Starting phenix.real_space_refine on Thu Mar 5 09:26:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sh2_25122/03_2026/7sh2_25122.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sh2_25122/03_2026/7sh2_25122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sh2_25122/03_2026/7sh2_25122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sh2_25122/03_2026/7sh2_25122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sh2_25122/03_2026/7sh2_25122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sh2_25122/03_2026/7sh2_25122.map" } resolution = 3.23 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 4 5.21 5 S 113 5.16 5 C 13174 2.51 5 N 3597 2.21 5 O 4009 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20933 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3309 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 389} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2489 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2569 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2617 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "E" Number of atoms: 2692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2692 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2178 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 8, 'TRANS': 260} Chain breaks: 6 Chain: "G" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 4, 'TRANS': 287} Chain breaks: 1 Chain: "H" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2145 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 5 Chain: "P" Number of atoms: 202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 202 Classifications: {'DNA': 10} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 9} Chain: "T" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 264 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 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, 'AGS': 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, 'AGS': 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, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.22 Number of scatterers: 20933 At special positions: 0 Unit cell: (135.792, 125.856, 142.416, 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 113 16.00 P 36 15.00 Mg 4 11.99 O 4009 8.00 N 3597 7.00 C 13174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4868 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 18 sheets defined 51.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 97 removed outlier: 3.530A pdb=" N LEU A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 127 removed outlier: 3.766A pdb=" N ILE A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.529A pdb=" N TYR A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 210 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 removed outlier: 3.572A pdb=" N LYS A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.530A pdb=" N THR A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.709A pdb=" N MET A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 376 through 384 Processing helix chain 'A' and resid 385 through 387 No H-bonds generated for 'chain 'A' and resid 385 through 387' Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.658A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 432 Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.529A pdb=" N LEU A 490 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.659A pdb=" N TYR B 15 " --> pdb=" O TRP B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 69 through 73 removed outlier: 4.229A pdb=" N ALA B 72 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 73 " --> pdb=" O SER B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 87 through 98 Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 220 through 228 Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.602A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.234A pdb=" N LYS B 258 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 281 through 302 Processing helix chain 'B' and resid 305 through 322 removed outlier: 3.717A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.929A pdb=" N VAL C 79 " --> pdb=" O TYR C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.584A pdb=" N THR C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 137 removed outlier: 3.508A pdb=" N GLU C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 3.538A pdb=" N LEU C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 190 through 202 removed outlier: 4.098A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 219 Processing helix chain 'C' and resid 228 through 237 removed outlier: 3.603A pdb=" N ILE C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 256 through 270 removed outlier: 3.891A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.813A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 Processing helix chain 'C' and resid 315 through 332 Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 43 through 54 removed outlier: 3.971A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 83 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 160 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 193 through 208 removed outlier: 5.294A pdb=" N ASP D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ARG D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.514A pdb=" N GLY