Starting phenix.real_space_refine on Fri Mar 6 05:47:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r6q_24286/03_2026/7r6q_24286.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r6q_24286/03_2026/7r6q_24286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r6q_24286/03_2026/7r6q_24286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r6q_24286/03_2026/7r6q_24286.map" model { file = "/net/cci-nas-00/data/ceres_data/7r6q_24286/03_2026/7r6q_24286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r6q_24286/03_2026/7r6q_24286.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 439 5.49 5 S 49 5.16 5 C 16755 2.51 5 N 5174 2.21 5 O 6616 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29033 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 21, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 32, 'rna3p': 54} Chain breaks: 1 Chain: "D" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3486 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 1 Chain: "G" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1560 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain breaks: 1 Chain: "K" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2291 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Chain: "n" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3467 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 401} Chain breaks: 3 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "t" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2328 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain breaks: 1 Chain: "X" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain breaks: 1 Chain: "m" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1513 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 20, 'TRANS': 159} Chain: "1" Number of atoms: 6301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 6301 Classifications: {'RNA': 295} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 37, 'rna3p_pur': 126, 'rna3p_pyr': 97} Link IDs: {'rna2p': 72, 'rna3p': 222} Chain breaks: 8 Chain: "v" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 475 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "2" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1206 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 22, 'rna3p_pyr': 26} Link IDs: {'rna2p': 8, 'rna3p': 48} Chain: "N" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1131 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "h" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 151 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain breaks: 1 Chain: "Z" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "g" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain breaks: 3 Chain: "w" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 574 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Chain: "i" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 468 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 Chain: "L" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 263 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain breaks: 1 Time building chain proxies: 6.68, per 1000 atoms: 0.23 Number of scatterers: 29033 At special positions: 0 Unit cell: (171.72, 135, 174.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 439 15.00 O 6616 8.00 N 5174 7.00 C 16755 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: 2.69 Conformation dependent library (CDL) restraints added in 887.2 milliseconds 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 19 sheets defined 52.1% alpha, 9.7% beta 123 base pairs and 203 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 72 through 78 Processing helix chain 'D' and resid 91 through 108 removed outlier: 3.576A pdb=" N ALA D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 110 through 114 removed outlier: 3.559A pdb=" N GLY D 114 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.849A pdb=" N GLU D 136 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU D 137 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 164 removed outlier: 3.526A pdb=" N GLY D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 182 removed outlier: 3.521A pdb=" N LEU D 176 " --> pdb=" O PRO D 172 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.559A pdb=" N GLU D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE D 241 " --> pdb=" O ASP D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 298 through 312 Processing helix chain 'D' and resid 324 through 336 Processing helix chain 'D' and resid 369 through 384 removed outlier: 3.663A pdb=" N HIS D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA D 381 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 408 removed outlier: 4.239A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 removed outlier: 3.535A pdb=" N LYS D 421 " --> pdb=" O PRO D 418 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE D 422 " --> pdb=" O GLU D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 418 through 422' Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 436 through 456 removed outlier: 3.589A pdb=" N SER D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 removed outlier: 3.546A pdb=" N LYS D 467 " --> pdb=" O GLN D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 476 Processing helix chain 'G' and resid 47 through 52 removed outlier: 4.051A pdb=" N VAL G 50 