Starting phenix.real_space_refine on Mon Apr 6 15:55:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q2a_72154/04_2026/9q2a_72154_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q2a_72154/04_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_72154/04_2026/9q2a_72154.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q2a_72154/04_2026/9q2a_72154.map" model { file = "/net/cci-nas-00/data/ceres_data/9q2a_72154/04_2026/9q2a_72154_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q2a_72154/04_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-2.1rc1-6017/lib/python3.9/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: 4.69, per 1000 atoms: 0.24 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: 1.99 Conformation dependent library (CDL) restraints added in 865.9 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: 0.68 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: 4.45 Time building geometry restraints manager: 2.53 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=" CA PRO C 18 " pdb=" CB PRO C 18 " ideal model delta sigma weight residual 1.532 1.523 0.009 7.10e-03 1.98e+04 1.57e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.41e+00 bond pdb=" N ILE B 141 " pdb=" CA ILE B 141 " ideal model delta sigma weight residual 1.474 1.457 0.018 1.57e-02 4.06e+03 1.29e+00 bond pdb=" CA GLN A 97 " pdb=" C GLN A 97 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.17e+00 bond pdb=" CB PRO X 38 " pdb=" CG PRO X 38 " ideal model delta sigma weight residual 1.492 1.544 -0.052 5.00e-02 4.00e+02 1.08e+00 ... (remaining 19795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 26223 1.40 - 2.80: 497 2.80 - 4.20: 85 4.20 - 5.60: 23 5.60 - 7.00: 18 Bond angle restraints: 26846 Sorted by residual: angle pdb=" N SER B 194 " pdb=" CA SER B 194 " pdb=" C SER B 194 " ideal model delta sigma weight residual 114.16 108.29 5.87 1.48e+00 4.57e-01 1.57e+01 angle pdb=" N CYS I 31 " pdb=" CA CYS I 31 " pdb=" C CYS I 31 " ideal model delta sigma weight residual 114.75 110.77 3.98 1.26e+00 6.30e-01 9.99e+00 angle pdb=" N ILE X 198 " pdb=" CA ILE X 198 " pdb=" C ILE X 198 " ideal model delta sigma weight residual 113.20 110.33 2.87 9.60e-01 1.09e+00 8.94e+00 angle pdb=" C VAL R 198 " pdb=" CA VAL R 198 " pdb=" CB VAL R 198 " ideal model delta sigma weight residual 113.70 110.94 2.76 9.50e-01 1.11e+00 8.44e+00 angle pdb=" CA VAL R 198 " pdb=" C VAL R 198 " pdb=" N PRO R 199 " ideal model delta sigma weight residual 120.83 119.16 1.67 5.90e-01 2.87e+00 8.01e+00 ... (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: 2809 0.059 - 0.117: 298 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: 6.200 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: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 20.740 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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= 0.602 Angle : 0.519 6.997 26846 Z= 0.314 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 covalent geometry : bond 0.00199 (19800) covalent geometry : angle 0.51898 (26846) hydrogen bonds : bond 0.15172 ( 985) hydrogen bonds : angle 6.47228 ( 2778) Misc. bond : bond 0.58774 ( 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 : 0.675 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: 0.6266 time to fit residues: 274.0767 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 : 0.705 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 X 196 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.133423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.090428 restraints weight = 38505.949| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.22 r_work: 0.3413 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19802 Z= 0.166 Angle : 0.649 11.911 26846 Z= 0.326 Chirality : 0.043 0.153 3139 Planarity : 0.004 0.048 3350 Dihedral : 11.119 135.631 2988 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 2.60 % Allowed : 12.49 % Favored : 84.90 % 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: 1.80 (0.16), residues: 1130 sheet: -0.03 (0.26), residues: 389 loop : -0.51 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 66 TYR 0.021 0.002 TYR G 205 PHE 0.018 0.002 PHE G 126 TRP 0.025 0.002 TRP D 314 HIS 0.010 0.001 HIS G 138 Details of bonding type rmsd covalent geometry : bond 0.00387 (19800) covalent geometry : angle 0.64867 (26846) hydrogen bonds : bond 0.04017 ( 985) hydrogen bonds : angle 4.92650 ( 2778) Misc. bond : bond 0.00234 ( 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 264 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.756 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: 0.5002 (mmm) cc_final: 0.4250 (mmm) REVERT: A 165 MET cc_start: 0.8448 (mmt) cc_final: 0.8115 (mmt) REVERT: A 193 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8330 (ttp-110) REVERT: A 289 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8101 (ptmm) REVERT: A 303 GLU cc_start: 0.7838 (pm20) cc_final: 0.7603 (tt0) REVERT: B 29 ASP cc_start: 0.8440 (m-30) cc_final: 0.7973 (m-30) REVERT: B 131 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.8061 (mtm) REVERT: C 10 MET cc_start: 0.7671 (ptm) cc_final: 0.7430 (ptt) REVERT: C 118 MET cc_start: 0.8873 (mtp) cc_final: 0.8413 (mtm) REVERT: G 72 ASP cc_start: 0.8020 (m-30) cc_final: 0.7762 (p0) REVERT: G 84 MET cc_start: 0.7362 (mmm) cc_final: 0.6939 (mpp) REVERT: G 91 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: G 158 MET cc_start: 0.5813 (ttm) cc_final: 0.5087 (ttm) REVERT: G 196 ASN cc_start: 0.7467 (p0) cc_final: 0.7095 (p0) REVERT: G 222 ASP cc_start: 0.6369 (t0) cc_final: 0.6115 (m-30) REVERT: I 125 MET cc_start: 0.0939 (pmm) cc_final: 0.0445 (pmm) REVERT: I 140 LEU cc_start: 0.8632 (mp) cc_final: 0.8400 (tp) REVERT: I 187 ASP cc_start: 0.2365 (OUTLIER) cc_final: 0.2055 (p0) REVERT: I 250 ARG cc_start: 0.7108 (tpp80) cc_final: 0.6600 (ptt90) REVERT: I 251 MET cc_start: 0.5003 (tpt) cc_final: 0.4024 (mtt) REVERT: I 326 MET cc_start: 0.5980 (pmm) cc_final: 0.5323 (tmm) REVERT: R 22 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8066 (tppt) REVERT: R 72 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7957 (mttp) REVERT: R 233 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7662 (ttm-80) outliers start: 54 outliers final: 22 residues processed: 249 average time/residue: 0.6000 time to fit residues: 168.0226 Evaluate side-chains 184 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 112 CYS Chi-restraints excluded: chain B residue 131 MET 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 184 GLU Chi-restraints excluded: chain G residue 81 LEU 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 142 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 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: 8.9990 chunk 164 optimal weight: 8.9990 chunk 32 optimal weight: 0.0870 chunk 217 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN G 23 GLN R 257 ASN X 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.131614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.088345 restraints weight = 38849.408| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.15 r_work: 0.3369 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19802 Z= 0.191 Angle : 0.606 8.006 26846 Z= 0.309 Chirality : 0.043 0.149 3139 Planarity : 0.004 0.048 3350 Dihedral : 10.649 125.490 2972 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 2.85 % Allowed : 13.22 % Favored : 83.94 % 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: 0.82 (0.17), residues: 2400 helix: 1.64 (0.16), residues: 1127 sheet: -0.07 (0.26), residues: 398 loop : -0.54 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 27 TYR 0.026 0.001 TYR G 205 PHE 0.023 0.002 PHE G 259 TRP 0.014 0.002 TRP D 314 HIS 0.008 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00453 (19800) covalent geometry : angle 0.60553 (26846) hydrogen bonds : bond 0.03711 ( 985) hydrogen bonds : angle 4.76804 ( 2778) Misc. bond : bond 0.00280 ( 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 240 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.642 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: 0.8332 (ttp-110) REVERT: A 289 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8087 (ptmm) REVERT: A 337 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 29 ASP cc_start: 0.8444 (m-30) cc_final: 0.7944 (m-30) REVERT: B 218 LYS cc_start: 0.7277 (tttt) cc_final: 0.6915 (mptt) REVERT: C 10 MET cc_start: 0.7676 (ptm) cc_final: 0.7468 (ptt) REVERT: C 194 LYS cc_start: 0.8901 (tptp) cc_final: 0.8263 (tptp) REVERT: C 197 GLU cc_start: 0.8348 (mp0) cc_final: 0.7926 (mp0) REVERT: D 292 MET cc_start: 0.6982 (OUTLIER) cc_final: 0.6247 (tpt) REVERT: G 72 ASP cc_start: 0.7986 (m-30) cc_final: 0.7690 (p0) REVERT: G 84 MET cc_start: 0.7371 (mmm) cc_final: 0.7008 (mpp) REVERT: G 158 MET cc_start: 0.5575 (ttm) cc_final: 0.4944 (ttm) REVERT: G 196 ASN cc_start: 0.7468 (p0) cc_final: 0.7134 (p0) REVERT: G 211 MET cc_start: 0.7986 (tpt) cc_final: 0.7758 (tpt) REVERT: G 222 ASP cc_start: 0.6796 (t0) cc_final: 0.6419 (m-30) REVERT: I 125 MET cc_start: 0.0870 (pmm) cc_final: 0.0404 (pmm) REVERT: I 250 ARG cc_start: 0.6917 (tpp80) cc_final: 0.6477 (ptt90) REVERT: I 251 MET cc_start: 0.5008 (tpt) cc_final: 0.3866 (mtt) REVERT: I 326 MET cc_start: 0.6168 (pmm) cc_final: 0.5466 (tmm) REVERT: R 72 