D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 removed outlier: 3.548A pdb=" N VAL D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 277 Processing helix chain 'D' and resid 279 through 294 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.745A pdb=" N VAL D 300 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 335 removed outlier: 3.585A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 19 through 32 removed outlier: 4.200A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 36 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 103 through 118 removed outlier: 4.484A pdb=" N ILE E 107 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 161 removed outlier: 3.809A pdb=" N ALA E 153 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 185 Processing helix chain 'E' and resid 194 through 209 Processing helix chain 'E' and resid 216 through 227 removed outlier: 3.666A pdb=" N LYS E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 through 291 Processing helix chain 'E' and resid 295 through 309 removed outlier: 3.506A pdb=" N ILE E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP E 309 " --> pdb=" O PHE E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 338 through 354 removed outlier: 3.611A pdb=" N LEU E 342 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP E 354 " --> pdb=" O MET E 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 30 removed outlier: 3.780A pdb=" N TYR F 16 " --> pdb=" O ALA F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.506A pdb=" N SER F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 220 Processing helix chain 'F' and resid 239 through 256 removed outlier: 4.392A pdb=" N GLY F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 422 Processing helix chain 'G' and resid 17 through 26 removed outlier: 4.335A pdb=" N ILE G 21 " --> pdb=" O HIS G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 33 removed outlier: 3.765A pdb=" N SER G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 96 removed outlier: 3.695A pdb=" N ILE G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL G 95 " --> pdb=" O ASP G 91 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 160 through 172 removed outlier: 4.298A pdb=" N GLU G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 249 removed outlier: 4.164A pdb=" N LYS G 247 " --> pdb=" O ASP G 243 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 329 removed outlier: 4.230A pdb=" N GLU G 323 " --> pdb=" O ALA G 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 27 Processing helix chain 'H' and resid 58 through 61 Processing helix chain 'H' and resid 67 through 71 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 98 through 103 removed outlier: 3.612A pdb=" N THR H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 209 Processing helix chain 'H' and resid 234 through 243 Processing helix chain 'H' and resid 245 through 249 removed outlier: 3.630A pdb=" N VAL H 248 " --> pdb=" O ASN H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 334 Processing helix chain 'H' and resid 334 through 339 removed outlier: 3.715A pdb=" N SER H 338 " --> pdb=" O THR H 334 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP H 339 " --> pdb=" O ILE H 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 334 through 339' Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 removed outlier: 5.787A pdb=" N THR A 149 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS A 261 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 106 " --> pdb=" O LYS A 261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 109 through 114 removed outlier: 6.127A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE B 46 " --> pdb=" O LEU B 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 82 removed outlier: 3.613A pdb=" N LEU C 80 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 147 " --> pdb=" O PHE C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 93 through 95 removed outlier: 4.049A pdb=" N LEU D 93 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR D 64 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 69 through 70 removed outlier: 3.566A pdb=" N VAL E 88 " --> pdb=" O GLU E 95 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 95 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE E 96 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU E 39 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 73 through 78 removed outlier: 4.085A pdb=" N ARG E 73 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ARG E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.372A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 78 through 81 removed outlier: 6.109A pdb=" N LEU F 79 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE F 6 " --> pdb=" O LEU F 79 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS F 4 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU F 5 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 121 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR F 120 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR F 159 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS F 122 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 157 " --> pdb=" O LYS F 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS F 203 " --> pdb=" O PHE F 