Starting phenix.real_space_refine on Sat Aug 8 18:37:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11aa_75580/08_2026/11aa_75580_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/11aa_75580/08_2026/11aa_75580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11aa_75580/08_2026/11aa_75580_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11aa_75580/08_2026/11aa_75580_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11aa_75580/08_2026/11aa_75580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11aa_75580/08_2026/11aa_75580.map" } resolution = 2.78 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= 0.006 sd= 1.079 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 355 5.49 5 Mg 5 5.21 5 S 57 5.16 5 C 17457 2.51 5 N 5236 2.21 5 O 6415 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29525 Number of models: 1 Model: "" Number of chains: 18 Chain: "1" Number of atoms: 4693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 4693 Classifications: {'RNA': 219} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 13, 'rna3p_pur': 102, 'rna3p_pyr': 79} Link IDs: {'rna2p': 37, 'rna3p': 181} Chain breaks: 5 Chain: "2" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1082 Classifications: {'RNA': 51} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 6, 'rna3p_pur': 19, 'rna3p_pyr': 22} Link IDs: {'rna2p': 10, 'rna3p': 40} Chain breaks: 2 Chain: "3" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1798 Classifications: {'RNA': 85} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 17, 'rna3p_pur': 28, 'rna3p_pyr': 28} Link IDs: {'rna2p': 29, 'rna3p': 55} Chain breaks: 1 Chain: "7" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 471 Classifications: {'peptide': 52} Link IDs: {'TRANS': 51} Chain: "G" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1385 Classifications: {'peptide': 178} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 169} Chain breaks: 1 Chain: "H" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1534 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain breaks: 2 Chain: "K" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2291 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 2 Chain: "L" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 723 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain breaks: 1 Chain: "N" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1314 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain breaks: 1 Chain: "b" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1801 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Chain: "i" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 641 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "m" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "n" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2760 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 317} Chain breaks: 3 Chain: "o" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1108 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "p" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3414 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 2 Chain: "s" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1764 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 23, 'TRANS': 188} Chain breaks: 2 Chain: "t" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1931 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain breaks: 2 Chain: "1" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.64, per 1000 atoms: 0.19 Number of scatterers: 29525 At special positions: 0 Unit cell: (130.724, 145.604, 180.676, 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 57 16.00 P 355 15.00 Mg 5 11.99 O 6415 8.00 N 5236 7.00 C 17457 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: 2.49 Conformation dependent library (CDL) restraints added in 938.1 milliseconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5150 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 22 sheets defined 51.9% alpha, 13.9% beta 109 base pairs and 156 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain '7' and resid 178 through 193 Processing helix chain '7' and resid 195 through 201 Processing helix chain '7' and resid 211 through 226 Processing helix chain 'G' and resid 55 through 69 removed outlier: 4.283A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 174 removed outlier: 4.726A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 190 removed outlier: 3.684A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'H' and resid 143 through 148 Processing helix chain 'H' and resid 157 through 162 Processing helix chain 'H' and resid 162 through 173 Processing helix chain 'H' and resid 218 through 226 Processing helix chain 'H' and resid 245 through 254 removed outlier: 3.929A pdb=" N LYS H 249 " --> pdb=" O SER H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 278 No H-bonds generated for 'chain 'H' and resid 276 through 278' Processing helix chain 'H' and resid 291 through 300 removed outlier: 3.896A pdb=" N LEU H 295 " --> pdb=" O ILE H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 303 No H-bonds generated for 'chain 'H' and resid 301 through 303' Processing helix chain 'H' and resid 329 through 338 removed outlier: 4.002A pdb=" N VAL H 333 " --> pdb=" O ASP H 329 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU H 338 " --> pdb=" O ASN H 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 Processing helix chain 'K' and resid 69 through 75 Processing helix chain 'K' and resid 107 through 115 Processing helix chain 'K' and resid 129 through 135 removed outlier: 3.534A pdb=" N ILE K 132 " --> pdb=" O ASP K 129 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS K 133 " --> pdb=" O SER K 130 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL K 135 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 145 removed outlier: 3.555A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 186 through 188 No H-bonds generated for 'chain 'K' and resid 186 through 188' Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.563A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 201 removed outlier: 3.870A pdb=" N LYS K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 295 through 302 removed outlier: 3.708A pdb=" N GLU K 300 " --> pdb=" O VAL K 297 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU K 301 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU K 302 " --> pdb=" O ASP K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 337 removed outlier: 3.664A pdb=" N GLU K 335 " --> pdb=" O LYS K 331 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE K 336 " --> pdb=" O GLY K 332 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 340 No H-bonds generated for 'chain 'K' and resid 338 through 340' Processing helix chain 'K' and resid 341 through 346 Processing helix chain 'L' and resid 13 through 26 removed outlier: 3.823A pdb=" N PHE L 26 " --> pdb=" O VAL L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 67 removed outlier: 4.505A pdb=" N ARG L 67 " --> pdb=" O VAL L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 86 through 94 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.836A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 