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.598A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (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 removed outlier: 3.507A pdb=" N LYS G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU G 93 " --> pdb=" O GLU G 89 " (cutoff:3.500A) 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 removed outlier: 3.504A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 164 through 173 removed outlier: 4.721A pdb=" N ALA G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.539A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (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 'G' and resid 239 through 247 removed outlier: 4.229A pdb=" N LYS G 245 " --> pdb=" O LYS G 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.557A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER K 49 " --> pdb=" O ILE K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 Processing helix chain 'K' and resid 106 through 114 removed outlier: 4.022A pdb=" N TRP K 110 " --> pdb=" O PHE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 145 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' 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 195 removed outlier: 3.928A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 201 removed outlier: 3.787A 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 removed outlier: 3.535A pdb=" N ASN K 262 " --> pdb=" O GLU K 258 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU K 265 " --> pdb=" O ASP K 261 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU K 268 " --> pdb=" O GLU K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 301 removed outlier: 4.155A pdb=" N ASP K 299 " --> pdb=" O ASP K 296 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU K 301 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 335 removed outlier: 3.679A pdb=" N GLU K 335 " --> pdb=" O LYS K 331 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 48 through 53 Processing helix chain 'n' and resid 64 through 73 removed outlier: 3.838A pdb=" N ILE n 68 " --> pdb=" O TYR n 64 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 96 removed outlier: 4.244A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 removed outlier: 3.691A pdb=" N ALA n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 144 removed outlier: 3.595A pdb=" N ALA n 128 " --> pdb=" O SER n 124 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 240 removed outlier: 3.770A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR n 227 " --> pdb=" O GLU n 223 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 254 removed outlier: 3.649A pdb=" N LYS n 254 " --> pdb=" O LEU n 250 " (cutoff:3.500A) Processing helix chain 'n' and resid 258 through 260 No H-bonds generated for 'chain 'n' and resid 258 through 260' Processing helix chain 'n' and resid 354 through 359 Processing helix chain 'n' and resid 373 through 382 removed outlier: 4.008A pdb=" N PHE n 378 " --> pdb=" O ASP n 374 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU n 379 " --> pdb=" O ILE n 375 " (cutoff:3.500A) Processing helix chain 'n' and resid 389 through 393 Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.938A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS n 438 " --> pdb=" O ASP n 434 " (cutoff:3.500A) Processing helix chain 'n' and resid 554 through 559 Processing helix chain 'n' and resid 560 through 594 removed outlier: 3.912A pdb=" N GLN n 594 " --> pdb=" O GLN n 590 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 113 through 115 No H-bonds generated for 'chain 'o' and resid 113 through 115' Processing helix chain 'o' and resid 141 through 153 removed outlier: 3.684A pdb=" N ALA o 145 " --> pdb=" O ASN o 141 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET o 146 " --> pdb=" O LYS o 142 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE o 147 " --> pdb=" O GLU o 143 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET o 152 " --> pdb=" O ALA o 148 " (cutoff:3.500A) Processing helix chain 'o' and resid 192 through 211 removed outlier: 3.621A pdb=" N MET o 200 " --> pdb=" O LEU o 196 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS o 201 " --> pdb=" O LYS o 197 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN o 202 " --> pdb=" O ASP o 198 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU o 211 " --> pdb=" O ARG o 207 " (cutoff:3.500A) Processing helix chain 'o' and resid 212 through 215 removed outlier: 3.843A pdb=" N GLY o 215 " --> pdb=" O ALA o 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 212 through 215' Processing helix chain 't' and resid 25 through 51 Processing helix chain 't' and resid 52 through 54 No H-bonds generated for 'chain 't' and resid 52 through 54' Processing helix chain 't' and resid 57 through 87 removed outlier: 3.572A 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 182 through 188 removed outlier: 4.326A pdb=" N LEU t 186 " --> pdb=" O ASN t 182 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) Processing helix chain 't' and resid 190 through 192 No H-bonds generated for 'chain 't' and resid 190 through 192' Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 240 removed outlier: 4.309A 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 256 Processing helix chain 't' and resid 260 through 269 removed outlier: 3.876A pdb=" N GLN t 269 " --> pdb=" O ASN t 265 " (cutoff:3.500A) Processing helix