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 34 through 35 Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 44 removed outlier: 4.047A pdb=" N THR F 43 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 231 through 232 removed outlier: 3.540A pdb=" N CYS F 438 " --> pdb=" O HIS F 434 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 231 through 232 removed outlier: 3.522A pdb=" N ASP F 445 " --> pdb=" O GLY F 462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 263 through 266 removed outlier: 5.008A pdb=" N HIS F 291 " --> pdb=" O GLU G 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 131 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N CYS F 295 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER G 127 " --> pdb=" O CYS F 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 80 through 84 removed outlier: 4.090A pdb=" N MET G 80 " --> pdb=" O ILE G 41 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE G 41 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU G 82 " --> pdb=" O ILE G 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL G 49 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN G 52 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 56 " --> pdb=" O ASN G 52 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL G 305 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS G 254 " --> pdb=" O LEU G 270 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET G 259 " --> pdb=" O PHE G 154 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER G 153 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS G 216 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL G 219 " --> pdb=" O ILE G 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 233 through 238 removed outlier: 3.657A pdb=" N ALA G 193 " --> pdb=" O TYR G 181 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE G 192 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL H 145 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 118 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 6 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 233 through 238 removed outlier: 4.113A pdb=" N GLU G 177 " --> pdb=" O LYS G 197 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL H 145 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR H 117 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE H 118 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 6 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 78 through 79 removed outlier: 3.625A pdb=" N GLN H 79 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 375 " --> pdb=" O ILE H 360 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN H 363 " --> pdb=" O ILE H 349 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 230 " --> pdb=" O SER H 350 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 283 through 285 removed outlier: 3.679A pdb=" N MET H 284 " --> pdb=" O ALA H 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 255 " --> pdb=" O SER H 262 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 264 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL H 252 " --> pdb=" O PHE H 324 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE H 324 " --> pdb=" O VAL H 252 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU H 254 " --> pdb=" O ILE H 322 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE H 322 " --> pdb=" O LEU H 254 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3018 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: 4.42 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6866 1.36 - 1.51: 5506 1.51 - 1.66: 8790 1.66 - 1.80: 100 1.80 - 1.95: 70 Bond restraints: 21332 Sorted by residual: bond pdb=" N MET F 224 " pdb=" CA MET F 224 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.29e-02 6.01e+03 2.42e+00 bond pdb=" CG1 ILE G 324 " pdb=" CD1 ILE G 324 " ideal model delta sigma weight residual 1.513 1.453 0.060 3.90e-02 6.57e+02 2.36e+00 bond pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C THR G 29 " pdb=" N PRO G 30 " ideal model delta sigma weight residual 1.335 1.349 -0.015 1.28e-02 6.10e+03 1.32e+00 bond pdb=" CA ASN F 286 " pdb=" CB ASN F 286 " ideal model delta sigma weight residual 1.535 1.557 -0.021 1.90e-02 2.77e+03 1.27e+00 ... (remaining 21327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28492 1.98 - 3.97: 347 3.97 - 5.95: 60 5.95 - 7.93: 17 7.93 - 9.92: 3 Bond angle restraints: 28919 Sorted by residual: angle pdb=" C SER E 79 " pdb=" CA SER E 79 " pdb=" CB SER E 79 " ideal model delta sigma weight residual 116.54 110.32 6.22 1.15e+00 7.56e-01 2.93e+01 angle pdb=" CA PRO F 48 " pdb=" N PRO F 48 " pdb=" CD PRO F 48 " ideal model delta sigma weight residual 112.00 105.04 6.96 1.40e+00 5.10e-01 2.47e+01 angle pdb=" C ILE G 324 " pdb=" N GLU G 325 " pdb=" CA GLU G 325 " ideal model delta sigma weight residual 120.29 114.08 6.21 1.42e+00 4.96e-01 1.92e+01 angle pdb=" N GLU G 325 " pdb=" CA GLU G 325 " pdb=" CB GLU G 325 " ideal model delta sigma weight residual 110.16 116.34 -6.18 1.48e+00 4.57e-01 1.74e+01 angle pdb=" N VAL G 16 " pdb=" CA VAL G 16 " pdb=" C VAL G 16 " ideal model delta sigma weight residual 113.53 109.51 4.02 9.80e-01 1.04e+00 1.68e+01 ... (remaining 28914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 12648 35.05 - 70.11: 327 70.11 - 105.16: 