Starting phenix.real_space_refine on Fri Aug 7 07:22:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q2a_72154/08_2026/9q2a_72154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q2a_72154/08_2026/9q2a_72154.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q2a_72154/08_2026/9q2a_72154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q2a_72154/08_2026/9q2a_72154.map" model { file = "/net/cci-nas-00/data/ceres_data/9q2a_72154/08_2026/9q2a_72154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q2a_72154/08_2026/9q2a_72154_trim.cif" } resolution = 2.67 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= 0.005 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: 6 Type Number sf(0) Gaussians P 33 5.49 5 Mg 6 5.21 5 S 110 5.16 5 C 12207 2.51 5 N 3379 2.21 5 O 3736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19471 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2650 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 11, 'TRANS': 324} Chain breaks: 1 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2510 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 313} Chain breaks: 1 Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2494 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 11, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2299 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 296} Chain breaks: 2 Chain: "G" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2279 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 288} Chain breaks: 2 Chain: "H" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "I" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2376 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 298} Chain breaks: 1 Chain: "R" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2449 Classifications: {'peptide': 318} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 297} Chain breaks: 2 Chain: "X" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1906 Classifications: {'peptide': 235} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 19471 At special positions: 0 Unit cell: (117.684, 129.826, 172.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 110 16.00 P 33 15.00 Mg 6 11.99 O 3736 8.00 N 3379 7.00 C 12207 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 814.8 milliseconds 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 18 sheets defined 53.4% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 13 through 17 Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 34 through 40 removed outlier: 3.677A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 53 through 69 Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 130 through 142 removed outlier: 3.663A pdb=" N LEU A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 165 through 188 Processing helix chain 'A' and resid 189 through 199 removed outlier: 3.609A pdb=" N ASP A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 215 through 233 Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 244 through 249 removed outlier: 3.834A pdb=" N PHE A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 277 Processing helix chain 'A' and resid 303 through 309 removed outlier: 4.138A pdb=" N ALA A 309 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 45 through 59 Processing helix chain 'B' and resid 67 through 75 removed outlier: 3.568A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 75 " --> pdb=" O LYS B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 113 through 126 Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 166 through 177 removed outlier: 3.640A pdb=" N LEU B 170 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'B' and resid 194 through 203 removed outlier: 3.976A pdb=" N GLU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.741A pdb=" N VAL B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.980A pdb=" N TRP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.839A pdb=" N GLU C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 143 through 144 No H-bonds generated for 'chain 'C' and resid 143 through 144' Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 188 Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 244 through 250 removed outlier: 4.117A pdb=" N PHE C 248 " --> pdb=" O ILE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 79 removed outlier: 3.960A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 93 Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 154 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 193 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.985A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 240 removed outlier: 3.775A pdb=" N ALA D 225 " --> pdb=" O ARG D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 removed outlier: 4.050A pdb=" N TRP D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 264 through 269' Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'G' and resid 26 through 32 removed outlier: 3.745A pdb=" N GLN G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 45 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.867A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 4.041A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 106 through 111 Processing helix chain 'G' and resid 132 through 145 removed outlier: 3.923A pdb=" N GLN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 176 removed outlier: 3.844A pdb=" N GLU G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 187 Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.572A pdb=" N GLN G 200 " --> pdb=" O ASN G 196 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN G 202 " --> pdb=" O ASP G 198 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 203 " --> pdb=" O HIS G 199 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 removed outlier: 4.575A pdb=" N LEU G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 260 Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.808A pdb=" N GLY I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 45 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.568A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 97 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.516A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL I 212 " --> pdb=" O SER I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.583A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.925A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 6 Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 23 through 30 removed outlier: 3.813A pdb=" N PHE R 30 " --> pdb=" O GLU R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 42 through 58 Processing helix chain 'R' and resid 65 through 71 Processing helix chain 