chain 't' and resid 281 through 299 removed outlier: 3.572A pdb=" N SER t 296 " --> pdb=" O ARG t 292 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ARG t 297 " --> pdb=" O GLU t 293 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 321 removed outlier: 3.535A pdb=" N LEU t 317 " --> pdb=" O ASP t 313 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 16 removed outlier: 3.708A pdb=" N ALA X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 266 removed outlier: 3.548A pdb=" N ARG m 265 " --> pdb=" O PRO m 262 " (cutoff:3.500A) Processing helix chain 'm' and resid 270 through 285 Processing helix chain 'm' and resid 290 through 298 Processing helix chain 'm' and resid 333 through 337 Processing helix chain 'm' and resid 341 through 345 Processing helix chain 'm' and resid 347 through 357 Processing helix chain 'm' and resid 383 through 397 removed outlier: 3.584A pdb=" N ARG m 387 " --> pdb=" O SER m 383 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR m 395 " --> pdb=" O SER m 391 " (cutoff:3.500A) Processing helix chain 'm' and resid 408 through 413 Processing helix chain 'v' and resid 178 through 193 Processing helix chain 'v' and resid 195 through 201 Processing helix chain 'v' and resid 211 through 227 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.658A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'h' and resid 101 through 110 Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'g' and resid 58 through 65 removed outlier: 3.843A pdb=" N TYR g 62 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA g 63 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR g 64 " --> pdb=" O GLN g 61 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 70 Processing helix chain 'w' and resid 456 through 479 removed outlier: 3.749A pdb=" N ASP w 460 " --> pdb=" O ALA w 456 " (cutoff:3.500A) Processing helix chain 'w' and resid 680 through 684 Processing helix chain 'w' and resid 696 through 704 removed outlier: 4.062A pdb=" N ASP w 702 " --> pdb=" O TRP w 698 " (cutoff:3.500A) Processing helix chain 'w' and resid 705 through 707 No H-bonds generated for 'chain 'w' and resid 705 through 707' Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.913A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 63 Processing helix chain 'i' and resid 82 through 99 removed outlier: 3.551A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 83 Processing helix chain 'L' and resid 105 through 117 Processing sheet with id=AA1, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.402A pdb=" N GLY D 146 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 117 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ALA D 170 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL D 119 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE D 118 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 193 " --> pdb=" O GLN D 223 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL D 82 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 316 through 319 removed outlier: 6.435A pdb=" N LEU D 317 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N THR D 346 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU D 319 " --> pdb=" O THR D 346 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE D 361 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N PHE D 393 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN D 363 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY D 267 " --> pdb=" O MET D 392 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU D 394 " --> pdb=" O GLY D 267 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N VAL D 269 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN D 266 " --> pdb=" O ASN D 413 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N TYR D 415 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR D 268 " --> pdb=" O TYR D 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AA4, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.183A pdb=" N LEU K 78 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 97 through 101 Processing sheet with id=AA6, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.300A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU K 124 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ASP K 183 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE K 126 " --> pdb=" O ASP K 183 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AA8, first strand: chain 'n' and resid 176 through 181 removed outlier: 6.684A pdb=" N GLN n 189 " --> pdb=" O ARG n 177 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL n 179 " --> pdb=" O TYR n 187 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR n 187 " --> pdb=" O VAL n 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'n' and resid 247 through 248 removed outlier: 3.764A pdb=" N LYS n 247 " --> pdb=" O ILE n 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'n' and resid 386 through 387 removed outlier: 6.131A pdb=" N GLN n 410 " --> pdb=" O ILE n 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'o' and resid 117 through 124 removed outlier: 4.848A pdb=" N LEU o 117 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU o 138 " --> pdb=" O LEU o 117 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU o 119 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N PHE o 136 " --> pdb=" O GLU o 119 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ARG