21 105.16 - 140.22: 2 140.22 - 175.27: 1 Dihedral angle restraints: 12999 sinusoidal: 5537 harmonic: 7462 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual 300.00 177.99 122.01 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 57.22 -124.95 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" C4' DA T 22 " pdb=" C3' DA T 22 " pdb=" O3' DA T 22 " pdb=" P DG T 23 " ideal model delta sinusoidal sigma weight residual -140.00 35.27 -175.27 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 12996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2543 0.043 - 0.085: 593 0.085 - 0.128: 193 0.128 - 0.170: 11 0.170 - 0.213: 6 Chirality restraints: 3346 Sorted by residual: chirality pdb=" CB ILE G 103 " pdb=" CA ILE G 103 " pdb=" CG1 ILE G 103 " pdb=" CG2 ILE G 103 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE G 251 " pdb=" CA ILE G 251 " pdb=" CG1 ILE G 251 " pdb=" CG2 ILE G 251 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA THR F 47 " pdb=" N THR F 47 " pdb=" C THR F 47 " pdb=" CB THR F 47 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.89e-01 ... (remaining 3343 not shown) Planarity restraints: 3560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 47 " -0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO F 48 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO F 48 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO F 48 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 167 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO C 168 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 488 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 489 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " 0.025 5.00e-02 4.00e+02 ... (remaining 3557 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 383 2.69 - 3.24: 19811 3.24 - 3.79: 33058 3.79 - 4.35: 42662 4.35 - 4.90: 71211 Nonbonded interactions: 167125 Sorted by model distance: nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.135 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.144 2.170 nonbonded pdb=" O3G AGS B 401 " pdb="MG MG B 402 " model vdw 2.169 2.170 nonbonded pdb=" O LEU G 326 " pdb=" OG1 THR G 330 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR F 92 " pdb=" OG1 THR F 218 " model vdw 2.202 3.040 ... (remaining 167120 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 6.140 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: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.460 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 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 : 0.002 0.060 21332 Z= 0.112 Angle : 0.560 9.916 28919 Z= 0.292 Chirality : 0.041 0.213 3346 Planarity : 0.004 0.124 3560 Dihedral : 15.294 175.269 8131 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.17), residues: 2497 helix: 1.46 (0.15), residues: 1225 sheet: 0.27 (0.27), residues: 440 loop : -1.43 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 36 TYR 0.015 0.001 TYR E 324 PHE 0.023 0.001 PHE F 205 TRP 0.026 0.001 TRP E 259 HIS 0.004 0.001 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00227 (21332) covalent geometry : angle 0.56039 (28919) hydrogen bonds : bond 0.16560 ( 1019) hydrogen bonds : angle 6.54763 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 289 time to evaluate : 0.757 Fit side-chains REVERT: A 168 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7812 (tp30) REVERT: A 307 GLU cc_start: 0.7134 (tp30) cc_final: 0.6829 (tp30) REVERT: C 245 LYS cc_start: 0.7448 (tptt) cc_final: 0.6955 (mtmm) REVERT: D 80 LYS cc_start: 0.7291 (tppt) cc_final: 0.6384 (tmtt) REVERT: F 14 ASP cc_start: 0.6320 (m-30) cc_final: 0.5925 (m-30) REVERT: H 148 TYR cc_start: 0.5798 (m-80) cc_final: 0.5591 (m-80) REVERT: H 371 LEU cc_start: 0.5549 (mt) cc_final: 0.5319 (mt) outliers start: 1 outliers final: 0 residues processed: 290 average time/residue: 0.1224 time to fit residues: 58.3499 Evaluate side-chains 213 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN B 35 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 305 HIS E 164 ASN F 226 ASN F 463 GLN G 9 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.191159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.156663 restraints weight = 29310.716| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.47 r_work: 0.3937 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21332 Z= 0.183 Angle : 0.628 9.180 28919 Z= 0.322 Chirality : 0.044 0.175 3346 Planarity : 0.005 0.049 3560 Dihedral : 11.892 176.329 3056 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 9.36 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2497 helix: 1.34 (0.15), residues: 1227 sheet: 0.19 (0.26), residues: 439 loop : -1.36 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 91 TYR 0.017 0.002 TYR C 75 PHE 0.026 0.002 PHE E 328 TRP 0.017 0.002 TRP C 256 HIS 0.009 0.001 HIS E 341 Details of bonding type rmsd covalent geometry : bond 0.00425 (21332) covalent geometry : angle 0.62821 (28919) hydrogen bonds : bond 0.04346 ( 1019) hydrogen bonds : angle 4.81421 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7929 (tp30) REVERT: A 174 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7243 (mtm110) REVERT: A 254 ILE cc_start: 0.7591 (mp) cc_final: 0.7108 (mm) REVERT: A 307 GLU cc_start: 0.7324 (tp30) cc_final: 0.6949 (tp30) REVERT: B 45 MET cc_start: 0.8018 (mtp) cc_final: 0.7798 (mtm) REVERT: C 91 ASP cc_start: 0.6853 (m-30) cc_final: 0.6633 (m-30) REVERT: F 14 ASP cc_start: 0.7170 (m-30) cc_final: 0.6736 (m-30) REVERT: F 415 TRP cc_start: 0.5872 (OUTLIER) cc_final: 0.4934 (p-90) REVERT: H 44 MET cc_start: 0.6005 (tpt) cc_final: 0.5240 (tpt) REVERT: H 371 LEU cc_start: 0.6664 (mt) cc_final: 0.6148 (mt) outliers start: 25 outliers final: 17 residues processed: 278 average time/residue: 0.1312 time to fit residues: 57.8966 Evaluate side-chains 239 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 415 TRP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 325 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 16 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 251 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 218 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 495 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 HIS C 180 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS D 313 ASN E 93 HIS E 164 ASN H 37 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.188807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.153835 restraints weight = 29236.988| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.17 r_work: 0.3921 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21332 Z= 0.158 Angle : 0.561 8.809 28919 Z= 0.291 Chirality : 0.042 0.201 3346 Planarity : 0.004 0.048 3560 Dihedral : 11.827 175.706 3056 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.91 % Allowed : 11.88 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.17), residues: 2497 helix: 1.41 (0.15), residues: 1217 sheet: 0.04 (0.26), residues: 433 loop : -1.34 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 91 TYR 0.029 0.002 TYR B 71 PHE 0.017 0.002 PHE C 40 TRP 0.021 0.002 TRP F 415 HIS 0.020 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00367 (21332) covalent geometry : angle 0.56143 (28919) hydrogen bonds : bond 0.04041 ( 1019) hydrogen bonds : angle 4.59296 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7993 (tp30) REVERT: A 174 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7394 (mtm110) REVERT: A 307 GLU cc_start: 0.7489 (tp30) cc_final: 0.7147 (tp30) REVERT: C 91 ASP cc_start: 0.7031 (m-30) cc_final: 0.6774 (m-30) REVERT: E 288 ASP cc_start: 0.7263 (t0) cc_final: 0.7055 (t0) REVERT: F 14 ASP cc_start: 0.7182 (m-30) cc_final: 0.6793 (m-30) REVERT: F 23 ILE cc_start: 0.7268 (mm) cc_final: 0.6856 (mm) REVERT: G 153 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8157 (m) REVERT: G 307 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: H 148 TYR cc_start: 0.6196 (m-80) cc_final: 0.5696 (m-80) REVERT: H 253 LYS cc_start: 0.6174 (tptp) cc_final: 0.5837 (tptt) outliers start: 44 outliers final: 28 residues processed: 271 average time/residue: 0.1359 time to fit residues: 58.1934 Evaluate side-chains 236 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 TYR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 ASN D 124 HIS D 313 ASN E 93 HIS E 164 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.189070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.153992 restraints weight = 29179.734| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 2.24 r_work: 0.3928 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21332 Z= 0.121 Angle : 0.527 8.306 28919 Z= 0.271 Chirality : 0.040 0.164 3346 Planarity : 0.003 0.049 3560 Dihedral : 11.717 175.444 3056 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.91 % Allowed : 13.79 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2497 helix: 1.58 (0.15), residues: 1217 sheet: 0.01 (0.26), residues: 433 loop : -1.31 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 20 TYR 0.024 0.001 TYR B 71 PHE 0.015 0.001 PHE G 202 TRP 0.019 0.001 TRP E 259 HIS 0.017 0.001 HIS E 93 Details of bonding type rmsd covalent geometry : bond 0.00278 (21332) covalent geometry : angle 0.52671 (28919) hydrogen bonds : bond 0.03511 ( 1019) hydrogen bonds : angle 4.43344 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 227 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7996 (tp30) REVERT: A 307 GLU cc_start: 0.7500 (tp30) cc_final: 0.7170 (tp30) REVERT: B 257 TRP cc_start: 0.8073 (OUTLIER) cc_final: 0.5640 (m-90) REVERT: C 91 ASP cc_start: 0.6920 (m-30) cc_final: 0.6669 (m-30) REVERT: E 105 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6909 (t70) REVERT: F 14 ASP cc_start: 0.7140 (m-30) cc_final: 0.6741 (m-30) REVERT: F 468 ILE cc_start: 0.8501 (mm) cc_final: 0.7923 (mm) REVERT: G 153 SER cc_start: 0.8617 (OUTLIER) cc_final: 0.8182 (m) REVERT: G 171 LYS cc_start: 0.7228 (ttpp) cc_final: 0.7007 (tptp) REVERT: G 307 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7129 (pt0) REVERT: H 148 TYR cc_start: 0.6190 (m-80) cc_final: 0.5732 (m-80) REVERT: H 253 LYS cc_start: 0.6205 (tptp) cc_final: 0.5902 (tptt) outliers start: 44 outliers final: 24 residues processed: 262 average time/residue: 0.1301 time to fit residues: 54.9316 Evaluate side-chains 232 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 96 ASN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 250 optimal weight: 0.3980 chunk 203 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 132 optimal weight: 0.0570 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 