resid \ 156 through 166 or (resid 167 and (name N or name CA or name C or name O or name \ CB )) or resid 168 through 170 or (resid 171 and (name N or name CA or name C o \ r name O or name CB )) or (resid 173 through 176 and (name N or name CA or name \ C or name O or name CB )) or resid 177 through 186 or (resid 187 and (name N or \ name CA or name C or name O or name CB )) or resid 188 through 189 or (resid 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 through 2 \ 18 or (resid 219 through 220 and (name N or name CA or name C or name O or name \ CB )) or resid 221 through 223 or (resid 224 and (name N or name CA or name C or \ name O or name CB )) or resid 225 through 241 or (resid 242 through 243 and (na \ me N or name CA or name C or name O or name CB )) or resid 244 through 246 or (r \ esid 247 and (name N or name CA or name C or name O or name CB )) or resid 248 t \ hrough 250 or (resid 251 and (name N or name CA or name C or name O or name CB ) \ ) or resid 252 through 279 or (resid 280 through 281 and (name N or name CA or n \ ame C or name O or name CB )) or resid 282 or (resid 283 through 286 and (name N \ or name CA or name C or name O or name CB )) or resid 287 through 401)) } 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: 5.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.120 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5266 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 : 0.004 0.052 8659 Z= 0.212 Angle : 1.052 15.757 11754 Z= 0.522 Chirality : 0.061 0.430 1434 Planarity : 0.005 0.045 1540 Dihedral : 12.784 82.805 3026 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.06 % Favored : 92.18 % Rotamer: Outliers : 0.12 % Allowed : 0.73 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.21), residues: 1190 helix: -4.63 (0.11), residues: 307 sheet: -0.16 (0.36), residues: 220 loop : -2.07 (0.21), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.003 0.001 TYR C 222 PHE 0.036 0.002 PHE D 137 HIS 0.005 0.001 HIS D 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 ( 8659) covalent geometry : angle 1.05157 / 0.52 (11754) hydrogen bonds : bond 0.33748 / 22.57 ( 160) hydrogen bonds : angle 9.90254 / 6.78 ( 444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ARG cc_start: 0.5658 (OUTLIER) cc_final: 0.1943 (ttp-170) REVERT: A 114 PRO cc_start: 0.7480 (Cg_exo) cc_final: 0.7197 (Cg_endo) REVERT: B 225 MET cc_start: 0.7325 (mpp) cc_final: 0.7077 (mpp) REVERT: C 100 ILE cc_start: 0.5586 (mm) cc_final: 0.5386 (mm) REVERT: D 29 MET cc_start: 0.4013 (mtt) cc_final: 0.3595 (mtm) REVERT: D 30 VAL cc_start: 0.5744 (t) cc_final: 0.5478 (t) REVERT: D 178 LEU cc_start: 0.6000 (tp) cc_final: 0.5323 (tt) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.0772 time to fit residues: 14.7031 Evaluate side-chains 104 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117] chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 165 ASN A 263 ASN C 28 HIS C 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.154281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.133661 restraints weight = 22658.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.136337 restraints weight = 16167.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.138270 restraints weight = 12388.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.139750 restraints weight = 10098.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.140760 restraints weight = 8595.264| |-----------------------------------------------------------------------------| r_work (final): 0.4703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8659 Z= 0.172 Angle : 0.702 9.111 11754 Z= 0.345 Chirality : 0.047 0.210 1434 Planarity : 0.004 0.036 1540 Dihedral : 5.030 40.935 1299 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.64 % Favored : 92.77 % Rotamer: Outliers : 1.45 % Allowed : 11.00 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.22), residues: 1190 helix: -3.64 (0.19), residues: 333 sheet: -0.38 (0.37), residues: 224 loop : -1.84 (0.22), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 283 TYR 0.003 0.001 TYR D 222 PHE 0.019 0.002 PHE D 182 HIS 0.002 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 8659) covalent geometry : angle 0.70184 / 0.34 (11754) hydrogen bonds : bond 0.04359 / 2.93 ( 160) hydrogen bonds : angle 6.58802 / 4.58 ( 444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.3320 (tpt) cc_final: 0.2787 (mmm) REVERT: A 114 PRO cc_start: 0.7888 (Cg_exo) cc_final: 0.7618 (Cg_endo) REVERT: C 29 MET cc_start: 0.6087 (ttt) cc_final: 0.5756 (ttp) outliers start: 12 outliers final: 6 residues processed: 112 average time/residue: 0.0674 time to fit residues: 11.6482 Evaluate side-chains 106 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [66, 58, 112, 69, 88, 67, 116, 22, 97, 0, 91] chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.154033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.133494 restraints weight = 23641.