109 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 159 through 163 removed outlier: 3.531A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'b' and resid 42 through 56 Processing helix chain 'b' and resid 72 through 81 removed outlier: 3.824A pdb=" N GLU b 76 " --> pdb=" O GLN b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 140 through 145 Processing helix chain 'b' and resid 146 through 161 Processing helix chain 'b' and resid 244 through 255 Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.626A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 Processing helix chain 'i' and resid 65 through 78 removed outlier: 3.727A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 99 Processing helix chain 'm' and resid 197 through 209 Processing helix chain 'm' and resid 211 through 215 removed outlier: 3.605A pdb=" N LYS m 214 " --> pdb=" O PRO m 211 " (cutoff:3.500A) Processing helix chain 'm' and resid 216 through 220 Processing helix chain 'm' and resid 228 through 233 removed outlier: 4.223A pdb=" N HIS m 232 " --> pdb=" O ASN m 228 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE m 233 " --> pdb=" O THR m 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 228 through 233' Processing helix chain 'm' and resid 238 through 264 Processing helix chain 'm' and resid 281 through 291 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 73 removed outlier: 3.503A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 96 removed outlier: 3.829A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 131 Processing helix chain 'n' and resid 132 through 145 Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 240 removed outlier: 3.868A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 254 Processing helix chain 'n' and resid 354 through 359 Processing helix chain 'n' and resid 372 through 383 removed outlier: 3.578A pdb=" N PHE n 378 " --> pdb=" O ASP n 374 " (cutoff:3.500A) Processing helix chain 'n' and resid 391 through 394 removed outlier: 3.565A pdb=" N ASP n 394 " --> pdb=" O ALA n 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 391 through 394' Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.675A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'n' and resid 444 through 448 removed outlier: 3.545A pdb=" N LEU n 448 " --> pdb=" O ASN n 445 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 153 removed outlier: 3.509A pdb=" N ALA o 145 " --> pdb=" O ASN o 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 192 through 214 Processing helix chain 'p' and resid 43 through 47 Processing helix chain 'p' and resid 50 through 61 Processing helix chain 'p' and resid 66 through 79 Proline residue: p 74 - end of helix Processing helix chain 'p' and resid 91 through 108 Proline residue: p 99 - end of helix Processing helix chain 'p' and resid 110 through 114 Processing helix chain 'p' and resid 123 through 138 Processing helix chain 'p' and resid 153 through 164 Processing helix chain 'p' and resid 171 through 182 Processing helix chain 'p' and resid 197 through 205 removed outlier: 3.654A pdb=" N GLY p 205 " --> pdb=" O ILE p 201 " (cutoff:3.500A) Processing helix chain 'p' and resid 206 through 217 Processing helix chain 'p' and resid 232 through 243 Processing helix chain 'p' and resid 272 through 274 No H-bonds generated for 'chain 'p' and resid 272 through 274' Processing helix chain 'p' and resid 275 through 287 Processing helix chain 'p' and resid 298 through 312 Processing helix chain 'p' and resid 324 through 338 Processing helix chain 'p' and resid 348 through 351 Processing helix chain 'p' and resid 369 through 377 Processing helix chain 'p' and resid 395 through 399 removed outlier: 3.799A pdb=" N LEU p 399 " --> pdb=" O PRO p 396 " (cutoff:3.500A) Processing helix chain 'p' and resid 400 through 408 removed outlier: 4.187A pdb=" N TYR p 404 " --> pdb=" O GLY p 400 " (cutoff:3.500A) Processing helix chain 'p' and resid 425 through 436 Processing helix chain 'p' and resid 436 through 456 Processing helix chain 'p' and resid 469 through 477 Processing helix chain 's' and resid 161 through 166 Processing helix chain 's' and resid 262 through 267 removed outlier: 3.538A pdb=" N VAL s 267 " --> pdb=" O ARG s 264 " (cutoff:3.500A) Processing helix chain 's' and resid 269 through 285 removed outlier: 3.590A pdb=" N ALA s 273 " --> pdb=" O SER s 269 " (cutoff:3.500A) Processing helix chain 's' and resid 290 through 305 Processing helix chain 's' and resid 333 through 337 Processing helix chain 's' and resid 341 through 345 Processing helix chain 's' and resid 347 through 357 Processing helix chain 's' and resid 358 through 362 Processing helix chain 's' and resid 373 through 377 Processing helix chain 's' and resid 382 through 397 Processing helix chain 't' and resid 57 through 87 removed outlier: 3.581A pdb=" N ILE t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 190 Processing helix chain 't' and resid 200 through 212 removed outlier: 3.594A pdb=" N GLY t 212 " --> pdb=" O ILE t 208 " (cutoff:3.500A) Processing helix chain 't' and resid 231 through 240 removed outlier: 3.972A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 241 through 243 No H-bonds generated for 'chain 't' and resid 241 through 243' Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 268 Processing helix chain 't' and resid 281 through 299 Processing helix chain 't' and resid 313 through 322 removed outlier: 3.500A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AA2, first strand: chain 'G' and resid 133 through 134 removed outlier: 6.421A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 203 through 209 removed outlier: 6.538A pdb=" N VAL H 240 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE H 206 " --> pdb=" O TYR H 238 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR H 238 " --> pdb=" O ILE H 206 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE H 208 " --> pdb=" O ASN H 236 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN H 236 " --> pdb=" O PHE H 208 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE H 235 " --> pdb=" O ASN H 154 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 305 through 312 removed outlier: 3.511A pdb=" N ILE H 311 " --> pdb=" O PHE H 322 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE H 322 " --> pdb=" O ILE H 311 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 64 through 65 removed outlier: 6.110A pdb=" N LYS K 64 " --> pdb=" O GLU p 416 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN p 266 " --> pdb=" O ASN p 413 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR p 415 " --> pdb=" O GLN p 266 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR p 268 " --> pdb=" O TYR p 415 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLY p 267 " --> pdb=" O MET p 392 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU p 394 " --> pdb=" O GLY p 267 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL p 269 " --> pdb=" O LEU p 394 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE p 361 " --> pdb=" O LEU p 391 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE p 393 " --> pdb=" O ILE p 361 