181 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS E 93 HIS E 164 ASN G 54 HIS H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.189347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.154597 restraints weight = 29094.933| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 2.17 r_work: 0.3935 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21332 Z= 0.114 Angle : 0.522 8.024 28919 Z= 0.267 Chirality : 0.040 0.163 3346 Planarity : 0.003 0.048 3560 Dihedral : 11.641 175.274 3056 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.87 % Allowed : 14.53 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2497 helix: 1.64 (0.15), residues: 1218 sheet: -0.03 (0.26), residues: 433 loop : -1.32 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 20 TYR 0.020 0.001 TYR E 92 PHE 0.016 0.001 PHE G 40 TRP 0.018 0.001 TRP E 259 HIS 0.006 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00257 (21332) covalent geometry : angle 0.52165 (28919) hydrogen bonds : bond 0.03366 ( 1019) hydrogen bonds : angle 4.35896 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8015 (tp30) REVERT: A 307 GLU cc_start: 0.7477 (tp30) cc_final: 0.7109 (tp30) REVERT: B 257 TRP cc_start: 0.8207 (OUTLIER) cc_final: 0.5698 (m-90) REVERT: C 91 ASP cc_start: 0.6896 (m-30) cc_final: 0.6633 (m-30) REVERT: E 329 ASP cc_start: 0.6248 (t0) cc_final: 0.6044 (t0) REVERT: F 14 ASP cc_start: 0.7154 (m-30) cc_final: 0.6750 (m-30) REVERT: G 153 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8172 (m) REVERT: G 307 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7211 (pt0) REVERT: H 148 TYR cc_start: 0.6130 (m-80) cc_final: 0.5691 (m-80) REVERT: H 253 LYS cc_start: 0.6105 (tptp) cc_final: 0.5795 (tptt) outliers start: 43 outliers final: 31 residues processed: 246 average time/residue: 0.1335 time to fit residues: 51.7069 Evaluate side-chains 237 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 54 HIS Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 157 optimal weight: 5.9990 chunk 234 optimal weight: 0.6980 chunk 111 optimal weight: 0.0870 chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN B 26 ASN B 35 GLN ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS H 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.186429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.151325 restraints weight = 29143.991| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 2.15 r_work: 0.3891 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21332 Z= 0.148 Angle : 0.553 9.345 28919 Z= 0.283 Chirality : 0.041 0.159 3346 Planarity : 0.004 0.048 3560 Dihedral : 11.682 175.843 3056 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.13 % Allowed : 14.97 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2497 helix: 1.51 (0.15), residues: 1218 sheet: -0.11 (0.26), residues: 441 loop : -1.33 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 166 TYR 0.021 0.001 TYR E 92 PHE 0.020 0.001 PHE G 202 TRP 0.017 0.001 TRP E 259 HIS 0.020 0.001 HIS G 54 Details of bonding type rmsd covalent geometry : bond 0.00350 (21332) covalent geometry : angle 0.55289 (28919) hydrogen bonds : bond 0.03627 ( 1019) hydrogen bonds : angle 4.39644 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8028 (tp30) REVERT: A 178 MET cc_start: 0.5418 (mmm) cc_final: 0.5114 (mmt) REVERT: A 307 GLU cc_start: 0.7514 (tp30) cc_final: 0.7163 (tp30) REVERT: B 257 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.5836 (m-90) REVERT: C 91 ASP cc_start: 0.6927 (m-30) cc_final: 0.6661 (m-30) REVERT: E 142 GLU cc_start: 0.8795 (mp0) cc_final: 0.8418 (mp0) REVERT: E 255 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6586 (mp) REVERT: F 14 ASP cc_start: 0.7188 (m-30) cc_final: 0.6782 (m-30) REVERT: F 415 TRP cc_start: 0.6177 (p-90) cc_final: 0.5576 (p-90) REVERT: G 153 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8237 (m) REVERT: G 307 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: H 148 TYR cc_start: 0.6174 (m-80) cc_final: 0.5688 (m-80) REVERT: H 253 LYS cc_start: 0.6225 (tptp) cc_final: 0.5903 (tptt) outliers start: 49 outliers final: 32 residues processed: 265 average time/residue: 0.1339 time to fit residues: 56.2030 Evaluate side-chains 246 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 137 CYS Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 297 ASN Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 249 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 92 optimal weight: 0.0020 chunk 66 optimal weight: 0.0970 chunk 91 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 251 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 30 optimal weight: 0.0670 chunk 73 optimal weight: 1.