o 121 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TYR o 134 " --> pdb=" O ARG o 121 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ALA o 123 " --> pdb=" O ARG o 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'o' and resid 156 through 157 Processing sheet with id=AB4, first strand: chain 't' and resid 14 through 20 Processing sheet with id=AB5, first strand: chain 't' and resid 129 through 134 removed outlier: 7.269A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 't' and resid 194 through 195 removed outlier: 3.815A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 't' and resid 213 through 215 Processing sheet with id=AB8, first strand: chain 'X' and resid 23 through 24 removed outlier: 4.118A pdb=" N LEU X 24 " --> pdb=" O ILE w 450 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE w 450 " --> pdb=" O LEU X 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'X' and resid 111 through 114 Processing sheet with id=AC1, first strand: chain 'N' and resid 36 through 38 removed outlier: 6.181A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) 848 hydrogen bonds defined for protein. 2394 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 516 hydrogen bond angles 0 basepair planarities 123 basepair parallelities 203 stacking parallelities Total time for adding SS restraints: 5.77 Time building geometry restraints manager: 3.58 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: 6223 1.33 - 1.45: 8440 1.45 - 1.57: 14855 1.57 - 1.69: 866 1.69 - 1.81: 85 Bond restraints: 30469 Sorted by residual: bond pdb=" CA GLN t 269 " pdb=" C GLN t 269 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.26e-02 6.30e+03 4.07e+00 bond pdb=" CG LEU n 139 " pdb=" CD1 LEU n 139 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" C ASN K 338 " pdb=" N PRO K 339 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.38e+00 bond pdb=" O5' A 1 266 " pdb=" C5' A 1 266 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 2.05e+00 bond pdb=" O5' U 6 225 " pdb=" C5' U 6 225 " ideal model delta sigma weight residual 1.424 1.444 -0.020 1.50e-02 4.44e+03 1.78e+00 ... (remaining 30464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 42440 1.68 - 3.35: 598 3.35 - 5.03: 74 5.03 - 6.71: 17 6.71 - 8.38: 4 Bond angle restraints: 43133 Sorted by residual: angle pdb=" C PRO n 245 " pdb=" N PRO n 246 " pdb=" CA PRO n 246 " ideal model delta sigma weight residual 119.76 123.02 -3.26 1.03e+00 9.43e-01 1.00e+01 angle pdb=" C3' C 6 59 " pdb=" O3' C 6 59 " pdb=" P U 6 60 " ideal model delta sigma weight residual 120.20 124.92 -4.72 1.50e+00 4.44e-01 9.89e+00 angle pdb=" O3' C 11551 " pdb=" C3' C 11551 " pdb=" C2' C 11551 " ideal model delta sigma weight residual 113.70 118.32 -4.62 1.50e+00 4.44e-01 9.47e+00 angle pdb=" CB MET m 322 " pdb=" CG MET m 322 " pdb=" SD MET m 322 " ideal model delta sigma weight residual 112.70 104.32 8.38 3.00e+00 1.11e-01 7.81e+00 angle pdb=" N GLY t 137 " pdb=" CA GLY t 137 " pdb=" C GLY t 137 " ideal model delta sigma weight residual 115.61 110.83 4.78 1.74e+00 3.30e-01 7.55e+00 ... (remaining 43128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 17979 35.90 - 71.80: 1130 71.80 - 107.70: 107 107.70 - 143.60: 6 143.60 - 179.49: 10 Dihedral angle restraints: 19232 sinusoidal: 12117 harmonic: 7115 Sorted by residual: dihedral pdb=" O4' C 6 59 " pdb=" C1' C 6 59 " pdb=" N1 C 6 59 " pdb=" C2 C 6 59 " ideal model delta sinusoidal sigma weight residual 232.00 52.51 179.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 6 223 " pdb=" C1' U 6 223 " pdb=" N1 U 6 223 " pdb=" C2 U 6 223 " ideal model delta sinusoidal sigma weight residual 232.00 53.33 178.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 11569 " pdb=" C1' U 11569 " pdb=" N1 U 11569 " pdb=" C2 U 11569 " ideal model delta sinusoidal sigma weight residual -128.00 48.52 -176.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 19229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4561 0.054 - 0.109: 527 0.109 - 0.163: 80 0.163 - 0.218: 6 0.218 - 0.272: 1 Chirality restraints: 5175 Sorted by residual: chirality pdb=" CA ASN K 338 " pdb=" N ASN K 338 " pdb=" C ASN K 338 " pdb=" CB ASN K 338 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE t 103 " pdb=" N ILE t 103 " pdb=" C ILE t 103 " pdb=" CB ILE t 103 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" C3' A 1 266 " pdb=" C4' A 1 266 " pdb=" O3' A 1 266 " pdb=" C2' A 1 266 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 5172 not shown) Planarity restraints: 3851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 11807 " -0.030 2.00e-02 2.50e+03 1.25e-02 4.71e+00 pdb=" N9 G 11807 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G 11807 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 11807 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 11807 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 11807 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G 11807 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G 11807 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 11807 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 11807 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 11807 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 11807 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 11646 " -0.029 2.00e-02 2.50e+03 1.25e-02 4.70e+00 pdb=" N9 G 11646 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G 