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7989 (mttp) REVERT: X 84 ASP cc_start: 0.8328 (p0) cc_final: 0.7907 (p0) REVERT: X 239 MET cc_start: 0.8549 (mpp) cc_final: 0.8304 (mpt) outliers start: 59 outliers final: 27 residues processed: 225 average time/residue: 0.5525 time to fit residues: 140.5368 Evaluate side-chains 186 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain B residue 5 LYS 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 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 112 LEU Chi-restraints excluded: chain G residue 124 GLU 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 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 178 GLN 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: 2.9990 chunk 140 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 167 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 172 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 186 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 169 optimal weight: 40.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN G 30 GLN G 294 HIS I 93 HIS X 40 HIS X 167 ASN X 233 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.130933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.087658 restraints weight = 38961.528| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.05 r_work: 0.3363 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19802 Z= 0.190 Angle : 0.598 12.137 26846 Z= 0.304 Chirality : 0.043 0.248 3139 Planarity : 0.004 0.049 3350 Dihedral : 10.617 123.406 2972 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 3.09 % Allowed : 13.99 % Favored : 82.92 % 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 (0.17), residues: 2400 helix: 1.51 (0.16), residues: 1128 sheet: -0.12 (0.26), residues: 398 loop : -0.54 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 300 TYR 0.029 0.002 TYR G 205 PHE 0.023 0.002 PHE G 259 TRP 0.010 0.002 TRP D 314 HIS 0.007 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00449 (19800) covalent geometry : angle 0.59839 (26846) hydrogen bonds : bond 0.03502 ( 985) hydrogen bonds : angle 4.69566 ( 2778) Misc. bond : bond 0.00273 ( 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 227 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 MET cc_start: 0.4995 (mmm) cc_final: 0.4729 (mmp) REVERT: A 193 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8319 (ttp-110) REVERT: A 289 LYS cc_start: 0.8462 (ttpp) cc_final: 0.7501 (tptt) REVERT: B 29 ASP cc_start: 0.8468 (m-30) cc_final: 0.7950 (m-30) REVERT: B 229 LYS cc_start: 0.8987 (ttpp) cc_final: 0.8678 (tmtt) REVERT: C 10 MET cc_start: 0.7570 (ptm) cc_final: 0.7365 (ptt) REVERT: C 118 MET cc_start: 0.8898 (mtp) cc_final: 0.8439 (mtm) REVERT: C 194 LYS cc_start: 0.8876 (tptp) cc_final: 0.8063 (tptp) REVERT: C 197 GLU cc_start: 0.8331 (mp0) cc_final: 0.7815 (mp0) REVERT: D 26 LYS cc_start: 0.7918 (tttm) cc_final: 0.7702 (tttp) REVERT: D 292 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6180 (tpt) REVERT: G 72 ASP cc_start: 0.8085 (m-30) cc_final: 0.7813 (p0) REVERT: G 84 MET cc_start: 0.7667 (mmm) cc_final: 0.7333 (mpp) REVERT: G 158 MET cc_start: 0.5894 (ttm) cc_final: 0.5315 (ttm) REVERT: G 196 ASN cc_start: 0.7431 (p0) cc_final: 0.7131 (p0) REVERT: G 294 HIS cc_start: 0.7867 (m90) cc_final: 0.7580 (m-70) REVERT: I 84 MET cc_start: 0.2958 (mmt) cc_final: 0.2640 (mpm) REVERT: I 250 ARG cc_start: 0.6739 (tpp80) cc_final: 0.6467 (ptt90) REVERT: I 251 MET cc_start: 0.5121 (tpt) cc_final: 0.3688 (mtp) REVERT: I 326 MET cc_start: 0.6145 (pmm) cc_final: 0.5501 (tmt) REVERT: R 72 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8029 (mttp) REVERT: X 84 ASP cc_start: 0.8370 (p0) cc_final: 0.7974 (p0) outliers start: 64 outliers final: 33 residues processed: 212 average time/residue: 0.5359 time to fit residues: 129.1905 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 : 0.768 ------------------------------------------------------------------------------- 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 5 LYS 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 B residue 304 VAL 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 91 LYS Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 228 MET 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 144 CYS 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 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 123 SER 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: 1.9990 chunk 151 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 159 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN X 167 ASN X 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.129841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.086413 