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN p 363 " --> pdb=" O PHE p 393 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS p 291 " --> pdb=" O TRP p 360 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE p 362 " --> pdb=" O LYS p 291 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE p 293 " --> pdb=" O ILE p 362 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU p 317 " --> pdb=" O ILE p 344 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N THR p 346 " --> pdb=" O LEU p 317 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU p 319 " --> pdb=" O THR p 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 243 through 250 removed outlier: 5.896A pdb=" N THR K 243 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASN K 84 " --> pdb=" O THR K 243 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN K 245 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL K 82 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS K 247 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU K 80 " --> pdb=" O HIS K 247 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY K 249 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP K 77 " --> pdb=" O THR K 283 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR K 283 " --> pdb=" O ASP K 77 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN K 79 " --> pdb=" O ILE K 281 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE K 281 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE K 81 " --> pdb=" O ILE K 279 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE K 279 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL K 83 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AA8, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.444A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU K 124 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASP K 183 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE K 126 " --> pdb=" O ASP K 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AB1, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AB2, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.525A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'b' and resid 59 through 61 removed outlier: 6.689A pdb=" N THR b 33 " --> pdb=" O ARG b 60 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 210 through 214 WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 218 through 227 current: chain 'b' and resid 136 through 139 removed outlier: 6.324A pdb=" N LEU b 137 " --> pdb=" O VAL m 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'n' and resid 176 through 182 removed outlier: 6.402A pdb=" N VAL n 176 " --> pdb=" O ASN n 191 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ASN n 191 " --> pdb=" O VAL n 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'n' and resid 247 through 248 removed outlier: 4.071A pdb=" N LYS n 247 " --> pdb=" O ILE n 263 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'n' and resid 386 through 389 Processing sheet with id=AB8, first strand: chain 'o' and resid 117 through 124 removed outlier: 5.298A pdb=" N LEU o 117 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU o 138 " --> pdb=" O LEU o 117 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU o 119 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE o 136 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG o 121 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N TYR o 134 " --> pdb=" O ARG o 121 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA o 123 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 145 through 148 removed outlier: 6.320A pdb=" N ILE p 117 " --> pdb=" O LEU p 168 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA p 170 " --> pdb=" O ILE p 117 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL p 119 " --> pdb=" O ALA p 170 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE p 118 " --> pdb=" O ILE p 194 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP p 196 " --> pdb=" O ILE p 118 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE p 120 " --> pdb=" O ASP p 196 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU p 193 " --> pdb=" O MET p 225 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE p 227 " --> pdb=" O LEU p 193 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE p 195 " --> pdb=" O PHE p 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 's' and resid 124 through 127 Processing sheet with id=AC2, first strand: chain 's' and resid 170 through 173 removed outlier: 4.015A pdb=" N GLY s 172 " --> pdb=" O ILE s 180 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 't' and resid 129 through 134 removed outlier: 6.980A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL t 194 " --> pdb=" O ILE t 310 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL t 312 " --> pdb=" O VAL t 194 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE t 196 " --> pdb=" O VAL t 312 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 't' and resid 213 through 216 1022 hydrogen bonds defined for protein. 2889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 269 hydrogen bonds 444 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 156 stacking parallelities Total time for adding SS restraints: 5.51 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6414 1.33 - 1.45: 8194 1.45 - 1.57: 15433 1.57 - 1.69: 699 1.69 - 1.81: 96 Bond restraints: 30836 Sorted by residual: bond pdb=" C6 A 1 123 " pdb=" N1 A 1 123 " ideal model delta sigma weight residual 1.351 1.340 0.011 7.00e-03 2.04e+04 2.46e+00 bond pdb=" C2 U 1 149 " pdb=" N3 U 1 149 " ideal model delta sigma weight residual 1.373 1.362 0.011 7.00e-03 2.04e+04 2.32e+00 bond pdb=" C VAL n 371 " pdb=" N PRO n 372 " ideal model delta sigma weight residual 1.332 1.347 -0.015 1.12e-02 7.97e+03 1.82e+00 bond pdb=" N9 G 1 251 " pdb=" C4 G 1 251 " ideal model delta sigma weight residual 1.375 1.385 -0.010 8.00e-03 1.56e+04 1.65e+00 bond pdb=" C GLU H 341 " pdb=" N LYS H 342 " ideal model delta sigma weight residual 1.333 1.367 -0.034 2.74e-02 1.33e+03 1.56e+00 ... (remaining 30831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 41651 1.55 - 3.11: 1456 3.11 - 4.66: 144 4.66 - 6.21: 9 6.21 - 7.77: 2 Bond angle restraints: 43262 Sorted by residual: angle pdb=" O5' A 3 47 " pdb=" C5' A 3 47 " pdb=" C4' A 3 47 " ideal model delta sigma weight residual 109.40 113.48 -4.08 8.00e-01 1.56e+00 2.60e+01 angle pdb=" O5' U 1 329 " pdb=" C5' U 1 329 " pdb=" C4' U 1 329 " ideal model delta sigma weight residual 109.40 113.11 -3.71 8.00e-01 1.56e+00 2.15e+01 angle pdb=" O5' C 1 73 " pdb=" C5' C 1 73 " pdb=" C4' C 1 73 " ideal model delta sigma weight residual 109.40 112.75 -3.35 8.00e-01 1.56e+00 1.75e+01 angle pdb=" O5' A 3 34 " pdb=" C5' A 3 34 " pdb=" C4' A 3 34 " ideal model delta sigma weight residual 109.40 112.69 -3.29 8.00e-01 1.56e+00 1.70e+01 angle pdb=" O5' A 3 48 " pdb=" C5' A 3 48 " pdb=" C4' A 3 48 " ideal model delta sigma weight residual 109.40 112.69 -3.29 8.00e-01 1.56e+00 1.69e+01 ... (remaining 43257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 17565 23.10 - 46.20: 1057 46.20 - 69.30: 525 69.30 - 92.40: 102 92.40 - 115.50: 2 