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.136310 restraints weight = 16697.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.138189 restraints weight = 12712.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.139769 restraints weight = 10368.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.140706 restraints weight = 8759.695| |-----------------------------------------------------------------------------| r_work (final): 0.4732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8659 Z= 0.135 Angle : 0.634 9.327 11754 Z= 0.307 Chirality : 0.045 0.164 1434 Planarity : 0.003 0.028 1540 Dihedral : 4.774 50.807 1295 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.80 % Favored : 93.61 % Rotamer: Outliers : 2.42 % Allowed : 15.24 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.23), residues: 1190 helix: -2.83 (0.23), residues: 332 sheet: -0.32 (0.37), residues: 220 loop : -1.62 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 235 TYR 0.004 0.000 TYR C 222 PHE 0.021 0.002 PHE A 210 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8659) covalent geometry : angle 0.63433 / 0.31 (11754) hydrogen bonds : bond 0.03024 / 2.07 ( 160) hydrogen bonds : angle 5.66618 / 3.98 ( 444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8082 (Cg_exo) cc_final: 0.7793 (Cg_endo) REVERT: B 220 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.5139 (mmp) REVERT: C 302 MET cc_start: 0.5382 (tpt) cc_final: 0.4881 (tpt) REVERT: D 143 MET cc_start: 0.7005 (mmm) cc_final: 0.5459 (mpp) outliers start: 20 outliers final: 12 residues processed: 116 average time/residue: 0.0642 time to fit residues: 11.4235 Evaluate side-chains 110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain D residue 161 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [1, 3, 26, 115, 18, 31, 98, 78, 41, 84, 29] chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 0.0870 chunk 26 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 84 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 289 ASN C 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.156071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.136989 restraints weight = 22856.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.139496 restraints weight = 16723.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.141018 restraints weight = 12258.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.141972 restraints weight = 10506.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.142439 restraints weight = 9636.149| |-----------------------------------------------------------------------------| r_work (final): 0.4738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5923 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8659 Z= 0.106 Angle : 0.598 8.436 11754 Z= 0.287 Chirality : 0.045 0.292 1434 Planarity : 0.003 0.025 1540 Dihedral : 4.708 58.094 1295 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.97 % Favored : 93.45 % Rotamer: Outliers : 2.42 % Allowed : 17.05 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.23), residues: 1190 helix: -2.36 (0.26), residues: 323 sheet: -0.36 (0.36), residues: 233 loop : -1.54 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.002 0.000 TYR D 222 PHE 0.014 0.001 PHE D 182 HIS 0.002 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8659) covalent geometry : angle 0.59753 / 0.29 (11754) hydrogen bonds : bond 0.02235 / 1.58 ( 160) hydrogen bonds : angle 5.24528 / 3.67 ( 444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8090 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: C 29 MET cc_start: 0.5750 (ttm) cc_final: 0.5206 (ttp) REVERT: C 302 MET cc_start: 0.5515 (tpt) cc_final: 0.5144 (tpt) REVERT: D 143 MET cc_start: 0.6391 (mmm) cc_final: 0.4984 (mpp) outliers start: 20 outliers final: 11 residues processed: 112 average time/residue: 0.0656 time to fit residues: 11.2836 Evaluate side-chains 107 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [111, 72, 98, 2, 118, 77, 33, 53, 84, 102, 60] chunk 111 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 2 optimal weight: 0.0270 chunk 118 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4954 r_free = 0.4954 target = 0.155985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.136303 restraints weight = 23098.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.139181 restraints weight = 16445.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.140312 restraints weight = 11747.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.140749 restraints weight = 10454.