'R' and resid 75 through 80 removed outlier: 3.662A pdb=" N HIS R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 93 Processing helix chain 'R' and resid 112 through 125 removed outlier: 4.156A pdb=" N GLN R 125 " --> pdb=" O CYS R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 131 removed outlier: 5.962A pdb=" N GLN R 129 " --> pdb=" O PHE R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 162 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 166 through 173 Processing helix chain 'R' and resid 174 through 178 Processing helix chain 'R' and resid 186 through 204 removed outlier: 4.346A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Proline residue: R 199 - end of helix Processing helix chain 'R' and resid 215 through 223 removed outlier: 3.876A pdb=" N PHE R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE R 223 " --> pdb=" O PHE R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 249 removed outlier: 3.596A pdb=" N ARG R 233 " --> pdb=" O ALA R 229 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG R 243 " --> pdb=" O GLY R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 290 removed outlier: 3.706A pdb=" N TRP R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 28 Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 88 through 100 Processing helix chain 'X' and resid 104 through 114 removed outlier: 3.849A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 140 removed outlier: 4.086A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N CYS X 138 " --> pdb=" O GLU X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 153 Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 170 through 188 Processing helix chain 'X' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 86 removed outlier: 6.040A pdb=" N VAL B 138 " --> pdb=" O HIS B 178 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N TYR B 180 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR B 140 " --> pdb=" O TYR B 180 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 137 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL B 207 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 139 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU B 209 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 141 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ILE B 254 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 207 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N THR B 256 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 209 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 104 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASN B 257 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE B 106 " --> pdb=" O ASN B 257 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 307 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 347 removed outlier: 4.004A pdb=" N ARG A 322 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 312 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR A 120 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU A 313 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLU A 122 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE A 315 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS A 124 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TRP A 317 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR A 121 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN A 284 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILE A 123 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU A 154 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA A 155 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N PHE A 211 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 157 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU R 63 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 removed outlier: 5.427A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS C 119 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU C 282 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR C 121 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ASN C 284 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 123 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AA7, first strand: chain 'B' and resid 259 through 260 Processing sheet with id=AA8, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.517A pdb=" N CYS C 85 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N THR D 103 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN D 249 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ILE D 105 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 102 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE D 276 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU D 104 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU D 278 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL D 106 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N THR D 280 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU D 277 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU D 295 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ASP D 279 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA D 293 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AB1, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.325A pdb=" N VAL X 78 " --> pdb=" O PHE X 116 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL X 118 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE X 80 " --> pdb=" O VAL X 118 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP X 42 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA X 193 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU X 44 " --> pdb=" O ALA X 193 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR X 195 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE X 46 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 251 through 253 Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 88 removed outlier: 4.337A pdb=" N THR G 87 " --> pdb=" O ILE R 181 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA R 137 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLU R 182 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N TYR R 139 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY R 136 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU R 209 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE R 102 " --> pdb=" O VAL R 294 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU R 296 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU R 104 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA R 298 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA R 106 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ARG