Dihedral angle restraints: 19251 sinusoidal: 11335 harmonic: 7916 Sorted by residual: dihedral pdb=" CA GLU H 215 " pdb=" C GLU H 215 " pdb=" N ALA H 216 " pdb=" CA ALA H 216 " ideal model delta harmonic sigma weight residual 180.00 -157.16 -22.84 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA MET K 231 " pdb=" C MET K 231 " pdb=" N ASN K 232 " pdb=" CA ASN K 232 " ideal model delta harmonic sigma weight residual -180.00 -163.21 -16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CG ARG p 80 " pdb=" CD ARG p 80 " pdb=" NE ARG p 80 " pdb=" CZ ARG p 80 " ideal model delta sinusoidal sigma weight residual 90.00 134.03 -44.03 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 19248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3334 0.031 - 0.062: 946 0.062 - 0.093: 325 0.093 - 0.124: 442 0.124 - 0.155: 51 Chirality restraints: 5098 Sorted by residual: chirality pdb=" C1' G 1 75 " pdb=" O4' G 1 75 " pdb=" C2' G 1 75 " pdb=" N9 G 1 75 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ILE p 355 " pdb=" N ILE p 355 " pdb=" C ILE p 355 " pdb=" CB ILE p 355 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA VAL H 308 " pdb=" N VAL H 308 " pdb=" C VAL H 308 " pdb=" CB VAL H 308 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 5095 not shown) Planarity restraints: 4182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 296 " -0.029 2.00e-02 2.50e+03 1.35e-02 4.99e+00 pdb=" N9 A 1 296 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A 1 296 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 296 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 1 296 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A 1 296 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 1 296 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 296 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A 1 296 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 1 296 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 21 " -0.178 9.50e-02 1.11e+02 7.99e-02 4.33e+00 pdb=" NE ARG L 21 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG L 21 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG L 21 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 21 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 144 " -0.168 9.50e-02 1.11e+02 7.56e-02 3.80e+00 pdb=" NE ARG N 144 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG N 144 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG N 144 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG N 144 " -0.003 2.00e-02 2.50e+03 ... (remaining 4179 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 206 2.59 - 3.16: 23277 3.16 - 3.74: 48812 3.74 - 4.32: 69632 4.32 - 4.90: 107757 Nonbonded interactions: 249684 Sorted by model distance: nonbonded pdb=" O2' U 1 117 " pdb=" OP2 U 1 119 " model vdw 2.007 3.040 nonbonded pdb=" OD2 ASP n 115 " pdb=" OH TYR s 308 " model vdw 2.089 3.040 nonbonded pdb=" OD1 ASP H 329 " pdb=" OG SER H 332 " model vdw 2.107 3.040 nonbonded pdb=" OP1 A 1 77 " pdb="MG MG 13403 " model vdw 2.110 2.170 nonbonded pdb=" OP2 A 1 317 " pdb="MG MG 13405 " model vdw 2.131 2.170 ... (remaining 249679 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: 2.130 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.930 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.034 30836 Z= 0.145 Angle : 0.591 7.766 43262 Z= 0.439 Chirality : 0.045 0.155 5098 Planarity : 0.004 0.080 4182 Dihedral : 17.222 115.496 14101 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.66 (0.17), residues: 2630 helix: 1.91 (0.16), residues: 1190 sheet: 0.47 (0.25), residues: 376 loop : 0.55 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG i 70 TYR 0.029 0.001 TYR H 307 PHE 0.018 0.001 PHE p 96 TRP 0.009 0.001 TRP N 120 HIS 0.005 0.001 HIS n 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.15 (30836) covalent geometry : angle 0.59108 / 0.44 (43262) hydrogen bonds : bond 0.12565 / 14.43 ( 1287) hydrogen bonds : angle 4.90213 / 6.49 ( 3333) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 43 THR cc_start: 0.9087 (m) cc_final: 0.8837 (m) REVERT: N 153 ASP cc_start: 0.7673 (m-30) cc_final: 0.7419 (m-30) REVERT: p 65 MET cc_start: 0.6843 (mpp) cc_final: 0.6564 (mpt) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.7546 time to fit residues: 352.9408 Evaluate side-chains 298 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 210 GLN H 225 GLN H 317 ASN H 326 GLN H 334 ASN K 247 HIS ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 ASN L 103 ASN L 105 ASN N 139 HIS N 156 HIS b 148 HIS i 91 ASN i 92 ASN n 456 HIS s 123 ASN t 225 HIS t 238 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.140736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108796 restraints weight = 36570.344| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.54 r_work: 0.2970 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30836 Z= 0.209 Angle : 0.555 6.135 43262 Z= 0.306 Chirality : 0.042 0.221 5098 Planarity : 0.005 0.060 4182 Dihedral : 18.350 110.093 8399 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.75 % Allowed : 7.57 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.54 (0.16), residues: 2630 helix: 1.82 (0.15), residues: 1207 sheet: 0.41 (0.25), residues: 376 loop : 0.45 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 285 TYR 0.024 0.002 TYR H 307 PHE 0.027 0.002 PHE p 96 TRP 0.012 0.002 TRP H 296 HIS 0.008 0.001 HIS N 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.21 (30836) covalent geometry : angle 0.55491 / 0.31 (43262) hydrogen bonds : bond 0.05446 / 5.89 ( 1287) hydrogen bonds : angle 4.24415 / 5.52 ( 3333) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 312 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 217 LEU cc_start: 0.8038 (mp) cc_final: 0.7441 (mp) REVERT: H 227 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7592 (ptpt) REVERT: H 250 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7437 (mp) REVERT: L 89 TYR cc_start: 0.8292 (t80) cc_final: 0.7960 (t80) REVERT: L 93 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8197 (mp) REVERT: L 117 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6978 (mttt) REVERT: N 31 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8175 (mmt180) REVERT: N 153 ASP cc_start: 0.8445 (m-30) cc_final: 0.8224 (m-30) REVERT: b 47 HIS cc_start: 0.8420 (m90) cc_final: 0.8135 (m-70) REVERT: i 68 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7775 (mmm-85) REVERT: m 272 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7821 (mm) REVERT: n 356 VAL cc_start: 0.8207 (t) cc_final: 0.7942 (p) REVERT: o 184 LEU cc_start: 0.7911 (mt) cc_final: 0.7660 (mt) REVERT: p 65 MET cc_start: 0.7645 (mpp) cc_final: 0.7312 (mpt) REVERT: t 138 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8365 (mmtm) outliers start: 42 outliers final: 14 residues processed: 333 average time/residue: 0.7298 time to fit residues: 281.3504 Evaluate side-chains 291 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 271 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 272 LEU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 21 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 317 ASN H 326 GLN H 334 ASN K 284 