11646 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 11646 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 11646 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 11646 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 11646 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G 11646 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 11646 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 11646 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 296 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A 1 296 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A 1 296 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 1 296 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 296 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 1 296 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 296 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 296 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 1 296 " 0.003 2.00e-02 2.50e+03 ... (remaining 3848 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2407 2.74 - 3.28: 26708 3.28 - 3.82: 50940 3.82 - 4.36: 64240 4.36 - 4.90: 97833 Nonbonded interactions: 242128 Sorted by model distance: nonbonded pdb=" OP2 G 2 103 " pdb=" O2' A 2 105 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR D 395 " pdb=" OD1 ASN D 397 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP K 184 " pdb=" OG SER K 208 " model vdw 2.207 3.040 nonbonded pdb=" OP2 G 1 297 " pdb=" N2 G 1 297 " model vdw 2.229 3.120 nonbonded pdb=" OP2 G 1 148 " pdb=" OH TYR N 4 " model vdw 2.230 3.040 ... (remaining 242123 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.160 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.003 0.057 30469 Z= 0.126 Angle : 0.515 8.385 43133 Z= 0.278 Chirality : 0.036 0.272 5175 Planarity : 0.004 0.046 3851 Dihedral : 19.636 179.495 14600 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2357 helix: 0.71 (0.16), residues: 1123 sheet: -0.33 (0.30), residues: 259 loop : -0.58 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 328 TYR 0.017 0.001 TYR G 97 PHE 0.023 0.001 PHE o 102 TRP 0.009 0.001 TRP N 28 HIS 0.005 0.001 HIS D 375 Details of bonding type rmsd covalent geometry : bond 0.00265 (30469) covalent geometry : angle 0.51498 (43133) hydrogen bonds : bond 0.14275 ( 1158) hydrogen bonds : angle 5.27815 ( 2910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.897 Fit side-chains REVERT: D 251 ASN cc_start: 0.6181 (m110) cc_final: 0.5926 (OUTLIER) REVERT: o 198 ASP cc_start: 0.7526 (t70) cc_final: 0.7127 (OUTLIER) REVERT: w 472 ASP cc_start: 0.7997 (m-30) cc_final: 0.7738 (t0) REVERT: L 104 ARG cc_start: 0.6620 (ptp90) cc_final: 0.5500 (ppt170) outliers start: 0 outliers final: 3 residues processed: 239 average time/residue: 0.8263 time to fit residues: 224.2646 Evaluate side-chains 168 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 231 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN D 251 ASN K 224 ASN K 295 GLN K 330 ASN t 34 GLN t 300 GLN i 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.101134 restraints weight = 43239.036| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.19 r_work: 0.3039 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30469 Z= 0.189 Angle : 0.563 8.547 43133 Z= 0.288 Chirality : 0.039 0.227 5175 Planarity : 0.004 0.048 3851 Dihedral : 21.084 178.718 9424 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.31 % Allowed : 8.17 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2357 helix: 0.91 (0.16), residues: 1143 sheet: -0.16 (0.31), residues: 249 loop : -0.56 (0.20), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG t 297 TYR 0.015 0.002 TYR G 97 PHE 0.028 0.002 PHE o 102 TRP 0.009 0.001 TRP N 120 HIS 0.006 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00421 (30469) covalent geometry : angle 0.56271 (43133) hydrogen bonds : bond 0.05094 ( 1158) hydrogen bonds : angle 4.01507 ( 2910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.962 Fit side-chains REVERT: D 162 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7038 (mpt) REVERT: D 251 ASN cc_start: 0.6481 (m-40) cc_final: 0.5319 (OUTLIER) REVERT: G 49 TYR cc_start: 0.8279 (p90) cc_final: 0.8033 (p90) REVERT: o 198 ASP cc_start: 0.8506 (t70) cc_final: 0.7940 (OUTLIER) REVERT: t 301 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5999 (p90) REVERT: X 21 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8274 (mmtm) REVERT: L 104 ARG cc_start: 0.7258 (ptp90) cc_final: 0.5385 (ppt170) outliers start: 28 outliers final: 13 residues processed: 193 average time/residue: 0.8596 time to fit residues: 187.7981 Evaluate side-chains 167 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain Z residue 55 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 181 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 259 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 112 optimal weight: 0.4980 chunk 148 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.122880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.102907 restraints weight = 43149.567| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.23 r_work: 0.3052 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30469 Z= 0.126 Angle : 0.501 9.275 43133 Z= 0.257 Chirality : 0.036 0.197 5175 Planarity : 0.004 0.046 3851 Dihedral : 21.013 178.992 9422 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.54 % Allowed : 10.78 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.18), residues: 2357 helix: 1.18 (0.16), residues: 1137 sheet: -0.00 (0.31), residues: 252 loop : -0.47 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG t 297 TYR 0.010 0.001 TYR D 447 PHE 0.018 0.001 PHE D 96 TRP 0.009 0.001 TRP N 120 HIS 0.005 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00273 (30469) covalent geometry : angle 0.50112 (43133) hydrogen bonds : bond 0.04380 ( 1158) hydrogen bonds : angle 3.81309 ( 2910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.743 Fit side-chains REVERT: D 251 ASN cc_start: 0.6692 (m-40) cc_final: 0.5372 (p0) REVERT: G 49 TYR cc_start: 0.8215 (p90) cc_final: 0.7783 (p90) REVERT: K 141 PHE cc_start: 0.8183 (t80) cc_final: 0.7783 (t80) REVERT: K 326 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7055 (pp) REVERT: n 138 MET cc_start: 0.9108 (tpp) cc_final: 0.8792 (tpp) REVERT: o 195 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8012 (tp40) REVERT: o 198 ASP cc_start: 0.8540 (t70) cc_final: 0.7965 (OUTLIER) REVERT: t 257 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8322 (mtm) REVERT: t 301 PHE cc_start: 0.6350 (OUTLIER) cc_final: 0.5928 (p90) REVERT: X 21 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8372 (mmtm) REVERT: v 186 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7935 (tm-30) REVERT: L 104 ARG cc_start: 0.7362 (ptp90) cc_final: 0.5310 (ppt170) outliers start: 33 outliers final: 15 residues processed: 195 average time/residue: 0.8088 time to fit residues: 180.6515 Evaluate side-chains 173 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 477 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 258 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 241 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 256 optimal weight: 0.0030 chunk 272 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 273 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 356 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.122711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102846 restraints weight = 42938.115| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.17 r_work: 0.3065 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30469 Z= 0.131 Angle : 0.501 9.696 43133 Z= 0.256 Chirality : 0.036 0.201 5175 Planarity : 0.004 0.045 3851 Dihedral : 20.959 178.607 9422 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.33 % Allowed : 11.58 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2357 helix: 1.29 (0.16), residues: 1139 sheet: 0.19 (0.31), residues: 243 loop : -0.46 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG t 297 TYR 0.011 0.001 TYR D 447 PHE 0.017 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.005 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00286 (30469) covalent geometry : angle 0.50127 (43133) hydrogen bonds : bond 0.04287 ( 1158) hydrogen bonds : angle 3.71100 ( 2910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 1.084 Fit side-chains REVERT: D 251 ASN cc_start: 0.6654 (m-40) cc_final: 0.5362 (p0) REVERT: G 49 TYR cc_start: 0.8161 (p90) cc_final: 0.7785 (p90) REVERT: K 141 PHE cc_start: 0.8201 (t80) cc_final: 0.7785 (t80) REVERT: K 326 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.6976 (pp) REVERT: n 138 MET cc_start: 0.9126 (tpp) cc_final: 0.8864 (tpp) REVERT: o 195 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: o 198 ASP cc_start: 0.8530 (t70) cc_final: 0.7953 (OUTLIER) REVERT: t 257 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8329 (mtm) REVERT: t 301 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5949 (p90) REVERT: X 21 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8287 (mmtm) REVERT: m 298 LYS cc_start: 0.7532 (mppt) cc_final: 0.7064 (mptp) REVERT: v 186 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: w 472 ASP cc_start: 0.8674 (m-30) cc_final: 0.7930 (t0) REVERT: w 481 ASP cc_start: 0.8020 (p0) cc_final: 0.7554 (p0) REVERT: L 104 ARG cc_start: 0.7466 (ptp90) cc_final: 0.5406 (ppt170) outliers start: 50 outliers final: 22 residues processed: 209 average time/residue: 0.7499 time to fit residues: 180.4812 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 142 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 264 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 166 optimal weight: 0.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN m 356 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104023 restraints weight = 42829.268| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.14 r_work: 0.3085 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30469 Z= 0.110 Angle : 0.487 9.578 43133 Z= 0.248 Chirality : 0.035 0.198 5175 Planarity : 0.004 0.045 3851 Dihedral : 20.947 179.417 9422 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.05 % Allowed : 12.70 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2357 helix: 1.43 (0.16), residues: 1133 sheet: 0.25 (0.32), residues: 243 loop : -0.43 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG t 297 TYR 0.011 0.001 TYR G 97 PHE 0.017 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00234 (30469) covalent geometry : angle 0.48655 (43133) hydrogen bonds : bond 0.04099 ( 1158) hydrogen bonds : angle 3.65307 ( 2910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.958 Fit side-chains REVERT: D 251 ASN cc_start: 0.6732 (m-40) cc_final: 