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.140921 restraints weight = 10065.625| |-----------------------------------------------------------------------------| r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8659 Z= 0.102 Angle : 0.595 9.873 11754 Z= 0.284 Chirality : 0.044 0.278 1434 Planarity : 0.002 0.026 1540 Dihedral : 4.551 56.284 1295 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.88 % Favored : 93.53 % Rotamer: Outliers : 2.90 % Allowed : 18.62 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.24), residues: 1190 helix: -1.97 (0.27), residues: 319 sheet: -0.33 (0.36), residues: 239 loop : -1.46 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.003 0.000 TYR B 222 PHE 0.012 0.001 PHE D 182 HIS 0.002 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 8659) covalent geometry : angle 0.59493 / 0.28 (11754) hydrogen bonds : bond 0.02104 / 1.48 ( 160) hydrogen bonds : angle 4.95597 / 3.47 ( 444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8147 (Cg_exo) cc_final: 0.7873 (Cg_endo) REVERT: C 29 MET cc_start: 0.5793 (ttm) cc_final: 0.5539 (ttp) REVERT: C 302 MET cc_start: 0.5540 (tpt) cc_final: 0.5223 (tpt) REVERT: D 143 MET cc_start: 0.6458 (mmm) cc_final: 0.5074 (mpp) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 0.0635 time to fit residues: 11.4992 Evaluate side-chains 113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [6, 55, 95, 15, 87, 33, 106, 38, 59, 102, 118] chunk 6 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 0.0170 chunk 33 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.4886 r_free = 0.4886 target = 0.151132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.130350 restraints weight = 22649.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.132538 restraints weight = 16595.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.134297 restraints weight = 12641.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.134821 restraints weight = 10293.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.134971 restraints weight = 9968.650| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8659 Z= 0.142 Angle : 0.656 11.755 11754 Z= 0.316 Chirality : 0.046 0.302 1434 Planarity : 0.003 0.043 1540 Dihedral : 4.975 59.846 1295 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.39 % Favored : 92.02 % Rotamer: Outliers : 3.14 % Allowed : 19.83 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.24), residues: 1190 helix: -1.88 (0.26), residues: 342 sheet: -0.37 (0.36), residues: 242 loop : -1.66 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 307 TYR 0.005 0.001 TYR C 222 PHE 0.019 0.001 PHE D 145 HIS 0.002 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8659) covalent geometry : angle 0.65610 / 0.32 (11754) hydrogen bonds : bond 0.02618 / 1.77 ( 160) hydrogen bonds : angle 5.43216 / 3.82 ( 444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8322 (Cg_exo) cc_final: 0.8065 (Cg_endo) REVERT: C 29 MET cc_start: 0.5969 (ttm) cc_final: 0.5632 (ttp) REVERT: D 143 MET cc_start: 0.6502 (mmm) cc_final: 0.5146 (mpp) outliers start: 26 outliers final: 17 residues processed: 118 average time/residue: 0.0641 time to fit residues: 11.6292 Evaluate side-chains 116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [31, 99, 53, 24, 107, 103, 12, 87, 111, 29, 112] chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 112 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.4900 r_free = 0.4900 target = 0.152149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.131206 restraints weight = 22440.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.133546 restraints weight = 16498.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.135927 restraints weight = 12421.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.136369 restraints weight = 9577.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.137148 restraints weight = 9646.342| |-----------------------------------------------------------------------------| r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8659 Z= 0.121 Angle : 0.644 14.865 11754 Z= 0.304 Chirality : 0.046 0.319 1434 Planarity : 0.003 0.026 1540 Dihedral : 4.849 54.645 1295 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.89 % Favored : 92.52 % Rotamer: Outliers : 2.90 % Allowed : 20.68 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.24), residues: 1190 helix: -1.76 (0.27), residues: 337 sheet: -0.45 (0.36), residues: 241 loop : -1.61 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.004 0.001 TYR D 222 PHE 0.014 0.001 PHE D 145 HIS 0.001 0.001 HIS C 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8659) covalent geometry : angle 0.64423 / 0.30 (11754) hydrogen bonds : bond 0.02205 / 1.52 ( 160) hydrogen bonds : angle 5.18366 / 3.63 ( 444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8309 (Cg_exo) cc_final: 0.8045 (Cg_endo) REVERT: B 118 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6897 (mt-10) REVERT: B 220 MET cc_start: 0.5007 (mmp) cc_final: 0.4687 (mmm) REVERT: C 29 MET cc_start: 0.5787 (ttm) cc_final: 0.5546 (ttp) REVERT: C 302 MET cc_start: 0.5147 (tpt) cc_final: 0.4851 (tpt) REVERT: D 143 MET cc_start: 0.6523 (mmm) cc_final: 0.5590 (mpp) REVERT: D 241 GLU cc_start: 0.5642 (OUTLIER) cc_final: 0.5036 (pm20) outliers start: 24 outliers final: 18 residues processed: 114 average time/residue: 0.0682 time to fit residues: 11.8642 Evaluate side-chains 113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 206 MET Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [55, 45, 50, 18, 37, 92, 1, 66, 84, 100, 43] chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.4878 r_free = 0.4878 target = 0.150560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.129701 restraints weight = 22408.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.132143 restraints weight = 16535.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.134205 restraints weight = 12413.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.134881 restraints weight = 9805.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.135631 restraints weight = 9647.885| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8659 Z= 0.122 Angle : 0.655 15.305 11754 Z= 0.308 Chirality : 0.046 0.331 1434 Planarity : 0.003 0.031 1540 Dihedral : 4.934 58.237 1295 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.31 % Favored : 92.10 % Rotamer: Outliers : 2.78 % Allowed : 21.40 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.24), residues: 1190 helix: -1.68 (0.27), residues: 342 sheet: -0.53 (0.35), residues: 254 loop : -1.62 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.006 0.001 TYR D 222 PHE 0.014 0.001 PHE D 145 HIS 0.001 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 8659) covalent geometry : angle 0.65481 / 0.31 (11754) hydrogen bonds : bond 0.02227 / 1.52 ( 160) hydrogen bonds : angle 5.16675 / 3.62 ( 444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8098 (Cg_endo) REVERT: B 97 MET cc_start: 0.6228 (ptm) cc_final: 0.6008 (ppp) REVERT: B 118 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: B 220 MET cc_start: 0.5137 (mmp) cc_final: 0.4555 (mmm) REVERT: C 29 MET cc_start: 0.5701 (ttm) cc_final: 0.5451 (ttp) REVERT: D 104 MET cc_start: 0.8093 (mmm) cc_final: 0.7819 (mmt) REVERT: D 143 MET cc_start: 0.6436 (mmm) cc_final: 0.5494 (mpp) REVERT: D 241 GLU cc_start: 0.5347 (OUTLIER) cc_final: 0.4748 (pm20) REVERT: D 242 MET cc_start: 0.8077 (ppp) cc_final: 0.7713 (ppp) outliers start: 23 outliers final: 17 residues processed: 111 average time/residue: 0.0627 time to fit residues: 11.0006 Evaluate side-chains 112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 301 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [3, 37, 13, 18, 33, 24, 1, 104, 109, 82, 80] chunk 3 optimal weight: 0.0970 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 80 optimal weight: 5.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.4895 r_free = 0.4895 target = 0.151589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.130828 restraints weight = 22187.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.133443 restraints weight = 16337.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.135436 restraints weight = 12174.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.136179 restraints weight = 9624.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.136804 restraints weight = 9518.516| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8659 Z= 0.113 Angle : 0.652 15.452 11754 Z= 0.305 Chirality : 0.046 0.320 1434 Planarity : 0.002 0.026 1540 Dihedral : 4.838 54.211 1295 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.30 % Favored : 93.11 % Rotamer: Outliers : 2.54 % Allowed : 21.89 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.24), residues: 1190 helix: -1.67 (0.27), residues: 351 sheet: -0.52 (0.35), residues: 254 loop : -1.56 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.006 0.001 TYR D 222 PHE 0.012 0.001 PHE D 145 HIS 0.001 0.000 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8659) covalent geometry : angle 0.65243 / 0.30 (11754) hydrogen bonds : bond 0.02062 / 1.42 ( 160) hydrogen bonds : angle 5.02839 / 3.52 ( 444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8356 (Cg_exo) cc_final: 0.8080 (Cg_endo) REVERT: B 97 MET cc_start: 0.6161 (ptm) cc_final: 0.5754 (ppp) REVERT: B 118 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: B 220 MET cc_start: 0.5099 (mmp) cc_final: 0.4560 (mmm) REVERT: C 29 MET cc_start: 0.5620 (ttm) cc_final: 0.5411 (ttp) REVERT: D 143 MET cc_start: 0.6529 (mmm) cc_final: 0.5103 (mpp) REVERT: D 241 GLU cc_start: 0.5404 (OUTLIER) cc_final: 0.4799 (pm20) REVERT: D 242 MET cc_start: 0.8085 (ppp) cc_final: 0.7786 (ppp) outliers start: 21 outliers final: 17 residues processed: 111 average time/residue: 0.0633 time to fit residues: 10.9840 Evaluate side-chains 113 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [5, 38, 46, 55, 92, 110, 41, 111, 28, 31, 99] chunk 5 optimal weight: 0.0970 chunk 38 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 92 optimal weight: 0.2980 chunk 110 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.151032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.130285 restraints weight = 22210.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.132789 restraints weight = 16405.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.134798 restraints weight = 12330.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.135474 restraints weight = 9726.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.136269 restraints weight = 9615.340| |-----------------------------------------------------------------------------| r_work (final): 0.4646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.5714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8659 Z= 0.115 Angle : 0.653 15.178 11754 Z= 0.306 Chirality : 0.046 0.324 1434 Planarity : 0.002 0.027 1540 Dihedral : 4.849 55.609 1295 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.81 % Favored : 92.61 % Rotamer: Outliers : 2.90 % Allowed : 21.77 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.24), residues: 1190 helix: -1.60 (0.27), residues: 346 sheet: -0.46 (0.36), residues: 250 loop : -1.53 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.006 0.001 TYR D 222 PHE 0.012 0.001 PHE D 145 HIS 0.001 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 8659) covalent geometry : angle 0.65275 / 0.31 (11754) hydrogen bonds : bond 0.02054 / 1.41 ( 160) hydrogen bonds : angle 4.99604 / 3.50 ( 444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.8352 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: A 217 MET cc_start: 0.7151 (tpp) cc_final: 0.6554 (tpp) REVERT: B 97 MET cc_start: 0.6118 (ptm) cc_final: 0.5831 (ppp) REVERT: B 118 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6669 (mt-10) REVERT: B 220 MET cc_start: 0.5091 (mmp) cc_final: 0.4584 (mmm) REVERT: D 143 MET cc_start: 0.6422 (mmm) cc_final: 0.5504 (mpp) REVERT: D 241 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.4790 (pm20) REVERT: D 242 MET cc_start: 0.8118 (ppp) cc_final: 0.7901 (ppp) outliers start: 24 outliers final: 18 residues processed: 114 average time/residue: 0.0563 time to fit residues: 10.1175 Evaluate side-chains 115 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain B residue 104 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 MET Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 241 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: [113, 28, 82, 33, 111, 12, 60, 24, 64, 101, 50] chunk 113 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 148 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 = 0.4832 r_free = 0.4832 target = 0.146737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.126106 restraints weight = 22723.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.128292 restraints weight = 17079.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.130234 restraints weight = 13070.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.130458 restraints weight = 10463.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.130850 restraints weight = 10140.630| |-----------------------------------------------------------------------------| r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8659 Z= 0.156 Angle : 0.726 17.119 11754 Z= 0.342 Chirality : 0.047 0.309 1434 Planarity : 0.003 0.031 1540 Dihedral : 5.326 62.908 1295 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.57 % Favored : 90.84 % Rotamer: Outliers : 2.66 % Allowed : 21.89 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.24), residues: 1190 helix: -1.59 (0.26), residues: 354 sheet: -0.71 (0.35), residues: 247 loop : -1.74 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 235 TYR 0.010 0.002 TYR D 222 PHE 0.020 0.002 PHE D 145 HIS 0.003 0.001 HIS C 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 8659) covalent geometry : angle 0.72579 / 0.34 (11754) hydrogen bonds : bond 0.02660 / 1.78 ( 160) hydrogen bonds : angle 5.49711 / 3.85 ( 444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1441.10 seconds wall clock time: 25 minutes 34.04 seconds (1534.04 seconds total)