R 300 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARG R 295 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG R 313 " --> pdb=" O TYR R 330 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N SER R 327 " --> pdb=" O GLY R 342 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N GLY R 342 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER R 329 " --> pdb=" O THR R 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB5, first strand: chain 'G' and resid 333 through 335 removed outlier: 4.229A pdb=" N PHE G 327 " --> pdb=" O ARG G 310 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG G 310 " --> pdb=" O PHE G 327 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU G 219 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N THR G 266 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL G 221 " --> pdb=" O THR G 266 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N TYR G 159 " --> pdb=" O ALA G 190 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA G 192 " --> pdb=" O TYR G 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'I' and resid 189 through 193 removed outlier: 6.766A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU I 218 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA I 217 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL I 264 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR I 309 " --> pdb=" O GLY I 305 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AB9, first strand: chain 'R' and resid 81 through 82 985 hydrogen bonds defined for protein. 2778 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: 4.47 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6210 1.34 - 1.45: 2259 1.45 - 1.57: 11111 1.57 - 1.69: 59 1.69 - 1.81: 161 Bond restraints: 19800 Sorted by residual: bond pdb=" C3' DT H 7 " pdb=" C2' DT H 7 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.91e+00 bond pdb=" C2' DT H 7 " pdb=" C1' DT H 7 " ideal model delta sigma weight residual 1.518 1.537 -0.019 1.00e-02 1.00e+04 3.69e+00 bond pdb=" C1' DT H 6 " pdb=" N1 DT H 6 " ideal model delta sigma weight residual 1.468 1.492 -0.024 1.40e-02 5.10e+03 3.02e+00 bond pdb=" C1' DT H 7 " pdb=" N1 DT H 7 " ideal model delta sigma weight residual 1.468 1.491 -0.023 1.40e-02 5.10e+03 2.58e+00 bond pdb=" C1' DT H 11 " pdb=" N1 DT H 11 " ideal model delta sigma weight residual 1.468 1.490 -0.022 1.40e-02 5.10e+03 2.56e+00 ... (remaining 19795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 26160 1.40 - 2.80: 560 2.80 - 4.20: 85 4.20 - 5.60: 23 5.60 - 7.00: 18 Bond angle restraints: 26846 Sorted by residual: angle pdb=" N3 DT H 17 " pdb=" C4 DT H 17 " pdb=" O4 DT H 17 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT H 13 " pdb=" C4 DT H 13 " pdb=" O4 DT H 13 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT H 14 " pdb=" C4 DT H 14 " pdb=" O4 DT H 14 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT H 9 " pdb=" C4 DT H 9 " pdb=" O4 DT H 9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT H 18 " pdb=" C4 DT H 18 " pdb=" O4 DT H 18 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 26841 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.39: 11852 31.39 - 62.79: 204 62.79 - 94.18: 22 94.18 - 125.58: 0 125.58 - 156.97: 1 Dihedral angle restraints: 12079 sinusoidal: 5057 harmonic: 7022 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 143.03 156.97 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" CA GLU B 193 " pdb=" C GLU B 193 " pdb=" N SER B 194 " pdb=" CA SER B 194 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE B 78 " pdb=" C PHE B 78 " pdb=" N SER B 79 " pdb=" CA SER B 79 " ideal model delta harmonic sigma weight residual 180.00 164.53 15.47 0 5.00e+00 4.00e-02 9.57e+00 ... (remaining 12076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2793 0.059 - 0.117: 314 0.117 - 0.176: 17 0.176 - 0.234: 0 0.234 - 0.293: 15 Chirality restraints: 3139 Sorted by residual: chirality pdb=" C2' ATP X 301 " pdb=" C1' ATP X 301 " pdb=" C3' ATP X 301 " pdb=" O2' ATP X 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP R 401 " pdb=" C1' ATP R 401 " pdb=" C3' ATP R 401 " pdb=" O2' ATP R 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C2' ATP D 401 " pdb=" C1' ATP D 401 " pdb=" C3' ATP D 401 " pdb=" O2' ATP D 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 3136 not shown) Planarity restraints: 3350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 241 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C ARG G 241 " 0.024 2.00e-02 2.50e+03 pdb=" O ARG G 241 " -0.009 2.00e-02 2.50e+03 pdb=" N GLN G 242 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 64 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO D 65 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 65 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 65 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 238 " -0.005 2.00e-02 2.50e+03 9.81e-03 9.63e-01 pdb=" C LEU R 238 " 0.017 2.00e-02 2.50e+03 pdb=" O LEU R 238 " -0.006 2.00e-02 2.50e+03 pdb=" N GLY R 239 " -0.006 2.00e-02 2.50e+03 ... (remaining 3347 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 170 2.44 - 3.06: 14662 3.06 - 3.67: 29904 3.67 - 4.29: 47235 4.29 - 4.90: 78385 Nonbonded interactions: 170356 Sorted by model distance: nonbonded pdb=" O3B ATP R 401 " pdb="MG MG R 402 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR X 55 " pdb="MG MG X 302 " model vdw 1.891 2.170 nonbonded pdb=" O3B ATP B 401 " pdb="MG MG B 402 " model vdw 1.905 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 1.916 2.170 nonbonded pdb=" O2B ATP R 401 " pdb="MG MG R 402 " model vdw 1.953 2.170 ... (remaining 170351 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 9 through 67 or resid 83 through 288 or resid 297 through \ 348 or resid 402)) selection = (chain 'C' and (resid 9 through 348 or resid 402)) } ncs_group { reference = chain 'G' selection = (chain 'I' and (resid 22 through 232 or resid 237 through 269 or resid 288 throu \ gh 339)) } 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 individual isotropic 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: 5.840 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.340 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 : 0.006 0.831 19802 Z= 0.607 Angle : 0.533 6.997 26846 Z= 0.351 Chirality : 0.041 0.293 3139 Planarity : 0.002 0.027 3350 Dihedral : 11.217 156.975 7531 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 40.