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 180 ASN G 164 HIS H 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.189760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.155353 restraints weight = 29246.945| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.13 r_work: 0.3942 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21332 Z= 0.103 Angle : 0.517 7.675 28919 Z= 0.265 Chirality : 0.040 0.160 3346 Planarity : 0.003 0.048 3560 Dihedral : 11.500 174.813 3056 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.70 % Allowed : 16.23 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2497 helix: 1.75 (0.15), residues: 1217 sheet: -0.09 (0.26), residues: 446 loop : -1.30 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 268 TYR 0.024 0.001 TYR E 92 PHE 0.018 0.001 PHE G 202 TRP 0.018 0.001 TRP E 259 HIS 0.003 0.000 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00226 (21332) covalent geometry : angle 0.51730 (28919) hydrogen bonds : bond 0.03110 ( 1019) hydrogen bonds : angle 4.24433 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8055 (tp30) REVERT: A 307 GLU cc_start: 0.7507 (tp30) cc_final: 0.7169 (tp30) REVERT: B 115 GLU cc_start: 0.8064 (tp30) cc_final: 0.7810 (mp0) REVERT: B 177 GLN cc_start: 0.7901 (mt0) cc_final: 0.7572 (mt0) REVERT: B 257 TRP cc_start: 0.8313 (OUTLIER) cc_final: 0.5724 (m-90) REVERT: C 91 ASP cc_start: 0.6906 (m-30) cc_final: 0.6656 (m-30) REVERT: E 142 GLU cc_start: 0.8746 (mp0) cc_final: 0.8415 (mp0) REVERT: E 305 PHE cc_start: 0.6914 (m-10) cc_final: 0.6705 (m-10) REVERT: F 14 ASP cc_start: 0.7145 (m-30) cc_final: 0.6754 (m-30) REVERT: G 153 SER cc_start: 0.8630 (OUTLIER) cc_final: 0.8209 (m) REVERT: G 307 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: H 148 TYR cc_start: 0.6103 (m-80) cc_final: 0.5627 (m-80) REVERT: H 253 LYS cc_start: 0.6176 (tptp) cc_final: 0.5864 (tptt) outliers start: 39 outliers final: 30 residues processed: 252 average time/residue: 0.1282 time to fit residues: 51.7982 Evaluate side-chains 240 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 430 LEU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 307 GLU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 27 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 178 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 20 optimal weight: 0.0170 chunk 245 optimal weight: 9.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS F 286 ASN H 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.188067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.153583 restraints weight = 29116.773| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 2.12 r_work: 0.3922 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3792 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21332 Z= 0.115 Angle : 0.530 9.880 28919 Z= 0.269 Chirality : 0.040 0.157 3346 Planarity : 0.003 0.048 3560 Dihedral : 11.488 175.335 3056 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.91 % Allowed : 16.28 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.18), residues: 2497 helix: 1.71 (0.15), residues: 1217 sheet: -0.11 (0.25), residues: 446 loop : -1.29 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 268 TYR 0.022 0.001 TYR E 92 PHE 0.018 0.001 PHE G 202 TRP 0.017 0.001 TRP E 259 HIS 0.005 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00263 (21332) covalent geometry : angle 0.52990 (28919) hydrogen bonds : bond 0.03230 ( 1019) hydrogen bonds : angle 4.25140 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 216 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7977 (tp30) REVERT: A 307 GLU cc_start: 0.7494 (tp30) cc_final: 0.7165 (tp30) REVERT: B 186 TYR cc_start: 0.6922 (p90) cc_final: 0.6637 (p90) REVERT: B 257 TRP cc_start: 0.8392 (OUTLIER) cc_final: 0.5854 (m-90) REVERT: C 91 ASP cc_start: 0.6877 (m-30) cc_final: 0.6615 (m-30) REVERT: E 142 GLU cc_start: 0.8778 (mp0) cc_final: 0.8434 (mp0) REVERT: E 255 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6684 (mp) REVERT: F 14 ASP cc_start: 0.7144 (m-30) cc_final: 0.6749 (m-30) REVERT: G 153 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8226 (m) REVERT: H 148 TYR cc_start: 0.6179 (m-80) cc_final: 0.5649 (m-80) REVERT: H 253 LYS cc_start: 0.6200 (tptp) cc_final: 0.5881 (tptt) outliers start: 44 outliers final: 33 residues processed: 249 average time/residue: 0.1338 time to fit residues: 53.6067 Evaluate side-chains 243 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 247 HIS Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 286 ASN Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 167 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 240 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 164 optimal weight: 0.6980 chunk 204 optimal weight: 2.9990 chunk 211 optimal weight: 0.0370 chunk 159 optimal weight: 0.7980 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS H 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.188097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.153703 restraints weight = 29131.022| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 2.11 r_work: 0.3919 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3789 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21332 Z= 0.117 Angle : 0.545 10.631 28919 Z= 0.275 Chirality : 0.041 0.298 3346 Planarity : 0.003 0.048 3560 Dihedral : 11.477 175.289 3056 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.13 % Allowed : 16.10 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2497 helix: 1.70 (0.15), residues: 1217 sheet: -0.07 (0.25), residues: 444 loop : -1.33 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 20 TYR 0.024 0.001 TYR E 92 PHE 0.019 0.001 PHE G 202 TRP 0.017 0.001 TRP E 259 HIS 0.005 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00268 (21332) covalent geometry : angle 0.54543 (28919) hydrogen bonds : bond 0.03225 ( 1019) hydrogen bonds : angle 4.22856 ( 3018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7977 (tp30) REVERT: A 178 MET cc_start: 0.5219 (mmm) cc_final: 0.4734 (mmt) REVERT: A 307 GLU cc_start: 0.7435 (tp30) cc_final: 0.7154 (tp30) REVERT: B 186 TYR cc_start: 0.6973 (p90) cc_final: 0.6748 (p90) REVERT: B 257 TRP cc_start: 0.8397 (OUTLIER) cc_final: 0.5884 (m-90) REVERT: C 91 ASP cc_start: 0.6864 (m-30) cc_final: 0.6607 (m-30) REVERT: E 142 GLU cc_start: 0.8746 (mp0) cc_final: 0.8420 (mp0) REVERT: E 255 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6709 (mm) REVERT: F 14 ASP cc_start: 0.7145 (m-30) cc_final: 0.6743 (m-30) REVERT: G 153 SER cc_start: 0.8653 (OUTLIER) cc_final: 0.8226 (m) REVERT: G 200 LEU cc_start: 0.6030 (mp) cc_final: 0.5755 (tp) REVERT: H 148 TYR cc_start: 0.6206 (m-80) cc_final: 0.5667 (m-80) outliers start: 49 outliers final: 38 residues processed: 251 average time/residue: 0.1294 time to fit residues: 52.3131 Evaluate side-chains 246 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain F residue 438 CYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 316 ILE Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 229 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 112 optimal weight: 0.0870 chunk 58 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.186831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.151173 restraints weight = 28990.335| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.34 r_work: 0.3859 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21332 Z= 0.116 Angle : 0.551 14.073 28919 Z= 0.274 Chirality : 0.041 0.309 3346 Planarity : 0.003 0.047 3560 Dihedral : 11.459 175.320 3056 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.78 % Allowed : 16.32 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2497 helix: 1.66 (0.15), residues: 1218 sheet: -0.09 (0.25), residues: 445 loop : -1.32 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 411 TYR 0.025 0.001 TYR E 92 PHE 0.020 0.001 PHE G 202 TRP 0.017 0.001 TRP E 259 HIS 0.006 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00265 (21332) covalent geometry : angle 0.55138 (28919) hydrogen bonds : bond 0.03251 ( 1019) hydrogen bonds : angle 4.21266 ( 3018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4994 Ramachandran restraints generated. 2497 Oldfield, 0 Emsley, 2497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 223 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7969 (tp30) REVERT: A 178 MET cc_start: 0.5271 (mmm) cc_final: 0.4719 (mmt) REVERT: A 307 GLU cc_start: 0.7371 (tp30) cc_final: 0.7122 (tp30) REVERT: B 186 TYR cc_start: 0.7132 (p90) cc_final: 0.6907 (p90) REVERT: B 257 TRP cc_start: 0.8432 (OUTLIER) cc_final: 0.5943 (m-90) REVERT: C 91 ASP cc_start: 0.6767 (m-30) cc_final: 0.6529 (m-30) REVERT: E 142 GLU cc_start: 0.8684 (mp0) cc_final: 0.8309 (mp0) REVERT: E 255 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6623 (mm) REVERT: E 324 TYR cc_start: 0.8013 (m-10) cc_final: 0.7789 (m-10) REVERT: F 14 ASP cc_start: 0.7233 (m-30) cc_final: 0.6842 (m-30) REVERT: F 231 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.3194 (tmm) REVERT: F 415 TRP cc_start: 0.6018 (p-90) cc_final: 0.5693 (p-90) REVERT: G 153 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8149 (m) REVERT: G 200 LEU cc_start: 0.5894 (mp) cc_final: 0.5648 (tp) REVERT: H 148 TYR cc_start: 0.6244 (m-80) cc_final: 0.5621 (m-80) outliers start: 41 outliers final: 32 residues processed: 255 average time/residue: 0.1280 time to fit residues: 52.5078 Evaluate side-chains 249 residues out of total 2301 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 351 HIS Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 257 TRP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 TYR Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 255 ILE Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 43 THR Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 409 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 153 SER Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 364 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 253 random chunks: chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 0.0970 chunk 98 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN H 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.181989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.145415 restraints weight = 29120.061| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.32 r_work: 0.3801 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 21332 Z= 0.163 Angle : 0.608 12.298 28919 Z= 0.306 Chirality : 0.042 0.320 3346 Planarity : 0.004 0.051 3560 Dihedral : 11.631 176.260 3056 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.87 % Allowed : 16.62 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2497 helix: 1.34 (0.15), residues: 1226 sheet: -0.19 (0.25), residues: 442 loop : -1.36 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 411 TYR 0.024 0.002 TYR E 92 PHE 0.019 0.001 PHE G 202 TRP 0.016 0.002 TRP E 259 HIS 0.005 0.001 HIS F 263 Details of bonding type rmsd covalent geometry : bond 0.00390 (21332) covalent geometry : angle 0.60760 (28919) hydrogen bonds : bond 0.03839 ( 1019) hydrogen bonds : angle 4.40596 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4962.30 seconds wall clock time: 85 minutes 53.26 seconds (5153.26 seconds total)