restraints weight = 38744.238| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.07 r_work: 0.3328 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 19802 Z= 0.237 Angle : 0.629 10.852 26846 Z= 0.318 Chirality : 0.044 0.276 3139 Planarity : 0.004 0.047 3350 Dihedral : 10.796 118.840 2972 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 3.18 % Allowed : 14.33 % 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: 0.53 (0.17), residues: 2400 helix: 1.34 (0.15), residues: 1133 sheet: -0.37 (0.25), residues: 414 loop : -0.52 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 108 TYR 0.029 0.002 TYR G 205 PHE 0.028 0.002 PHE G 129 TRP 0.011 0.002 TRP R 47 HIS 0.006 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00561 (19800) covalent geometry : angle 0.62942 (26846) hydrogen bonds : bond 0.03612 ( 985) hydrogen bonds : angle 4.77959 ( 2778) Misc. bond : bond 0.00334 ( 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 230 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 164 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8603 (ttp-110) cc_final: 0.8356 (ttp-110) REVERT: A 267 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.5926 (tt0) REVERT: A 289 LYS cc_start: 0.8423 (ttpp) cc_final: 0.7449 (tptt) REVERT: B 1 MET cc_start: 0.6833 (tpp) cc_final: 0.6624 (tmt) REVERT: B 29 ASP cc_start: 0.8463 (m-30) cc_final: 0.7947 (m-30) REVERT: B 229 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8647 (tmtt) REVERT: C 118 MET cc_start: 0.8927 (mtp) cc_final: 0.8614 (mtm) REVERT: C 194 LYS cc_start: 0.8876 (tptp) cc_final: 0.8031 (tptp) REVERT: C 197 GLU cc_start: 0.8374 (mp0) cc_final: 0.7893 (mp0) REVERT: G 84 MET cc_start: 0.7911 (mmm) cc_final: 0.7624 (mpp) REVERT: G 158 MET cc_start: 0.5728 (ttm) cc_final: 0.5143 (ttm) REVERT: G 196 ASN cc_start: 0.7524 (p0) cc_final: 0.7193 (p0) REVERT: G 211 MET cc_start: 0.8139 (tpt) cc_final: 0.7851 (tpt) REVERT: G 222 ASP cc_start: 0.6114 (OUTLIER) cc_final: 0.5561 (m-30) REVERT: I 125 MET cc_start: 0.1012 (pmm) cc_final: 0.0361 (pmm) REVERT: I 250 ARG cc_start: 0.6774 (tpp80) cc_final: 0.6361 (ptt90) REVERT: I 251 MET cc_start: 0.5260 (tpt) cc_final: 0.3677 (mtp) REVERT: I 326 MET cc_start: 0.6131 (pmm) cc_final: 0.5520 (tmt) REVERT: R 18 LYS cc_start: 0.9134 (tmtt) cc_final: 0.8771 (tmmt) REVERT: R 72 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8028 (mttp) REVERT: X 42 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: X 84 ASP cc_start: 0.8425 (p0) cc_final: 0.8134 (p0) outliers start: 66 outliers final: 40 residues processed: 212 average time/residue: 0.5405 time to fit residues: 130.6940 Evaluate side-chains 195 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 267 GLN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 5 LYS 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 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 77 THR 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 303 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 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 144 CYS Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 222 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 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 42 ASP Chi-restraints excluded: chain X residue 86 HIS Chi-restraints excluded: chain X residue 123 SER Chi-restraints excluded: chain X residue 198 ILE Chi-restraints excluded: chain X residue 251 ASN 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: 0.5980 chunk 193 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 143 optimal weight: 7.9990 chunk 201 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 165 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 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 = 0.4211 r_free = 0.4211 target = 0.131416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.088512 restraints weight = 38700.838| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.08 r_work: 0.3369 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3635 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= 0.146 Angle : 0.584 14.318 26846 Z= 0.295 Chirality : 0.042 0.251 3139 Planarity : 0.004 0.047 3350 Dihedral : 10.573 123.464 2972 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 2.80 % Allowed : 15.44 % Favored : 81.77 % 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: 1.43 (0.16), residues: 1127 sheet: -0.33 (0.25), residues: 415 loop : -0.47 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 108 TYR 0.020 0.001 TYR B 68 PHE 0.038 0.001 PHE G 259 TRP 0.009 0.001 TRP A 317 HIS 0.006 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00343 (19800) covalent geometry : angle 0.58392 (26846) hydrogen bonds : bond 0.03197 ( 985) hydrogen bonds : angle 4.62519 ( 2778) Misc. bond : bond 0.00206 ( 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 224 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8388 (ttp-110) REVERT: A 267 GLN cc_start: 0.7140 (OUTLIER) cc_final: 0.5899 (tt0) REVERT: A 277 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7708 (ttp-110) REVERT: A 289 LYS cc_start: 0.8425 (ttpp) cc_final: 0.7446 (tptt) REVERT: B 1 MET cc_start: 0.6700 (tpp) cc_final: 0.6496 (tpt) REVERT: B 29 ASP cc_start: 0.8402 (m-30) cc_final: 0.7846 (m-30) REVERT: B 229 LYS cc_start: 0.9088 (ttpp) cc_final: 0.8731 (tmtt) REVERT: C 118 MET cc_start: 0.8909 (mtp) cc_final: 0.8453 (mtm) REVERT: C 194 LYS cc_start: 0.8871 (tptp) cc_final: 0.8027 (tptp) REVERT: C 197 GLU cc_start: 0.8418 (mp0) cc_final: 0.7900 (mp0) REVERT: G 46 PHE cc_start: 0.7285 (m-80) cc_final: 0.6921 (m-80) REVERT: G 84 MET cc_start: 0.7934 (mmm) cc_final: 0.7617 (mpp) REVERT: G 96 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7601 (ttm110) REVERT: G 158 MET cc_start: 0.5831 (ttm) cc_final: 0.5287 (ttm) REVERT: G 196 ASN cc_start: 0.7511 (p0) cc_final: 0.7196 (p0) REVERT: G 211 MET cc_start: 0.7922 (tpt) cc_final: 0.7591 (tpt) REVERT: G 222 ASP cc_start: 0.6142 (OUTLIER) cc_final: 0.5559 (m-30) REVERT: G 248 PHE cc_start: 0.8888 (t80) cc_final: 0.8686 (t80) REVERT: G 251 MET cc_start: 0.8336 (tpt) cc_final: 0.8119 (tpp) REVERT: G 294 HIS cc_start: 0.7840 (m90) cc_final: 0.7620 (m-70) REVERT: I 84 MET cc_start: 0.2963 (mmt) cc_final: 0.2628 (mpm) REVERT: I 125 MET cc_start: 0.0846 (pmm) cc_final: 0.0268 (pmm) REVERT: I 250 ARG cc_start: 0.6720 (tpp80) cc_final: 0.6360 (ptt90) REVERT: I 251 MET cc_start: 0.5252 (tpt) cc_final: 0.3700 (mtp) REVERT: I 326 MET cc_start: 0.6139 (pmm) cc_final: 0.5531 (tmt) REVERT: R 11 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8723 (ptm160) REVERT: R 72 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8025 (mttp) REVERT: X 42 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7455 (t0) REVERT: X 83 THR cc_start: 0.8671 (p) cc_final: 0.8254 (p) REVERT: X 84 ASP cc_start: 0.8383 (p0) cc_final: 0.7993 (p0) outliers start: 58 outliers final: 30 residues processed: 211 average time/residue: 0.5444 time to fit residues: 131.0140 Evaluate side-chains 187 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 267 GLN Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain B residue 5 LYS 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 D residue 303 THR 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 144 CYS Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain R residue 11 ARG 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 42 ASP Chi-restraints excluded: chain X residue 86 HIS 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: 0.8980 chunk 172 optimal weight: 0.0000 chunk 109 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN X 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.132437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.089998 restraints weight = 38722.788| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.03 r_work: 0.3402 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3794 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= 0.121 Angle : 0.578 12.765 26846 Z= 0.290 Chirality : 0.041 0.262 3139 Planarity : 0.004 0.046 3350 Dihedral : 10.347 121.585 2972 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.25 % Rotamer: Outliers : 2.89 % Allowed : 15.34 % Favored : 81.77 % 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: 1.52 (0.16), residues: 1131 sheet: -0.21 (0.25), residues: 414 loop : -0.49 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.021 0.001 TYR B 68 PHE 0.020 0.001 PHE G 126 TRP 0.010 0.001 TRP D 314 HIS 0.006 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00278 (19800) covalent geometry : angle 0.57824 (26846) hydrogen bonds : bond 0.02970 ( 985) hydrogen bonds : angle 4.50186 ( 2778) Misc. bond : bond 0.00154 ( 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 227 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8374 (ttp-110) REVERT: A 267 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: A 277 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7747 (ttp-110) REVERT: A 289 LYS cc_start: 0.8419 (ttpp) cc_final: 0.7438 (tptt) REVERT: B 29 ASP cc_start: 0.8468 (m-30) cc_final: 0.7924 (m-30) REVERT: B 210 ASP cc_start: 0.8672 (t0) cc_final: 0.8378 (t70) REVERT: B 218 LYS cc_start: 0.7115 (tttt) cc_final: 0.6716 (mppt) REVERT: B 229 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8746 (tmtt) REVERT: C 118 MET cc_start: 0.8906 (mtp) cc_final: 0.8498 (mtm) REVERT: C 194 LYS cc_start: 0.8856 (tptp) cc_final: 0.8445 (tptp) REVERT: C 197 GLU cc_start: 0.8425 (mp0) cc_final: 0.8081 (mp0) REVERT: D 292 MET cc_start: 0.6859 (tpt) cc_final: 0.6493 (tpt) REVERT: G 46 PHE cc_start: 0.7346 (m-80) cc_final: 0.6984 (m-80) REVERT: G 84 MET cc_start: 0.7960 (mmm) cc_final: 0.7646 (mpp) REVERT: G 96 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7556 (ttm110) REVERT: G 158 MET cc_start: 0.5863 (ttm) cc_final: 0.5245 (ttm) REVERT: G 196 ASN cc_start: 0.7490 (p0) cc_final: 0.7200 (p0) REVERT: G 238 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8555 (tm) REVERT: I 125 MET cc_start: 0.0658 (pmm) cc_final: 0.0147 (pmm) REVERT: I 187 ASP cc_start: 0.2504 (OUTLIER) cc_final: 0.2178 (p0) REVERT: I 250 ARG cc_start: 0.6548 (tpp80) cc_final: 0.6238 (ptt90) REVERT: I 251 MET cc_start: 0.5141 (tpt) cc_final: 0.3517 (mtp) REVERT: I 326 MET cc_start: 0.6147 (pmm) cc_final: 0.5498 (tmt) REVERT: R 11 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8733 (ptm160) REVERT: R 72 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8122 (mttp) REVERT: X 26 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8979 (pm20) REVERT: X 42 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7472 (t0) REVERT: X 83 THR cc_start: 0.8615 (p) cc_final: 0.8204 (p) REVERT: X 84 ASP cc_start: 0.8296 (p0) cc_final: 0.7866 (p0) outliers start: 60 outliers final: 29 residues processed: 212 average time/residue: 0.5255 time to fit residues: 127.5567 Evaluate side-chains 195 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 267 GLN 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 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 238 LEU 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 12 ILE 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 42 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 46 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 204 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN G 294 HIS X 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.130329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086653 restraints weight = 38761.466| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.17 r_work: 0.3328 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 19802 Z= 0.235 Angle : 0.653 11.654 26846 Z= 0.327 Chirality : 0.044 0.289 3139 Planarity : 0.004 0.055 3350 Dihedral : 10.612 112.013 2972 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.70 % Allowed : 16.02 % Favored : 81.28 % 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: 0.50 (0.17), residues: 2400 helix: 1.30 (0.16), residues: 1139 sheet: -0.40 (0.25), residues: 412 loop : -0.48 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 168 TYR 0.020 0.002 TYR C 327 PHE 0.039 0.002 PHE G 259 TRP 0.012 0.002 TRP R 47 HIS 0.009 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00557 (19800) covalent geometry : angle 0.65282 (26846) hydrogen bonds : bond 0.03542 ( 985) hydrogen bonds : angle 4.72899 ( 2778) Misc. bond : bond 0.00298 ( 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 208 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 152 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.5521 (tt0) REVERT: A 289 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7534 (tptt) REVERT: B 29 ASP cc_start: 0.8492 (m-30) cc_final: 0.7961 (m-30) REVERT: B 218 LYS cc_start: 0.7269 (tttt) cc_final: 0.6359 (tttt) REVERT: C 118 MET cc_start: 0.8953 (mtp) cc_final: 0.8544 (mtm) REVERT: C 194 LYS cc_start: 0.8838 (tptp) cc_final: 0.8509 (tptp) REVERT: C 197 GLU cc_start: 0.8451 (mp0) cc_final: 0.8230 (mp0) REVERT: G 46 PHE cc_start: 0.7252 (m-80) cc_final: 0.6959 (m-80) REVERT: G 84 MET cc_start: 0.7923 (mmm) cc_final: 0.7562 (mpp) REVERT: G 96 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7581 (ttm110) REVERT: G 158 MET cc_start: 0.5837 (ttm) cc_final: 0.5240 (ttm) REVERT: G 196 ASN cc_start: 0.7565 (p0) cc_final: 0.7256 (p0) REVERT: G 294 HIS cc_start: 0.7733 (m90) cc_final: 0.7381 (m90) REVERT: G 326 MET cc_start: 0.6831 (mmm) cc_final: 0.6473 (mmm) REVERT: I 125 MET cc_start: 0.0612 (pmm) cc_final: 0.0127 (pmm) REVERT: I 187 ASP cc_start: 0.2378 (OUTLIER) cc_final: 0.2055 (p0) REVERT: I 250 ARG cc_start: 0.6702 (tpp80) cc_final: 0.6338 (ptt90) REVERT: I 326 MET cc_start: 0.6142 (pmm) cc_final: 0.5551 (tmt) REVERT: R 11 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8767 (ptm160) REVERT: R 18 LYS cc_start: 0.9191 (tmtt) cc_final: 0.8887 (tmmt) REVERT: R 72 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8146 (mttp) REVERT: X 42 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7539 (t0) REVERT: X 83 THR cc_start: 0.8773 (p) cc_final: 0.8355 (p) REVERT: X 84 ASP cc_start: 0.8403 (p0) cc_final: 0.8014 (p0) outliers start: 56 outliers final: 32 residues processed: 192 average time/residue: 0.5279 time to fit residues: 116.0005 Evaluate side-chains 189 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 267 GLN 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 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 49 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 96 ARG Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 149 ASP 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 12 ILE 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 42 ASP 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: 0.9980 chunk 79 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 chunk 115 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.0050 chunk 46 optimal weight: 0.3980 chunk 170 optimal weight: 7.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN X 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.132309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089680 restraints weight = 38363.381| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.06 r_work: 0.3391 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19802 Z= 0.122 Angle : 0.608 12.264 26846 Z= 0.303 Chirality : 0.042 0.321 3139 Planarity : 0.004 0.046 3350 Dihedral : 10.320 120.934 2970 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.50 % Favored : 97.46 % Rotamer: Outliers : 2.03 % Allowed : 17.27 % Favored : 80.70 % 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: 1.42 (0.16), residues: 1140 sheet: -0.36 (0.25), residues: 425 loop : -0.47 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 193 TYR 0.037 0.001 TYR G 205 PHE 0.017 0.001 PHE G 129 TRP 0.010 0.001 TRP A 305 HIS 0.007 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00280 (19800) covalent geometry : angle 0.60784 (26846) hydrogen bonds : bond 0.02988 ( 985) hydrogen bonds : angle 4.51570 ( 2778) Misc. bond : bond 0.00137 ( 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: 42 poor density : 163 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.5742 (tt0) REVERT: A 277 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7760 (ttp-110) REVERT: A 289 LYS cc_start: 0.8434 (ttpp) cc_final: 0.7449 (tptt) REVERT: B 1 MET cc_start: 0.6673 (ttm) cc_final: 0.6460 (tmm) REVERT: B 29 ASP cc_start: 0.8481 (m-30) cc_final: 0.7955 (m-30) REVERT: B 210 ASP cc_start: 0.8644 (t0) cc_final: 0.8364 (t70) REVERT: C 118 MET cc_start: 0.8926 (mtp) cc_final: 0.8521 (mtm) REVERT: C 194 LYS cc_start: 0.8829 (tptp) cc_final: 0.8398 (tptp) REVERT: C 197 GLU cc_start: 0.8457 (mp0) cc_final: 0.8068 (mp0) REVERT: G 46 PHE cc_start: 0.7468 (m-80) cc_final: 0.7069 (m-80) REVERT: G 84 MET cc_start: 0.7946 (mmm) cc_final: 0.7600 (mpp) REVERT: G 96 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7572 (ttm110) REVERT: G 112 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7350 (tp) REVERT: G 158 MET cc_start: 0.5778 (ttm) cc_final: 0.5163 (ttm) REVERT: G 196 ASN cc_start: 0.7542 (p0) cc_final: 0.7278 (p0) REVERT: I 125 MET cc_start: 0.0595 (pmm) cc_final: 0.0138 (pmm) REVERT: I 158 MET cc_start: 0.3608 (mmt) cc_final: 0.2066 (mpt) REVERT: I 187 ASP cc_start: 0.2486 (OUTLIER) cc_final: 0.2163 (p0) REVERT: I 250 ARG cc_start: 0.6652 (tpp80) cc_final: 0.6235 (ptt90) REVERT: I 251 MET cc_start: 0.5227 (tpt) cc_final: 0.3514 (mtp) REVERT: I 326 MET cc_start: 0.6146 (pmm) cc_final: 0.5525 (tmt) REVERT: R 18 LYS cc_start: 0.9202 (tmtt) cc_final: 0.8845 (tmmt) REVERT: R 72 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8113 (mttp) REVERT: X 26 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8929 (pm20) REVERT: X 42 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7514 (t0) REVERT: X 83 THR cc_start: 0.8621 (p) cc_final: 0.8236 (p) REVERT: X 84 ASP cc_start: 0.8251 (p0) cc_final: 0.7984 (p0) outliers start: 42 outliers final: 26 residues processed: 195 average time/residue: 0.5377 time to fit residues: 119.4990 Evaluate side-chains 186 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 267 GLN 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 B residue 304 VAL Chi-restraints excluded: chain C residue 105 SER 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 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 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 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: 0.8980 chunk 13 optimal weight: 1.9990 chunk 168 optimal weight: 40.0000 chunk 208 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 215 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN G 294 HIS X 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.089271 restraints weight = 38622.295| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.11 r_work: 0.3371 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19802 Z= 0.152 Angle : 0.633 13.512 26846 Z= 0.313 Chirality : 0.042 0.324 3139 Planarity : 0.004 0.045 3350 Dihedral : 10.297 111.198 2970 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Rotamer: Outliers : 1.98 % Allowed : 17.51 % Favored : 80.51 % 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: 0.64 (0.17), residues: 2400 helix: 1.43 (0.16), residues: 1138 sheet: -0.30 (0.25), residues: 409 loop : -0.47 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 11 TYR 0.021 0.001 TYR C 327 PHE 0.039 0.001 PHE G 259 TRP 0.010 0.002 TRP R 47 HIS 0.024 0.001 HIS G 294 Details of bonding type rmsd covalent geometry : bond 0.00361 (19800) covalent geometry : angle 0.63339 (26846) hydrogen bonds : bond 0.03131 ( 985) hydrogen bonds : angle 4.53074 ( 2778) Misc. bond : bond 0.00187 ( 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 196 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.5787 (tt0) REVERT: A 277 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7760 (ttp-110) REVERT: A 289 LYS cc_start: 0.8454 (ttpp) cc_final: 0.7505 (tptt) REVERT: A 320 LYS cc_start: 0.7939 (tppt) cc_final: 0.7594 (ttmm) REVERT: B 29 ASP cc_start: 0.8437 (m-30) cc_final: 0.7892 (m-30) REVERT: B 210 ASP cc_start: 0.8704 (t0) cc_final: 0.8444 (t70) REVERT: C 118 MET cc_start: 0.8932 (mtp) cc_final: 0.8526 (mtm) REVERT: C 187 HIS cc_start: 0.8156 (t-170) cc_final: 0.7623 (m170) REVERT: C 194 LYS cc_start: 0.8817 (tptp) cc_final: 0.8430 (tptp) REVERT: C 197 GLU cc_start: 0.8499 (mp0) cc_final: 0.8099 (mp0) REVERT: G 46 PHE cc_start: 0.7510 (m-80) cc_final: 0.7095 (m-80) REVERT: G 84 MET cc_start: 0.7967 (mmm) cc_final: 0.7569 (mpp) REVERT: G 96 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7620 (ttm110) REVERT: G 158 MET cc_start: 0.5888 (ttm) cc_final: 0.5271 (ttm) REVERT: G 196 ASN cc_start: 0.7571 (p0) cc_final: 0.7305 (p0) REVERT: G 205 TYR cc_start: 0.9302 (m-80) cc_final: 0.8980 (m-80) REVERT: G 326 MET cc_start: 0.7096 (mmm) cc_final: 0.5310 (mmm) REVERT: I 125 MET cc_start: 0.0579 (pmm) cc_final: 0.0130 (pmm) REVERT: I 187 ASP cc_start: 0.2394 (OUTLIER) cc_final: 0.2087 (p0) REVERT: I 250 ARG cc_start: 0.6671 (tpp80) cc_final: 0.6312 (ptt90) REVERT: I 326 MET cc_start: 0.6144 (pmm) cc_final: 0.5559 (tmt) REVERT: R 72 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8185 (mttp) REVERT: R 206 MET cc_start: 0.8987 (mtt) cc_final: 0.8620 (mmm) REVERT: X 26 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8890 (pm20) REVERT: X 42 ASP cc_start: 0.8214 (m-30) cc_final: 0.7539 (t0) REVERT: X 83 THR cc_start: 0.8646 (p) cc_final: 0.8251 (p) REVERT: X 84 ASP cc_start: 0.8276 (p0) cc_final: 0.8006 (p0) outliers start: 41 outliers final: 28 residues processed: 188 average time/residue: 0.5467 time to fit residues: 116.7697 Evaluate side-chains 180 residues out of total 2073 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 267 GLN 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 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 124 GLU Chi-restraints excluded: chain G residue 144 CYS 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: 0.8980 chunk 45 optimal weight: 0.7980 chunk 201 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 165 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.131789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.089097 restraints weight = 38627.615| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.12 r_work: 0.3379 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4110 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= 0.139 Angle : 0.624 13.016 26846 Z= 0.308 Chirality : 0.042 0.315 3139 Planarity : 0.004 0.044 3350 Dihedral : 10.247 109.708 2970 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.93 % Allowed : 17.70 % Favored : 80.37 % 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: 1.49 (0.16), residues: 1132 sheet: -0.33 (0.25), residues: 423 loop : -0.45 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 11 TYR 0.020 0.001 TYR I 54 PHE 0.024 0.001 PHE G 126 TRP 0.010 0.001 TRP A 317 HIS 0.006 0.001 HIS I 294 Details of bonding type rmsd covalent geometry : bond 0.00328 (19800) covalent geometry : angle 0.62364 (26846) hydrogen bonds : bond 0.03050 ( 985) hydrogen bonds : angle 4.48493 ( 2778) Misc. bond : bond 0.00165 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7553.26 seconds wall clock time: 129 minutes 16.12 seconds (7756.12 seconds total)