ASN L 66 ASN i 35 ASN n 191 ASN s 123 ASN s 155 ASN s 356 ASN t 303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108839 restraints weight = 36621.726| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.51 r_work: 0.2968 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30836 Z= 0.155 Angle : 0.498 6.438 43262 Z= 0.275 Chirality : 0.040 0.190 5098 Planarity : 0.004 0.044 4182 Dihedral : 18.310 108.519 8399 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.25 % Allowed : 8.78 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.57 (0.16), residues: 2630 helix: 1.91 (0.15), residues: 1203 sheet: 0.50 (0.25), residues: 370 loop : 0.35 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 285 TYR 0.020 0.001 TYR H 307 PHE 0.023 0.001 PHE p 96 TRP 0.018 0.001 TRP s 354 HIS 0.005 0.001 HIS N 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (30836) covalent geometry : angle 0.49777 / 0.28 (43262) hydrogen bonds : bond 0.04861 / 5.27 ( 1287) hydrogen bonds : angle 4.06208 / 5.28 ( 3333) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 293 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: G 230 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7566 (ptpt) REVERT: H 217 LEU cc_start: 0.7895 (mp) cc_final: 0.7503 (mp) REVERT: H 225 GLN cc_start: 0.8048 (mt0) cc_final: 0.7694 (mt0) REVERT: H 250 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7642 (mp) REVERT: K 34 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8038 (tpt-90) REVERT: L 89 TYR cc_start: 0.8262 (t80) cc_final: 0.7897 (t80) REVERT: L 93 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8092 (mp) REVERT: L 117 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6989 (mttt) REVERT: L 119 TYR cc_start: 0.7820 (t80) cc_final: 0.7586 (t80) REVERT: N 31 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8128 (mmt180) REVERT: b 28 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7132 (ptm) REVERT: m 288 ILE cc_start: 0.8273 (mp) cc_final: 0.8014 (mp) REVERT: m 289 LYS cc_start: 0.7293 (mttp) cc_final: 0.6930 (mptt) REVERT: n 112 TYR cc_start: 0.8195 (p90) cc_final: 0.7963 (p90) REVERT: n 251 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8171 (tppt) REVERT: n 356 VAL cc_start: 0.8092 (t) cc_final: 0.7850 (p) REVERT: n 440 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7136 (pp20) REVERT: o 184 LEU cc_start: 0.7916 (mt) cc_final: 0.7703 (mt) REVERT: p 65 MET cc_start: 0.7712 (mpp) cc_final: 0.7250 (mpt) REVERT: p 167 MET cc_start: 0.8670 (tpp) cc_final: 0.8373 (ttp) REVERT: p 414 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: s 125 TYR cc_start: 0.7627 (m-80) cc_final: 0.7426 (m-80) REVERT: s 297 MET cc_start: 0.6808 (mmp) cc_final: 0.6194 (mmp) REVERT: s 359 TYR cc_start: 0.7140 (t80) cc_final: 0.6901 (t80) REVERT: t 73 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: t 138 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8294 (mmtm) outliers start: 54 outliers final: 15 residues processed: 322 average time/residue: 0.7540 time to fit residues: 282.1082 Evaluate side-chains 299 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain K residue 34 ARG Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 28 MET Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain p residue 225 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain p residue 414 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 83 ASP Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 136 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 283 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 238 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 225 GLN H 317 ASN K 284 ASN L 66 ASN s 123 ASN s 155 ASN t 225 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.109230 restraints weight = 36520.875| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.48 r_work: 0.2974 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30836 Z= 0.131 Angle : 0.472 6.855 43262 Z= 0.261 Chirality : 0.038 0.169 5098 Planarity : 0.004 0.043 4182 Dihedral : 18.292 107.964 8399 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.41 % Allowed : 9.61 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.62 (0.16), residues: 2630 helix: 1.96 (0.15), residues: 1211 sheet: 0.47 (0.25), residues: 381 loop : 0.38 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 285 TYR 0.019 0.001 TYR H 307 PHE 0.023 0.001 PHE p 96 TRP 0.012 0.001 TRP s 354 HIS 0.004 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (30836) covalent geometry : angle 0.47178 / 0.26 (43262) hydrogen bonds : bond 0.04545 / 4.93 ( 1287) hydrogen bonds : angle 3.97057 / 5.15 ( 3333) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 230 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7566 (ptpt) REVERT: H 217 LEU cc_start: 0.7881 (mp) cc_final: 0.7525 (mp) REVERT: H 227 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7910 (ptmt) REVERT: H 306 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: K 139 ASP cc_start: 0.8058 (m-30) cc_final: 0.7831 (m-30) REVERT: L 117 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6947 (mttt) REVERT: L 119 TYR cc_start: 0.7831 (t80) cc_final: 0.7581 (t80) REVERT: N 31 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8114 (mmt180) REVERT: N 174 ILE cc_start: 0.7768 (mt) cc_final: 0.7249 (pt) REVERT: b 28 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.6978 (ptm) REVERT: i 66 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8073 (tm-30) REVERT: m 288 ILE cc_start: 0.8252 (mp) cc_final: 0.8011 (mp) REVERT: m 289 LYS cc_start: 0.7264 (mttp) cc_final: 0.6933 (mptt) REVERT: n 72 MET cc_start: 0.7667 (mmt) cc_final: 0.7370 (mmt) REVERT: n 112 TYR cc_start: 0.8281 (p90) cc_final: 0.8076 (p90) REVERT: n 251 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8164 (tppt) REVERT: n 440 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7139 (pp20) REVERT: o 143 GLU cc_start: 0.8422 (pm20) cc_final: 0.7973 (pm20) REVERT: o 147 ILE cc_start: 0.8607 (mm) cc_final: 0.8352 (mp) REVERT: o 184 LEU cc_start: 0.7908 (mt) cc_final: 0.7693 (mt) REVERT: p 167 MET cc_start: 0.8654 (tpp) cc_final: 0.8341 (ttp) REVERT: s 297 MET cc_start: 0.6452 (mmp) cc_final: 0.6103 (mmp) REVERT: s 301 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: t 73 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: t 138 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8308 (mmtm) REVERT: t 170 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7562 (mp0) outliers start: 58 outliers final: 17 residues processed: 314 average time/residue: 0.7316 time to fit residues: 267.1691 Evaluate side-chains 295 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 267 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 306 GLU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 28 MET Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 263 ARG Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain n residue 440 GLU Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 91 optimal weight: 0.0570 chunk 97 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 260 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 58 optimal weight: 0.5980 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 