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.38 % Rotamer: Outliers : 1.45 % Allowed : 4.15 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.18), residues: 2400 helix: 2.18 (0.17), residues: 1111 sheet: -0.04 (0.26), residues: 400 loop : -0.60 (0.22), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 310 TYR 0.005 0.001 TYR G 315 PHE 0.007 0.001 PHE C 346 TRP 0.006 0.001 TRP R 47 HIS 0.003 0.000 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.14 (19800) covalent geometry : angle 0.53260 / 0.35 (26846) hydrogen bonds : bond 0.15172 / 10.13 ( 985) hydrogen bonds : angle 6.47228 / 4.68 ( 2778) Misc. bond : bond 0.58774 / 30.93 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 373 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8424 (ptmm) REVERT: B 17 ASP cc_start: 0.8396 (m-30) cc_final: 0.8023 (m-30) REVERT: B 29 ASP cc_start: 0.8369 (m-30) cc_final: 0.7924 (m-30) REVERT: B 68 TYR cc_start: 0.8678 (t80) cc_final: 0.8428 (t80) REVERT: B 230 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8327 (mm-30) REVERT: C 10 MET cc_start: 0.8009 (ptm) cc_final: 0.7336 (ptt) REVERT: D 18 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8255 (mm-40) REVERT: D 292 MET cc_start: 0.6701 (mmm) cc_final: 0.5879 (tpt) REVERT: G 72 ASP cc_start: 0.8185 (m-30) cc_final: 0.7945 (p0) REVERT: G 73 LYS cc_start: 0.8556 (tptm) cc_final: 0.8244 (tmtt) REVERT: G 84 MET cc_start: 0.6914 (mmm) cc_final: 0.6288 (mpt) REVERT: G 196 ASN cc_start: 0.7222 (p0) cc_final: 0.6743 (p0) REVERT: G 205 TYR cc_start: 0.9350 (m-80) cc_final: 0.8964 (m-80) REVERT: I 250 ARG cc_start: 0.7638 (tpp80) cc_final: 0.6844 (ptt90) REVERT: X 27 ILE cc_start: 0.8974 (mt) cc_final: 0.8720 (mp) REVERT: X 28 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7138 (tp30) outliers start: 30 outliers final: 8 residues processed: 392 average time/residue: 0.6029 time to fit residues: 264.9194 Evaluate side-chains 190 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 216 TYR Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain X residue 28 GLU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 HIS A 250 HIS B 116 GLN B 130 ASN B 298 ASN C 274 ASN D 123 ASN G 94 GLN G 138 HIS ** G 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN I 101 GLN I 145 GLN I 242 GLN I 272 GLN R 344 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.133509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.090717 restraints weight = 38580.022| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.06 r_work: 0.3420 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19802 Z= 0.177 Angle : 0.668 13.166 26846 Z= 0.337 Chirality : 0.044 0.242 3139 Planarity : 0.005 0.048 3350 Dihedral : 11.288 138.528 2988 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 2.46 % Allowed : 12.54 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2400 helix: 1.78 (0.16), residues: 1129 sheet: -0.01 (0.26), residues: 386 loop : -0.52 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 66 TYR 0.019 0.002 TYR G 191 PHE 0.016 0.002 PHE G 126 TRP 0.028 0.002 TRP D 314 HIS 0.009 0.001 HIS R 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (19800) covalent geometry : angle 0.66823 / 0.34 (26846) hydrogen bonds : bond 0.04041 / 2.73 ( 985) hydrogen bonds : angle 4.97952 / 3.54 ( 2778) Misc. bond : bond 0.00241 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4910 (mmm) cc_final: 0.4311 (mmm) REVERT: A 193 ARG cc_start: 0.8580 (ttp-110) cc_final: 0.8307 (ttp-110) REVERT: A 289 LYS cc_start: 0.8491 (ttpp) cc_final: 0.8119 (ptmm) REVERT: A 303 GLU cc_start: 0.7791 (pm20) cc_final: 0.7585 (tt0) REVERT: B 29 ASP cc_start: 0.8548 (m-30) cc_final: 0.8052 (m-30) REVERT: C 10 MET cc_start: 0.7690 (ptm) cc_final: 0.7445 (ptt) REVERT: C 118 MET cc_start: 0.8848 (mtp) cc_final: 0.8379 (mtm) REVERT: G 72 ASP cc_start: 0.7977 (m-30) cc_final: 0.7747 (p0) REVERT: G 84 MET cc_start: 0.7382 (mmm) cc_final: 0.6960 (mpp) REVERT: G 91 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (mp0) REVERT: G 158 MET cc_start: 0.6028 (ttm) cc_final: 0.5280 (ttm) REVERT: G 196 ASN cc_start: 0.7427 (p0) cc_final: 0.7087 (p0) REVERT: G 216 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5727 (m-80) REVERT: G 222 ASP cc_start: 0.6393 (t0) cc_final: 0.6173 (m-30) REVERT: I 125 MET cc_start: 0.0526 (pmm) cc_final: -0.0010 (pmm) REVERT: I 140 LEU cc_start: 0.8606 (mp) cc_final: 0.8401 (tp) REVERT: I 187 ASP cc_start: 0.2390 (OUTLIER) cc_final: 0.2031 (p0) REVERT: I 250 ARG cc_start: 0.6987 (tpp80) cc_final: 0.6587 (ptt90) REVERT: I 251 MET cc_start: 0.5068 (tpt) cc_final: 0.4052 (mtt) REVERT: I 326 MET cc_start: 0.6054 (pmm) cc_final: 0.5320 (tmm) REVERT: R 22 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8006 (tppt) REVERT: R 72 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7927 (mttp) REVERT: R 233 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7644 (ttp-110) outliers start: 51 outliers final: 21 residues processed: 243 average time/residue: 0.5771 time to fit residues: 158.5037 Evaluate side-chains 180 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 216 TYR Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 107 ILE Chi-restraints excluded: chain X residue 123 SER Chi-restraints excluded: chain X residue 200 GLN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 149 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN G 23 GLN ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.130041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086336 restraints weight = 38978.677| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.15 r_work: 0.3342 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 19802 Z= 0.256 Angle : 0.653 8.986 26846 Z= 0.334 Chirality : 0.045 0.158 3139 Planarity : 0.005 0.048 3350 Dihedral : 10.876 120.994 2974 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 2.99 % Allowed : 13.46 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.17), residues: 2400 helix: 1.53 (0.16), residues: 1126 sheet: -0.18 (0.25), residues: 395 loop : -0.55 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 300 TYR 0.024 0.002 TYR G 205 PHE 0.022 0.002 PHE G 259 TRP 0.013 0.002 TRP D 314 HIS 0.008 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 (19800) covalent geometry : angle 0.65329 / 0.33 (26846) hydrogen bonds : bond 0.04029 / 2.70 ( 985) hydrogen bonds : angle 4.92620 / 3.47 ( 2778) Misc. bond : bond 0.00272 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 170 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8338 (ttp-110) REVERT: A 289 LYS cc_start: 0.8439 (ttpp) cc_final: 0.8076 (ptmm) REVERT: B 29 ASP cc_start: 0.8493 (m-30) cc_final: 0.7979 (m-30) REVERT: B 218 LYS cc_start: 0.7356 (tttt) cc_final: 0.6928 (mptt) REVERT: C 10 MET cc_start: 0.7731 (ptm) cc_final: 0.7522 (ptt) REVERT: C 197 GLU cc_start: 0.8253 (mp0) cc_final: 0.7861 (mp0) REVERT: D 292 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6190 (tpt) REVERT: G 84 MET cc_start: 0.7318 (mmm) cc_final: 0.6942 (mpp) REVERT: G 158 MET cc_start: 0.5668 (ttm) cc_final: 0.5077 (ttm) REVERT: G 196 ASN cc_start: 0.7492 (p0) cc_final: 0.7156 (p0) REVERT: G 211 MET cc_start: 0.7796 (tpt) cc_final: 0.7564 (tpt) REVERT: G 222 ASP cc_start: 0.6766 (t0) cc_final: 0.6382 (m-30) REVERT: G 294 HIS cc_start: 0.8038 (m90) cc_final: 0.7819 (m-70) REVERT: I 125 MET cc_start: 0.1002 (pmm) cc_final: 0.0506 (pmm) REVERT: I 140 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8446 (tp) REVERT: I 250 ARG cc_start: 0.7068 (tpp80) cc_final: 0.6579 (ptt90) REVERT: I 251 MET cc_start: 0.5090 (tpt) cc_final: 0.3936 (mtt) REVERT: I 326 MET cc_start: 0.6230 (pmm) cc_final: 0.5452 (tmm) REVERT: R 18 LYS cc_start: 0.9516 (ttpp) cc_final: 0.9264 (tmmt) REVERT: R 72 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7952 (mttp) REVERT: R 233 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7647 (ttp-110) REVERT: X 84 ASP cc_start: 0.8429 (p0) cc_final: 0.8057 (p0) outliers start: 62 outliers final: 29 residues processed: 217 average time/residue: 0.5546 time to fit residues: 137.5335 Evaluate side-chains 188 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain R residue 9 ASN Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 123 SER Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 196 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 167 optimal weight: 30.0000 chunk 159 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 169 optimal weight: 30.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN I 93 HIS X 40 HIS X 167 ASN X 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.129554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.085622 restraints weight = 38882.688| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.20 r_work: 0.3326 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19802 Z= 0.250 Angle : 0.636 12.741 26846 Z= 0.324 Chirality : 0.044 0.188 3139 Planarity : 0.004 0.059 3350 Dihedral : 10.857 120.399 2972 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 3.09 % Allowed : 13.94 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.17), residues: 2400 helix: 1.35 (0.15), residues: 1127 sheet: -0.29 (0.25), residues: 398 loop : -0.58 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 322 TYR 0.027 0.002 TYR G 205 PHE 0.023 0.002 PHE G 129 TRP 0.011 0.002 TRP R 47 HIS 0.007 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.25 (19800) covalent geometry : angle 0.63601 / 0.32 (26846) hydrogen bonds : bond 0.03799 / 2.53 ( 985) hydrogen bonds : angle 4.88971 / 3.43 ( 2778) Misc. bond : bond 0.00261 / 0.13 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 162 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4982 (mmm) cc_final: 0.4562 (mmp) REVERT: A 193 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8318 (ttp-110) REVERT: A 253 ASP cc_start: 0.7882 (m-30) cc_final: 0.7153 (OUTLIER) REVERT: A 289 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7459 (tptt) REVERT: B 29 ASP cc_start: 0.8472 (m-30) cc_final: 0.7958 (m-30) REVERT: B 127 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 229 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8650 (tmtt) REVERT: C 118 MET cc_start: 0.8917 (mtp) cc_final: 0.8591 (mtm) REVERT: C 197 GLU cc_start: 0.8414 (mp0) cc_final: 0.8017 (mp0) REVERT: D 292 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6159 (tpt) REVERT: G 84 MET cc_start: 0.7620 (mmm) cc_final: 0.7301 (mpp) REVERT: G 158 MET cc_start: 0.5795 (ttm) cc_final: 0.5160 (ttm) REVERT: G 196 ASN cc_start: 0.7474 (p0) cc_final: 0.7114 (p0) REVERT: I 140 LEU cc_start: 0.8663 (mp) cc_final: 0.8435 (tp) REVERT: I 158 MET cc_start: 0.3602 (mmt) cc_final: 0.2609 (mpt) REVERT: I 250 ARG cc_start: 0.6990 (tpp80) cc_final: 0.6515 (ptt90) REVERT: I 251 MET cc_start: 0.5201 (tpt) cc_final: 0.3960 (mtt) REVERT: I 326 MET cc_start: 0.6113 (pmm) cc_final: 0.5549 (tmt) REVERT: R 72 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8047 (mttp) REVERT: R 108 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7325 (mtp180) REVERT: R 233 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7754 (ttp-110) REVERT: X 42 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: X 84 ASP cc_start: 0.8457 (p0) cc_final: 0.8149 (p0) outliers start: 64 outliers final: 31 residues processed: 212 average time/residue: 0.5826 time to fit residues: 141.0414 Evaluate side-chains 182 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain R residue 9 ASN Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 108 ARG Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 123 SER Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 30 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 110 optimal weight: 0.5980 chunk 128 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 30 GLN G 294 HIS X 167 ASN X 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.131288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.087948 restraints weight = 38579.641| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.19 r_work: 0.3361 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19802 Z= 0.146 Angle : 0.579 10.943 26846 Z= 0.295 Chirality : 0.041 0.154 3139 Planarity : 0.004 0.050 3350 Dihedral : 10.693 125.774 2972 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 2.65 % Allowed : 14.86 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.17), residues: 2400 helix: 1.47 (0.16), residues: 1129 sheet: -0.35 (0.25), residues: 413 loop : -0.53 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.032 0.001 TYR G 205 PHE 0.026 0.001 PHE G 129 TRP 0.010 0.002 TRP A 305 HIS 0.007 0.001 HIS G 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (19800) covalent geometry : angle 0.57880 / 0.30 (26846) hydrogen bonds : bond 0.03310 / 2.21 ( 985) hydrogen bonds : angle 4.69391 / 3.30 ( 2778) Misc. bond : bond 0.00184 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8333 (ttp-110) REVERT: A 289 LYS cc_start: 0.8423 (ttpp) cc_final: 0.7448 (tptt) REVERT: B 1 MET cc_start: 0.6921 (tpp) cc_final: 0.6704 (tmt) REVERT: B 29 ASP cc_start: 0.8455 (m-30) cc_final: 0.7936 (m-30) REVERT: B 218 LYS cc_start: 0.7218 (tttt) cc_final: 0.6901 (mptt) REVERT: B 229 LYS cc_start: 0.9052 (ttpp) cc_final: 0.8716 (tmtt) REVERT: C 118 MET cc_start: 0.8910 (mtp) cc_final: 0.8469 (mtm) REVERT: C 194 LYS cc_start: 0.8883 (tptp) cc_final: 0.8564 (tptp) REVERT: C 197 GLU cc_start: 0.8436 (mp0) cc_final: 0.8215 (mp0) REVERT: G 84 MET cc_start: 0.7692 (mmm) cc_final: 0.7337 (mpp) REVERT: G 158 MET cc_start: 0.5426 (ttm) cc_final: 0.4713 (ttm) REVERT: G 196 ASN cc_start: 0.7481 (p0) cc_final: 0.7125 (p0) REVERT: G 222 ASP cc_start: 0.5755 (OUTLIER) cc_final: 0.5120 (m-30) REVERT: G 294 HIS cc_start: 0.7906 (m90) cc_final: 0.7633 (m-70) REVERT: I 125 MET cc_start: 0.0891 (pmm) cc_final: 0.0318 (pmm) REVERT: I 140 LEU cc_start: 0.8566 (mp) cc_final: 0.8363 (tp) REVERT: I 158 MET cc_start: 0.3680 (mmt) cc_final: 0.2722 (mpt) REVERT: I 187 ASP cc_start: 0.2348 (OUTLIER) cc_final: 0.2019 (p0) REVERT: I 250 ARG cc_start: 0.6917 (tpp80) cc_final: 0.6447 (ptt90) REVERT: I 251 MET cc_start: 0.5157 (tpt) cc_final: 0.3677 (mtp) REVERT: I 326 MET cc_start: 0.6131 (pmm) cc_final: 0.5571 (tmm) REVERT: R 72 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8081 (mttp) REVERT: R 233 ARG cc_start: 0.7977 (ttm110) cc_final: 0.7769 (ttp-110) REVERT: X 84 ASP cc_start: 0.8436 (p0) cc_final: 0.8030 (p0) outliers start: 55 outliers final: 30 residues processed: 205 average time/residue: 0.5238 time to fit residues: 122.9493 Evaluate side-chains 183 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain R residue 9 ASN Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 106 optimal weight: 0.7980 chunk 193 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 201 optimal weight: 0.0370 chunk 30 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN X 167 ASN X 196 GLN X 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.089524 restraints weight = 38652.487| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.14 r_work: 0.3384 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19802 Z= 0.130 Angle : 0.576 15.219 26846 Z= 0.290 Chirality : 0.041 0.371 3139 Planarity : 0.004 0.049 3350 Dihedral : 10.525 124.384 2972 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Rotamer: Outliers : 2.80 % Allowed : 15.20 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2400 helix: 1.55 (0.16), residues: 1131 sheet: -0.22 (0.26), residues: 412 loop : -0.53 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 162 TYR 0.022 0.001 TYR B 68 PHE 0.032 0.001 PHE G 259 TRP 0.010 0.001 TRP A 305 HIS 0.006 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19800) covalent geometry : angle 0.57565 / 0.29 (26846) hydrogen bonds : bond 0.03095 / 2.06 ( 985) hydrogen bonds : angle 4.58163 / 3.22 ( 2778) Misc. bond : bond 0.00141 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8590 (ttp-110) cc_final: 0.8343 (ttp-110) REVERT: A 277 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7735 (ttp-110) REVERT: A 289 LYS cc_start: 0.8413 (ttpp) cc_final: 0.7440 (tptt) REVERT: B 1 MET cc_start: 0.6885 (tpp) cc_final: 0.6634 (tpt) REVERT: B 29 ASP cc_start: 0.8406 (m-30) cc_final: 0.7903 (m-30) REVERT: B 229 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8706 (tmtt) REVERT: C 118 MET cc_start: 0.8925 (mtp) cc_final: 0.8478 (mtm) REVERT: C 194 LYS cc_start: 0.8877 (tptp) cc_final: 0.8533 (tptp) REVERT: C 197 GLU cc_start: 0.8465 (mp0) cc_final: 0.8213 (mp0) REVERT: D 292 MET cc_start: 0.6962 (tpt) cc_final: 0.6688 (tpt) REVERT: G 46 PHE cc_start: 0.7204 (m-80) cc_final: 0.6888 (m-80) REVERT: G 84 MET cc_start: 0.7912 (mmm) cc_final: 0.7544 (mpp) REVERT: G 96 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7487 (ttm110) REVERT: G 158 MET cc_start: 0.5417 (ttm) cc_final: 0.4763 (ttm) REVERT: G 196 ASN cc_start: 0.7491 (p0) cc_final: 0.7159 (p0) REVERT: G 222 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5432 (m-30) REVERT: I 125 MET cc_start: 0.0825 (pmm) cc_final: 0.0267 (pmm) REVERT: I 210 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3941 (ttt) REVERT: I 250 ARG cc_start: 0.6945 (tpp80) cc_final: 0.6518 (ptt90) REVERT: I 251 MET cc_start: 0.5206 (tpt) cc_final: 0.3739 (mtp) REVERT: I 326 MET cc_start: 0.6164 (pmm) cc_final: 0.5581 (tmt) REVERT: R 72 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8081 (mttp) REVERT: X 42 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7442 (t0) REVERT: X 83 THR cc_start: 0.8626 (p) cc_final: 0.8191 (p) REVERT: X 84 ASP cc_start: 0.8334 (p0) cc_final: 0.7915 (p0) outliers start: 58 outliers final: 30 residues processed: 209 average time/residue: 0.5304 time to fit residues: 127.0040 Evaluate side-chains 188 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 153 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain R residue 9 ASN Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 42 ASP Chi-restraints excluded: chain X residue 82 ASP Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 136 MET Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 9 optimal weight: 0.5980 chunk 172 optimal weight: 0.0370 chunk 109 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 156 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN G 294 HIS I 272 GLN ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 167 ASN X 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.132910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.090452 restraints weight = 38712.043| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 3.04 r_work: 0.3409 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19802 Z= 0.120 Angle : 0.575 12.933 26846 Z= 0.290 Chirality : 0.041 0.153 3139 Planarity : 0.004 0.047 3350 Dihedral : 10.354 120.990 2972 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.88 % Favored : 97.08 % Rotamer: Outliers : 2.32 % Allowed : 16.11 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.18), residues: 2400 helix: 1.60 (0.16), residues: 1132 sheet: -0.21 (0.25), residues: 412 loop : -0.52 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 11 TYR 0.035 0.001 TYR G 205 PHE 0.035 0.001 PHE G 259 TRP 0.010 0.001 TRP A 305 HIS 0.006 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19800) covalent geometry : angle 0.57537 / 0.29 (26846) hydrogen bonds : bond 0.02933 / 1.95 ( 985) hydrogen bonds : angle 4.47358 / 3.15 ( 2778) Misc. bond : bond 0.00138 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 171 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8587 (ttp-110) cc_final: 0.8349 (ttp-110) REVERT: A 277 ARG cc_start: 0.8228 (mtp-110) cc_final: 0.7807 (ttp-110) REVERT: A 289 LYS cc_start: 0.8409 (ttpp) cc_final: 0.7418 (tptt) REVERT: A 303 GLU cc_start: 0.7582 (pm20) cc_final: 0.7158 (tt0) REVERT: B 29 ASP cc_start: 0.8491 (m-30) cc_final: 0.7998 (m-30) REVERT: B 210 ASP cc_start: 0.8678 (t0) cc_final: 0.8443 (t70) REVERT: B 229 LYS cc_start: 0.9072 (ttpp) cc_final: 0.8722 (tmtt) REVERT: C 118 MET cc_start: 0.8916 (mtp) cc_final: 0.8471 (mtm) REVERT: C 194 LYS cc_start: 0.8865 (tptp) cc_final: 0.8507 (tptp) REVERT: C 197 GLU cc_start: 0.8477 (mp0) cc_final: 0.8190 (mp0) REVERT: G 46 PHE cc_start: 0.7275 (m-80) cc_final: 0.6938 (m-80) REVERT: G 84 MET cc_start: 0.7948 (mmm) cc_final: 0.7604 (mpp) REVERT: G 96 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7561 (ttm110) REVERT: G 158 MET cc_start: 0.5569 (ttm) cc_final: 0.4844 (ttm) REVERT: G 196 ASN cc_start: 0.7449 (p0) cc_final: 0.7139 (p0) REVERT: G 294 HIS cc_start: 0.7798 (m90) cc_final: 0.7525 (m-70) REVERT: I 125 MET cc_start: 0.0731 (pmm) cc_final: 0.0124 (pmm) REVERT: I 140 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7730 (mp) REVERT: I 187 ASP cc_start: 0.2555 (OUTLIER) cc_final: 0.2200 (p0) REVERT: I 210 MET cc_start: 0.4385 (OUTLIER) cc_final: 0.4166 (ttt) REVERT: I 250 ARG cc_start: 0.6651 (tpp80) cc_final: 0.6360 (ptt90) REVERT: I 251 MET cc_start: 0.5302 (tpt) cc_final: 0.3708 (mtp) REVERT: I 326 MET cc_start: 0.6125 (pmm) cc_final: 0.5482 (tmt) REVERT: R 11 ARG cc_start: 0.8964 (ptm-80) cc_final: 0.8728 (ptm160) REVERT: X 42 ASP cc_start: 0.8081 (m-30) cc_final: 0.7416 (t0) REVERT: X 84 ASP cc_start: 0.8251 (p0) cc_final: 0.7779 (p0) outliers start: 48 outliers final: 26 residues processed: 204 average time/residue: 0.5623 time to fit residues: 131.8132 Evaluate side-chains 192 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 345 SER Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 136 MET Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 46 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN ** R 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 167 ASN X 196 GLN X 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.131185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.088289 restraints weight = 38780.442| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.09 r_work: 0.3358 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19802 Z= 0.194 Angle : 0.619 12.935 26846 Z= 0.311 Chirality : 0.042 0.148 3139 Planarity : 0.004 0.044 3350 Dihedral : 10.481 112.537 2972 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.08 % Favored : 96.88 % Rotamer: Outliers : 2.70 % Allowed : 15.77 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2400 helix: 1.48 (0.16), residues: 1135 sheet: -0.28 (0.25), residues: 410 loop : -0.52 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 168 TYR 0.020 0.001 TYR B 68 PHE 0.040 0.002 PHE G 259 TRP 0.010 0.002 TRP R 47 HIS 0.005 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (19800) covalent geometry : angle 0.61892 / 0.31 (26846) hydrogen bonds : bond 0.03291 / 2.19 ( 985) hydrogen bonds : angle 4.60748 / 3.25 ( 2778) Misc. bond : bond 0.00187 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 LYS cc_start: 0.8426 (ttpp) cc_final: 0.7425 (tptt) REVERT: B 29 ASP cc_start: 0.8441 (m-30) cc_final: 0.7931 (m-30) REVERT: B 229 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8713 (tmtt) REVERT: C 118 MET cc_start: 0.8911 (mtp) cc_final: 0.8473 (mtm) REVERT: C 194 LYS cc_start: 0.8857 (tptp) cc_final: 0.8516 (tptp) REVERT: C 197 GLU cc_start: 0.8458 (mp0) cc_final: 0.8239 (mp0) REVERT: G 46 PHE cc_start: 0.7242 (m-80) cc_final: 0.6960 (m-80) REVERT: G 84 MET cc_start: 0.7910 (mmm) cc_final: 0.7528 (mpp) REVERT: G 96 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7546 (ttm110) REVERT: G 158 MET cc_start: 0.5454 (ttm) cc_final: 0.4838 (ttm) REVERT: G 196 ASN cc_start: 0.7544 (p0) cc_final: 0.7225 (p0) REVERT: G 215 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7694 (tpt-90) REVERT: I 125 MET cc_start: 0.0611 (pmm) cc_final: 0.0026 (pmm) REVERT: I 140 LEU cc_start: 0.7962 (tp) cc_final: 0.7743 (mp) REVERT: I 187 ASP cc_start: 0.2623 (OUTLIER) cc_final: 0.2259 (p0) REVERT: I 250 ARG cc_start: 0.6801 (tpp80) cc_final: 0.6327 (ptt90) REVERT: I 251 MET cc_start: 0.5230 (tpt) cc_final: 0.3619 (mtp) REVERT: I 326 MET cc_start: 0.6131 (pmm) cc_final: 0.5503 (tmt) REVERT: R 11 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8693 (ptm160) REVERT: R 18 LYS cc_start: 0.9199 (tmtt) cc_final: 0.8934 (ttpp) REVERT: R 40 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8962 (t0) REVERT: R 72 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8125 (mttp) REVERT: R 206 MET cc_start: 0.9155 (mtt) cc_final: 0.8950 (mtp) REVERT: X 42 ASP cc_start: 0.8143 (m-30) cc_final: 0.7463 (t0) REVERT: X 83 THR cc_start: 0.8667 (p) cc_final: 0.8246 (p) REVERT: X 84 ASP cc_start: 0.8298 (p0) cc_final: 0.7881 (p0) outliers start: 56 outliers final: 32 residues processed: 201 average time/residue: 0.5728 time to fit residues: 131.4494 Evaluate side-chains 191 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 125 MET Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 215 ARG Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 40 ASN Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 251 ASN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 145 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 88 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN G 294 HIS X 167 ASN X 196 GLN X 233 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.132889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.090492 restraints weight = 38266.928| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.06 r_work: 0.3404 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19802 Z= 0.123 Angle : 0.613 13.773 26846 Z= 0.307 Chirality : 0.041 0.143 3139 Planarity : 0.004 0.047 3350 Dihedral : 10.312 117.500 2972 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.83 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 16.84 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2400 helix: 1.55 (0.16), residues: 1131 sheet: -0.22 (0.26), residues: 409 loop : -0.50 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 108 TYR 0.037 0.001 TYR G 205 PHE 0.050 0.001 PHE G 259 TRP 0.010 0.001 TRP A 317 HIS 0.008 0.001 HIS G 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (19800) covalent geometry : angle 0.61278 / 0.31 (26846) hydrogen bonds : bond 0.02933 / 1.96 ( 985) hydrogen bonds : angle 4.49036 / 3.17 ( 2778) Misc. bond : bond 0.00126 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7751 (ttp-110) REVERT: A 289 LYS cc_start: 0.8402 (ttpp) cc_final: 0.7400 (tptt) REVERT: B 29 ASP cc_start: 0.8482 (m-30) cc_final: 0.7946 (m-30) REVERT: B 210 ASP cc_start: 0.8649 (t0) cc_final: 0.8406 (t70) REVERT: B 218 LYS cc_start: 0.7119 (tttt) cc_final: 0.6798 (mptt) REVERT: B 229 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8739 (tmtt) REVERT: C 118 MET cc_start: 0.8905 (mtp) cc_final: 0.8469 (mtm) REVERT: C 194 LYS cc_start: 0.8843 (tptp) cc_final: 0.8419 (tptp) REVERT: C 197 GLU cc_start: 0.8470 (mp0) cc_final: 0.8098 (mp0) REVERT: G 46 PHE cc_start: 0.7281 (m-80) cc_final: 0.7006 (m-80) REVERT: G 84 MET cc_start: 0.7938 (mmm) cc_final: 0.7465 (mpp) REVERT: G 96 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7524 (ttm110) REVERT: G 158 MET cc_start: 0.5450 (ttm) cc_final: 