243 ASN H 317 ASN K 200 ASN K 212 HIS i 63 ASN n 116 HIS s 123 ASN s 356 ASN t 225 HIS t 300 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106743 restraints weight = 36470.122| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.53 r_work: 0.2928 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30836 Z= 0.196 Angle : 0.530 7.849 43262 Z= 0.289 Chirality : 0.042 0.223 5098 Planarity : 0.005 0.051 4182 Dihedral : 18.329 108.064 8399 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.46 % Allowed : 11.03 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.48 (0.16), residues: 2630 helix: 1.84 (0.15), residues: 1212 sheet: 0.51 (0.25), residues: 362 loop : 0.25 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 285 TYR 0.024 0.002 TYR i 53 PHE 0.026 0.002 PHE p 96 TRP 0.012 0.002 TRP N 120 HIS 0.005 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (30836) covalent geometry : angle 0.53021 / 0.29 (43262) hydrogen bonds : bond 0.05185 / 5.59 ( 1287) hydrogen bonds : angle 4.05365 / 5.25 ( 3333) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 277 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: G 230 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7509 (ptpt) REVERT: H 227 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8008 (ptmt) REVERT: K 139 ASP cc_start: 0.8126 (m-30) cc_final: 0.7842 (m-30) REVERT: L 117 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7026 (mttt) REVERT: L 119 TYR cc_start: 0.7873 (t80) cc_final: 0.7561 (t80) REVERT: N 31 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8149 (mmt180) REVERT: b 28 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.6928 (ptm) REVERT: i 67 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8566 (tttt) REVERT: m 288 ILE cc_start: 0.8319 (mp) cc_final: 0.8086 (mp) REVERT: m 289 LYS cc_start: 0.7306 (mttp) cc_final: 0.6934 (mptt) REVERT: n 72 MET cc_start: 0.7679 (mmt) cc_final: 0.7466 (mmt) REVERT: n 112 TYR cc_start: 0.8340 (p90) cc_final: 0.8104 (p90) REVERT: n 251 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8169 (tppt) REVERT: o 138 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: o 143 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (pm20) REVERT: o 184 LEU cc_start: 0.7926 (mt) cc_final: 0.7699 (mt) REVERT: o 202 GLN cc_start: 0.7951 (mt0) cc_final: 0.7680 (tt0) REVERT: p 65 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7448 (mtp) REVERT: s 301 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: t 73 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7875 (tt0) REVERT: t 138 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8408 (mmtm) REVERT: t 170 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7597 (mp0) outliers start: 59 outliers final: 22 residues processed: 307 average time/residue: 0.7560 time to fit residues: 270.3656 Evaluate side-chains 297 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 243 ASN Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 31 ARG Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 28 MET Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain i residue 35 ASN Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain n residue 110 ASP Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 138 GLU Chi-restraints excluded: chain o residue 143 GLU Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 225 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Chi-restraints excluded: chain t residue 303 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 117 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 284 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 109 optimal weight: 0.0980 chunk 94 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 225 GLN H 243 ASN H 271 HIS L 66 ASN b 159 ASN n 116 HIS s 356 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107805 restraints weight = 36567.253| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.46 r_work: 0.2955 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30836 Z= 0.132 Angle : 0.468 9.164 43262 Z= 0.260 Chirality : 0.038 0.188 5098 Planarity : 0.004 0.047 4182 Dihedral : 18.318 107.341 8399 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.16 % Allowed : 12.15 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.67 (0.16), residues: 2630 helix: 2.02 (0.15), residues: 1205 sheet: 0.59 (0.25), residues: 366 loop : 0.33 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 285 TYR 0.019 0.001 TYR H 307 PHE 0.022 0.001 PHE p 96 TRP 0.013 0.001 TRP N 120 HIS 0.004 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (30836) covalent geometry : angle 0.46759 / 0.26 (43262) hydrogen bonds : bond 0.04544 / 4.93 ( 1287) hydrogen bonds : angle 3.96983 / 5.11 ( 3333) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: G 230 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7620 (ptpt) REVERT: H 225 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7853 (mt0) REVERT: H 227 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7913 (ptmt) REVERT: K 139 ASP cc_start: 0.8056 (m-30) cc_final: 0.7724 (m-30) REVERT: L 117 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7244 (mmtt) REVERT: L 119 TYR cc_start: 0.7813 (t80) cc_final: 0.7516 (t80) REVERT: N 174 ILE cc_start: 0.7891 (mt) cc_final: 0.7393 (pt) REVERT: b 28 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.6866 (ptm) REVERT: i 67 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8523 (tttt) REVERT: m 288 ILE cc_start: 0.8181 (mp) cc_final: 0.7946 (mp) REVERT: m 289 LYS cc_start: 0.7285 (mttp) cc_final: 0.6913 (mptt) REVERT: n 72 MET cc_start: 0.7685 (mmt) cc_final: 0.7479 (mmt) REVERT: n 251 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8143 (tppt) REVERT: o 184 LEU cc_start: 0.7899 (mt) cc_final: 0.7672 (mt) REVERT: p 65 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7471 (mtp) REVERT: p 167 MET cc_start: 0.8686 (tpp) cc_final: 0.8421 (ttp) REVERT: s 297 MET cc_start: 0.6557 (mmp) cc_final: 0.6192 (mmp) REVERT: s 301 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: t 170 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7543 (mp0) outliers start: 52 outliers final: 18 residues processed: 298 average time/residue: 0.7447 time to fit residues: 259.0609 Evaluate side-chains 293 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 28 MET Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 260 GLU Chi-restraints excluded: chain m residue 263 ARG Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Chi-restraints excluded: chain t residue 303 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 128 optimal weight: 0.0010 chunk 76 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 243 ASN H 271 HIS s 155 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108663 restraints weight = 36575.462| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.41 r_work: 0.2973 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30836 Z= 0.110 Angle : 0.448 6.944 43262 Z= 0.250 Chirality : 0.037 0.178 5098 Planarity : 0.004 0.042 4182 Dihedral : 18.273 107.051 8399 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.91 % Allowed : 12.57 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.78 (0.17), residues: 2630 helix: 2.12 (0.15), residues: 1203 sheet: 0.67 (0.25), residues: 367 loop : 0.38 (0.20), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 285 TYR 0.019 0.001 TYR H 307 PHE 0.022 0.001 PHE p 96 TRP 0.013 0.001 TRP N 120 HIS 0.003 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (30836) covalent geometry : angle 0.44797 / 0.25 (43262) hydrogen bonds : bond 0.04281 / 4.66 ( 1287) hydrogen bonds : angle 3.91121 / 5.02 ( 3333) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: G 230 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7599 (ptpt) REVERT: H 225 GLN cc_start: 0.8122 (mt0) cc_final: 0.7864 (mt0) REVERT: K 139 ASP cc_start: 0.8059 (m-30) cc_final: 0.7768 (m-30) REVERT: K 285 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7617 (mtp-110) REVERT: L 117 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7223 (mmtt) REVERT: L 119 TYR cc_start: 0.7792 (t80) cc_final: 0.7472 (t80) REVERT: N 174 ILE cc_start: 0.7821 (mt) cc_final: 0.7481 (pt) REVERT: i 67 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8507 (tttt) REVERT: m 288 ILE cc_start: 0.8148 (mp) cc_final: 0.7936 (mp) REVERT: m 289 LYS cc_start: 0.7271 (mttp) cc_final: 0.6906 (mptt) REVERT: n 72 MET cc_start: 0.7698 (mmt) cc_final: 0.7424 (mmt) REVERT: n 251 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8117 (tppt) REVERT: o 143 GLU cc_start: 0.8431 (pm20) cc_final: 0.8102 (pm20) REVERT: o 147 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8537 (mp) REVERT: o 184 LEU cc_start: 0.7882 (mt) cc_final: 0.7665 (mt) REVERT: p 65 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7306 (mtp) REVERT: p 167 MET cc_start: 0.8671 (tpp) cc_final: 0.8400 (ttp) REVERT: s 297 MET cc_start: 0.6654 (mmp) cc_final: 0.6280 (mmp) REVERT: s 301 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: t 73 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: t 170 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7524 (mp0) outliers start: 46 outliers final: 16 residues processed: 299 average time/residue: 0.7439 time to fit residues: 259.8130 Evaluate side-chains 289 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain i residue 53 TYR Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 263 ARG Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Chi-restraints excluded: chain t residue 303 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 287 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 72 optimal weight: 0.1980 chunk 99 optimal weight: 0.9980 chunk 70 optimal weight: 0.0980 chunk 2 optimal weight: 10.0000 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 138 HIS H 271 HIS H 317 ASN b 159 ASN i 35 ASN s 155 ASN t 225 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.141575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109536 restraints weight = 36619.734| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.53 r_work: 0.2992 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30836 Z= 0.104 Angle : 0.439 11.198 43262 Z= 0.244 Chirality : 0.037 0.249 5098 Planarity : 0.004 0.048 4182 Dihedral : 18.241 106.667 8399 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.54 % Allowed : 13.57 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.85 (0.17), residues: 2630 helix: 2.14 (0.15), residues: 1211 sheet: 0.77 (0.25), residues: 361 loop : 0.43 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 285 TYR 0.021 0.001 TYR H 307 PHE 0.022 0.001 PHE p 96 TRP 0.013 0.001 TRP N 120 HIS 0.003 0.001 HIS m 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (30836) covalent geometry : angle 0.43905 / 0.24 (43262) hydrogen bonds : bond 0.04058 / 4.41 ( 1287) hydrogen bonds : angle 3.84241 / 4.93 ( 3333) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 277 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: G 230 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7592 (ptpt) REVERT: K 139 ASP cc_start: 0.8072 (m-30) cc_final: 0.7790 (m-30) REVERT: K 285 ARG cc_start: 0.8015 (ttm110) cc_final: 0.7515 (mtp-110) REVERT: L 117 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7239 (mmtt) REVERT: L 119 TYR cc_start: 0.7792 (t80) cc_final: 0.7435 (t80) REVERT: N 174 ILE cc_start: 0.7787 (mt) cc_final: 0.7513 (pt) REVERT: i 35 ASN cc_start: 0.8302 (OUTLIER) cc_final: 0.8091 (p0) REVERT: m 278 MET cc_start: 0.8519 (mmt) cc_final: 0.7582 (mmt) REVERT: m 288 ILE cc_start: 0.7992 (mp) cc_final: 0.7776 (mp) REVERT: m 289 LYS cc_start: 0.7266 (mttp) cc_final: 0.6899 (mptt) REVERT: n 72 MET cc_start: 0.7662 (mmt) cc_final: 0.7443 (mmt) REVERT: n 251 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8104 (tppt) REVERT: o 143 GLU cc_start: 0.8413 (pm20) cc_final: 0.8051 (pm20) REVERT: o 147 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8459 (mp) REVERT: o 184 LEU cc_start: 0.7887 (mt) cc_final: 0.7681 (mt) REVERT: o 202 GLN cc_start: 0.7946 (mt0) cc_final: 0.7670 (mt0) REVERT: p 65 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7263 (mtp) REVERT: p 167 MET cc_start: 0.8653 (tpp) cc_final: 0.8378 (ttp) REVERT: s 297 MET cc_start: 0.6575 (mmp) cc_final: 0.6284 (mmp) REVERT: s 301 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: t 73 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7849 (tt0) REVERT: t 170 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7496 (mp0) outliers start: 37 outliers final: 16 residues processed: 296 average time/residue: 0.7554 time to fit residues: 260.7455 Evaluate side-chains 289 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain i residue 35 ASN Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 263 ARG Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Chi-restraints excluded: chain t residue 303 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 73 optimal weight: 0.0070 chunk 244 optimal weight: 2.9990 chunk 187 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 242 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 236 optimal weight: 0.0030 overall best weight: 1.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 225 GLN H 243 ASN L 66 ASN m 209 GLN s 155 ASN t 225 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108759 restraints weight = 36366.172| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.50 r_work: 0.2976 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30836 Z= 0.128 Angle : 0.458 9.680 43262 Z= 0.252 Chirality : 0.038 0.239 5098 Planarity : 0.004 0.043 4182 Dihedral : 18.232 106.766 8399 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.54 % Allowed : 13.77 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.80 (0.16), residues: 2630 helix: 2.10 (0.15), residues: 1212 sheet: 0.66 (0.25), residues: 368 loop : 0.42 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG K 285 TYR 0.021 0.001 TYR H 307 PHE 0.023 0.001 PHE p 96 TRP 0.011 0.001 TRP N 120 HIS 0.003 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (30836) covalent geometry : angle 0.45798 / 0.25 (43262) hydrogen bonds : bond 0.04250 / 4.61 ( 1287) hydrogen bonds : angle 3.86342 / 4.95 ( 3333) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 270 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 139 ASP cc_start: 0.8120 (m-30) cc_final: 0.7845 (m-30) REVERT: K 285 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7628 (mtp-110) REVERT: L 117 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7241 (mmtt) REVERT: L 119 TYR cc_start: 0.7804 (t80) cc_final: 0.7456 (t80) REVERT: N 68 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7799 (mtt180) REVERT: N 124 ASP cc_start: 0.8839 (p0) cc_final: 0.8631 (p0) REVERT: N 174 ILE cc_start: 0.7821 (mt) cc_final: 0.7531 (pt) REVERT: m 278 MET cc_start: 0.8538 (mmt) cc_final: 0.7713 (mmt) REVERT: m 288 ILE cc_start: 0.8150 (mp) cc_final: 0.7937 (mp) REVERT: m 289 LYS cc_start: 0.7234 (mttp) cc_final: 0.6852 (mptt) REVERT: n 72 MET cc_start: 0.7667 (mmt) cc_final: 0.7442 (mmt) REVERT: n 251 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8125 (tppt) REVERT: o 143 GLU cc_start: 0.8421 (pm20) cc_final: 0.8023 (pm20) REVERT: o 147 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8479 (mp) REVERT: o 184 LEU cc_start: 0.7889 (mt) cc_final: 0.7681 (mt) REVERT: p 65 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7278 (mtp) REVERT: p 167 MET cc_start: 0.8668 (tpp) cc_final: 0.8399 (ttp) REVERT: s 297 MET cc_start: 0.6605 (mmp) cc_final: 0.6371 (mmp) REVERT: s 301 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: t 73 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: t 170 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7510 (mp0) outliers start: 37 outliers final: 20 residues processed: 291 average time/residue: 0.7281 time to fit residues: 246.5670 Evaluate side-chains 298 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 300 GLU Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 102 GLN Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 75 LYS Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 263 ARG Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Chi-restraints excluded: chain t residue 303 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 9 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 ASN m 209 GLN t 225 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105256 restraints weight = 36435.416| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.41 r_work: 0.2913 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30836 Z= 0.238 Angle : 0.576 13.411 43262 Z= 0.309 Chirality : 0.044 0.245 5098 Planarity : 0.005 0.055 4182 Dihedral : 18.341 107.843 8399 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.71 % Allowed : 13.77 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.10 % 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: 1.49 (0.16), residues: 2630 helix: 1.87 (0.15), residues: 1205 sheet: 0.52 (0.25), residues: 362 loop : 0.23 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 285 TYR 0.025 0.002 TYR H 307 PHE 0.027 0.002 PHE p 96 TRP 0.014 0.002 TRP o 220 HIS 0.007 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (30836) covalent geometry : angle 0.57553 / 0.31 (43262) hydrogen bonds : bond 0.05497 / 5.91 ( 1287) hydrogen bonds : angle 4.09792 / 5.26 ( 3333) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 230 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7642 (ptpt) REVERT: K 139 ASP cc_start: 0.8158 (m-30) cc_final: 0.7880 (m-30) REVERT: L 117 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7277 (mmtt) REVERT: L 119 TYR cc_start: 0.7821 (t80) cc_final: 0.7455 (t80) REVERT: N 68 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7790 (mtt180) REVERT: N 174 ILE cc_start: 0.7882 (mt) cc_final: 0.7416 (pt) REVERT: b 33 THR cc_start: 0.9131 (t) cc_final: 0.8887 (t) REVERT: m 201 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7113 (mpp) REVERT: m 288 ILE cc_start: 0.8349 (mp) cc_final: 0.8022 (mt) REVERT: m 289 LYS cc_start: 0.7333 (mttp) cc_final: 0.6938 (mptt) REVERT: n 72 MET cc_start: 0.7767 (mmt) cc_final: 0.7482 (mmt) REVERT: n 251 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8223 (tppt) REVERT: o 143 GLU cc_start: 0.8463 (pm20) cc_final: 0.7984 (pm20) REVERT: o 147 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8568 (mp) REVERT: o 184 LEU cc_start: 0.7896 (mt) cc_final: 0.7695 (mt) REVERT: p 65 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7514 (mtp) REVERT: p 167 MET cc_start: 0.8732 (tpp) cc_final: 0.8446 (ttp) REVERT: s 297 MET cc_start: 0.6650 (mmp) cc_final: 0.6442 (mmp) REVERT: s 301 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: s 369 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8426 (mm-40) REVERT: t 73 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: t 170 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7584 (mp0) outliers start: 41 outliers final: 16 residues processed: 299 average time/residue: 0.7436 time to fit residues: 258.9233 Evaluate side-chains 294 residues out of total 2403 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 268 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 LYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 341 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 117 LYS Chi-restraints excluded: chain N residue 68 ARG Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain b residue 67 THR Chi-restraints excluded: chain i residue 35 ASN Chi-restraints excluded: chain m residue 195 VAL Chi-restraints excluded: chain m residue 201 MET Chi-restraints excluded: chain m residue 263 ARG Chi-restraints excluded: chain n residue 251 LYS Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 147 ILE Chi-restraints excluded: chain p residue 65 MET Chi-restraints excluded: chain p residue 358 VAL Chi-restraints excluded: chain s residue 301 GLU Chi-restraints excluded: chain t residue 73 GLU Chi-restraints excluded: chain t residue 129 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 169 VAL Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 292 ARG Chi-restraints excluded: chain t residue 303 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 188 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 164 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 ASN n 116 HIS p 219 ASN s 155 ASN t 225 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105641 restraints weight = 36620.517| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.45 r_work: 0.2908 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 30836 Z= 0.231 Angle : 0.679 59.120 43262 Z= 0.387 Chirality : 0.043 0.608 5098 Planarity : 0.005 0.056 4182 Dihedral : 18.343 107.854 8399 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.33 % Allowed : 14.48 % Favored : 84.19 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.10 % 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: 1.46 (0.16), residues: 2630 helix: 1.85 (0.15), residues: 1205 sheet: 0.51 (0.25), residues: 362 loop : 0.22 (0.19), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 285 TYR 0.023 0.002 TYR H 307 PHE 0.026 0.002 PHE p 96 TRP 0.012 0.002 TRP o 220 HIS 0.006 0.001 HIS b 148 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.23 (30836) covalent geometry : angle 0.67942 / 0.39 (43262) hydrogen bonds : bond 0.05368 / 5.78 ( 1287) hydrogen bonds : angle 4.10086 / 5.27 ( 3333) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8996.90 seconds wall clock time: 154 minutes 37.24 seconds (9277.24 seconds total)