0.4795 (ttm) REVERT: G 196 ASN cc_start: 0.7489 (p0) cc_final: 0.7213 (p0) REVERT: G 211 MET cc_start: 0.8100 (tpt) cc_final: 0.7876 (tpt) REVERT: G 294 HIS cc_start: 0.7560 (m90) cc_final: 0.7139 (m90) REVERT: G 326 MET cc_start: 0.6774 (mmm) cc_final: 0.6326 (mmm) REVERT: I 125 MET cc_start: 0.0596 (pmm) cc_final: 0.0037 (pmm) REVERT: I 140 LEU cc_start: 0.7985 (tp) cc_final: 0.7760 (mp) REVERT: I 158 MET cc_start: 0.3726 (mmt) cc_final: 0.3445 (mpt) REVERT: I 187 ASP cc_start: 0.2571 (OUTLIER) cc_final: 0.2237 (p0) REVERT: I 250 ARG cc_start: 0.6655 (tpp80) cc_final: 0.6272 (ptt90) REVERT: I 251 MET cc_start: 0.5117 (tpt) cc_final: 0.3489 (mtp) REVERT: I 326 MET cc_start: 0.6184 (pmm) cc_final: 0.5540 (tmt) REVERT: R 72 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8148 (mttp) REVERT: R 206 MET cc_start: 0.9094 (mtt) cc_final: 0.8894 (mtp) REVERT: X 26 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8899 (pm20) REVERT: X 42 ASP cc_start: 0.8107 (m-30) cc_final: 0.7432 (t0) REVERT: X 83 THR cc_start: 0.8583 (p) cc_final: 0.8200 (p) REVERT: X 84 ASP cc_start: 0.8231 (p0) cc_final: 0.7926 (p0) outliers start: 41 outliers final: 25 residues processed: 195 average time/residue: 0.5182 time to fit residues: 115.7677 Evaluate side-chains 183 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 46 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 208 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 143 GLN X 167 ASN X 196 GLN X 233 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.132190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089597 restraints weight = 38615.552| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.04 r_work: 0.3384 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19802 Z= 0.155 Angle : 0.631 14.636 26846 Z= 0.314 Chirality : 0.042 0.209 3139 Planarity : 0.004 0.055 3350 Dihedral : 10.175 109.987 2970 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.78 % Allowed : 17.27 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.17), residues: 2400 helix: 1.48 (0.16), residues: 1131 sheet: -0.27 (0.25), residues: 412 loop : -0.47 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 108 TYR 0.030 0.002 TYR I 216 PHE 0.019 0.001 PHE G 126 TRP 0.009 0.001 TRP R 47 HIS 0.006 0.001 HIS I 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (19800) covalent geometry : angle 0.63092 / 0.31 (26846) hydrogen bonds : bond 0.03141 / 2.10 ( 985) hydrogen bonds : angle 4.55038 / 3.21 ( 2778) Misc. bond : bond 0.00148 / 0.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4800 Ramachandran restraints generated. 2400 Oldfield, 0 Emsley, 2400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 ARG cc_start: 0.8211 (mtp-110) cc_final: 0.7728 (ttp-110) REVERT: A 289 LYS cc_start: 0.8411 (ttpp) cc_final: 0.7413 (tptt) REVERT: B 29 ASP cc_start: 0.8401 (m-30) cc_final: 0.7897 (m-30) REVERT: B 210 ASP cc_start: 0.8699 (t0) cc_final: 0.8423 (t70) REVERT: B 218 LYS cc_start: 0.7029 (tttt) cc_final: 0.6825 (mptt) REVERT: B 229 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8672 (tmtt) REVERT: C 118 MET cc_start: 0.8911 (mtp) cc_final: 0.8468 (mtm) REVERT: C 187 HIS cc_start: 0.8267 (t-170) cc_final: 0.8055 (t-170) REVERT: C 194 LYS cc_start: 0.8839 (tptp) cc_final: 0.8416 (tptp) REVERT: C 197 GLU cc_start: 0.8463 (mp0) cc_final: 0.8075 (mp0) REVERT: D 23 HIS cc_start: 0.8863 (m90) cc_final: 0.8283 (m90) REVERT: G 46 PHE cc_start: 0.7353 (m-80) cc_final: 0.6988 (m-80) REVERT: G 84 MET cc_start: 0.7894 (mmm) cc_final: 0.7411 (mpp) REVERT: G 96 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7572 (ttm110) REVERT: G 158 MET cc_start: 0.5550 (ttm) cc_final: 0.4998 (ttm) REVERT: G 196 ASN cc_start: 0.7530 (p0) cc_final: 0.7245 (p0) REVERT: G 205 TYR cc_start: 0.9313 (m-80) cc_final: 0.8957 (m-80) REVERT: G 294 HIS cc_start: 0.7586 (m90) cc_final: 0.7300 (m90) REVERT: G 326 MET cc_start: 0.6993 (mmm) cc_final: 0.6561 (mmm) REVERT: I 84 MET cc_start: 0.2359 (mmt) cc_final: 0.2059 (mpm) REVERT: I 125 MET cc_start: 0.0626 (pmm) cc_final: 0.0129 (pmm) REVERT: I 187 ASP cc_start: 0.2560 (OUTLIER) cc_final: 0.2221 (p0) REVERT: I 250 ARG cc_start: 0.6692 (tpp80) cc_final: 0.6270 (ptt90) REVERT: I 251 MET cc_start: 0.5151 (tpt) cc_final: 0.3503 (mtp) REVERT: I 326 MET cc_start: 0.6136 (pmm) cc_final: 0.5516 (tmt) REVERT: R 72 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8136 (mttp) REVERT: R 206 MET cc_start: 0.9107 (mtt) cc_final: 0.8895 (mtp) REVERT: X 42 ASP cc_start: 0.8121 (m-30) cc_final: 0.7443 (t0) REVERT: X 83 THR cc_start: 0.8607 (p) cc_final: 0.8237 (p) REVERT: X 84 ASP cc_start: 0.8252 (p0) cc_final: 0.7950 (p0) REVERT: X 185 ASN cc_start: 0.8608 (t0) cc_final: 0.8204 (t0) outliers start: 37 outliers final: 28 residues processed: 187 average time/residue: 0.5163 time to fit residues: 111.0017 Evaluate side-chains 185 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 259 PHE Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain I residue 187 ASP Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain R residue 72 LYS Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain X residue 37 SER Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 207 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 201 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 165 optimal weight: 30.0000 chunk 29 optimal weight: 0.3980 chunk 170 optimal weight: 20.0000 chunk 19 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 167 ASN X 196 GLN X 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.132315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.089949 restraints weight = 38616.546| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.05 r_work: 0.3390 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19802 Z= 0.140 Angle : 0.623 13.516 26846 Z= 0.310 Chirality : 0.042 0.189 3139 Planarity : 0.004 0.050 3350 Dihedral : 10.124 109.562 2970 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.75 % Favored : 97.21 % Rotamer: Outliers : 1.98 % Allowed : 17.03 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2400 helix: 1.49 (0.16), residues: 1131 sheet: -0.28 (0.25), residues: 423 loop : -0.49 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG R 108 TYR 0.024 0.001 TYR I 54 PHE 0.021 0.001 PHE G 126 TRP 0.010 0.001 TRP A 317 HIS 0.006 0.001 HIS D 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (19800) covalent geometry : angle 0.62340 / 0.31 (26846) hydrogen bonds : bond 0.03047 / 2.04 ( 985) hydrogen bonds : angle 4.51300 / 3.19 ( 2778) Misc. bond : bond 0.00136 / 0.07 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7730.10 seconds wall clock time: 132 minutes 19.80 seconds (7939.80 seconds total)