0.5353 (p0) REVERT: K 141 PHE cc_start: 0.8207 (t80) cc_final: 0.7808 (t80) REVERT: K 326 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.6937 (pp) REVERT: n 138 MET cc_start: 0.9101 (tpp) cc_final: 0.8762 (tpp) REVERT: o 121 ARG cc_start: 0.8621 (mtt180) cc_final: 0.8414 (mtt180) REVERT: o 165 ARG cc_start: 0.8148 (ptp-110) cc_final: 0.7935 (ptp90) REVERT: o 195 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7997 (tp40) REVERT: o 198 ASP cc_start: 0.8490 (t70) cc_final: 0.7904 (OUTLIER) REVERT: t 257 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8306 (mtm) REVERT: t 301 PHE cc_start: 0.6372 (OUTLIER) cc_final: 0.5900 (p90) REVERT: X 21 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8308 (mmtm) REVERT: v 186 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7884 (tm-30) REVERT: w 472 ASP cc_start: 0.8671 (m-30) cc_final: 0.7909 (t0) REVERT: w 481 ASP cc_start: 0.8002 (p0) cc_final: 0.7549 (p0) REVERT: L 85 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7370 (pp) REVERT: L 104 ARG cc_start: 0.7435 (ptp90) cc_final: 0.5191 (ptm160) outliers start: 44 outliers final: 21 residues processed: 205 average time/residue: 0.7712 time to fit residues: 181.3144 Evaluate side-chains 184 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 142 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 112 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 118 optimal weight: 0.4980 chunk 151 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 276 optimal weight: 0.7980 chunk 253 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN K 295 GLN n 157 ASN m 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104590 restraints weight = 42831.250| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.14 r_work: 0.3095 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30469 Z= 0.108 Angle : 0.479 9.721 43133 Z= 0.244 Chirality : 0.035 0.199 5175 Planarity : 0.004 0.044 3851 Dihedral : 20.906 179.587 9422 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.01 % Allowed : 13.40 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2357 helix: 1.55 (0.16), residues: 1133 sheet: 0.34 (0.32), residues: 243 loop : -0.41 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG t 297 TYR 0.010 0.001 TYR D 447 PHE 0.016 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00231 (30469) covalent geometry : angle 0.47900 (43133) hydrogen bonds : bond 0.03966 ( 1158) hydrogen bonds : angle 3.59028 ( 2910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.932 Fit side-chains REVERT: D 225 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7896 (mpp) REVERT: D 251 ASN cc_start: 0.6796 (m-40) cc_final: 0.5385 (p0) REVERT: G 246 MET cc_start: 0.6496 (mtt) cc_final: 0.5856 (tmt) REVERT: K 141 PHE cc_start: 0.8226 (t80) cc_final: 0.7833 (t80) REVERT: K 326 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.6916 (pp) REVERT: n 138 MET cc_start: 0.9111 (tpp) cc_final: 0.8800 (tpp) REVERT: n 404 MET cc_start: 0.7132 (mpp) cc_final: 0.6690 (mpp) REVERT: o 195 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.7977 (tp40) REVERT: o 198 ASP cc_start: 0.8472 (t70) cc_final: 0.7884 (OUTLIER) REVERT: t 257 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8291 (mtm) REVERT: t 301 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5935 (p90) REVERT: X 21 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8289 (mmtm) REVERT: v 186 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: N 67 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8109 (mtm180) REVERT: L 85 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7318 (pp) REVERT: L 104 ARG cc_start: 0.7453 (ptp90) cc_final: 0.5105 (ppt170) outliers start: 43 outliers final: 20 residues processed: 203 average time/residue: 0.7936 time to fit residues: 184.0520 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 176 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN G 59 GLN K 295 GLN m 356 ASN v 210 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100227 restraints weight = 42990.791| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.17 r_work: 0.3022 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30469 Z= 0.214 Angle : 0.563 9.684 43133 Z= 0.287 Chirality : 0.039 0.225 5175 Planarity : 0.004 0.047 3851 Dihedral : 20.912 179.138 9422 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.24 % Allowed : 13.45 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2357 helix: 1.35 (0.16), residues: 1134 sheet: 0.28 (0.32), residues: 243 loop : -0.51 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG t 297 TYR 0.017 0.002 TYR K 292 PHE 0.016 0.002 PHE D 96 TRP 0.007 0.002 TRP N 120 HIS 0.007 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00480 (30469) covalent geometry : angle 0.56337 (43133) hydrogen bonds : bond 0.04882 ( 1158) hydrogen bonds : angle 3.73511 ( 2910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.891 Fit side-chains REVERT: D 209 GLU cc_start: 0.7942 (mp0) cc_final: 0.7676 (mp0) REVERT: D 225 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7922 (mpp) REVERT: D 251 ASN cc_start: 0.6878 (m-40) cc_final: 0.5458 (p0) REVERT: G 49 TYR cc_start: 0.8257 (p90) cc_final: 0.8040 (p90) REVERT: G 246 MET cc_start: 0.6530 (mtt) cc_final: 0.5894 (tmt) REVERT: K 141 PHE cc_start: 0.8326 (t80) cc_final: 0.7982 (t80) REVERT: K 326 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.6996 (pp) REVERT: n 138 MET cc_start: 0.9200 (tpp) cc_final: 0.8908 (tpp) REVERT: n 404 MET cc_start: 0.7225 (mpp) cc_final: 0.6749 (mpp) REVERT: o 198 ASP cc_start: 0.8508 (t70) cc_final: 0.7921 (OUTLIER) REVERT: t 257 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8121 (mtm) REVERT: t 301 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.5867 (p90) REVERT: X 21 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8480 (mmtm) REVERT: v 186 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: N 67 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8205 (mtm180) REVERT: L 85 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7337 (pp) REVERT: L 104 ARG cc_start: 0.7644 (ptp90) cc_final: 0.5221 (ppt170) outliers start: 48 outliers final: 28 residues processed: 196 average time/residue: 0.7832 time to fit residues: 175.9618 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain m residue 411 SER Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 35 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 157 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN K 295 GLN t 51 ASN m 356 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.103730 restraints weight = 43026.933| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.14 r_work: 0.3082 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30469 Z= 0.113 Angle : 0.490 9.895 43133 Z= 0.251 Chirality : 0.036 0.199 5175 Planarity : 0.004 0.047 3851 Dihedral : 20.902 179.223 9422 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.77 % Allowed : 14.01 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2357 helix: 1.50 (0.16), residues: 1137 sheet: 0.35 (0.32), residues: 243 loop : -0.42 (0.20), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG t 297 TYR 0.010 0.001 TYR D 447 PHE 0.016 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00242 (30469) covalent geometry : angle 0.48965 (43133) hydrogen bonds : bond 0.04089 ( 1158) hydrogen bonds : angle 3.61135 ( 2910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.900 Fit side-chains REVERT: D 209 GLU cc_start: 0.7941 (mp0) cc_final: 0.7697 (mp0) REVERT: D 236 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6475 (pm20) REVERT: D 251 ASN cc_start: 0.6702 (m-40) cc_final: 0.5440 (p0) REVERT: G 246 MET cc_start: 0.6607 (mtt) cc_final: 0.5953 (tmt) REVERT: K 141 PHE cc_start: 0.8256 (t80) cc_final: 0.7870 (t80) REVERT: K 292 TYR cc_start: 0.8378 (t80) cc_final: 0.8091 (t80) REVERT: K 326 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6787 (pp) REVERT: n 138 MET cc_start: 0.9127 (tpp) cc_final: 0.8823 (tpp) REVERT: n 393 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: n 404 MET cc_start: 0.7146 (mpp) cc_final: 0.6696 (mpp) REVERT: o 198 ASP cc_start: 0.8447 (t70) cc_final: 0.7850 (OUTLIER) REVERT: t 257 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8300 (mtm) REVERT: t 301 PHE cc_start: 0.6225 (OUTLIER) cc_final: 0.5794 (p90) REVERT: X 21 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8359 (mmtm) REVERT: v 186 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: N 67 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8142 (mtm180) REVERT: w 450 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5539 (tp) REVERT: w 686 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7798 (mtp85) REVERT: L 85 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7351 (pp) REVERT: L 104 ARG cc_start: 0.7610 (ptp90) cc_final: 0.5280 (ptm160) outliers start: 38 outliers final: 19 residues processed: 193 average time/residue: 0.7998 time to fit residues: 176.1940 Evaluate side-chains 187 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain m residue 411 SER Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain w residue 686 ARG Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 167 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 0.0010 chunk 82 optimal weight: 0.6980 chunk 225 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN K 295 GLN m 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104070 restraints weight = 42928.078| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.14 r_work: 0.3087 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30469 Z= 0.112 Angle : 0.486 9.909 43133 Z= 0.248 Chirality : 0.035 0.200 5175 Planarity : 0.004 0.051 3851 Dihedral : 20.874 179.453 9422 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.73 % Allowed : 14.38 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2357 helix: 1.55 (0.16), residues: 1141 sheet: 0.37 (0.32), residues: 243 loop : -0.43 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG t 297 TYR 0.010 0.001 TYR D 447 PHE 0.015 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00243 (30469) covalent geometry : angle 0.48606 (43133) hydrogen bonds : bond 0.04018 ( 1158) hydrogen bonds : angle 3.57479 ( 2910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.879 Fit side-chains REVERT: D 236 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6481 (pm20) REVERT: D 251 ASN cc_start: 0.6798 (m-40) cc_final: 0.5461 (p0) REVERT: G 246 MET cc_start: 0.6613 (mtt) cc_final: 0.5967 (tmt) REVERT: K 141 PHE cc_start: 0.8251 (t80) cc_final: 0.7876 (t80) REVERT: K 292 TYR cc_start: 0.8380 (t80) cc_final: 0.8090 (t80) REVERT: K 326 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6771 (pp) REVERT: n 138 MET cc_start: 0.9123 (tpp) cc_final: 0.8831 (tpp) REVERT: n 404 MET cc_start: 0.7214 (mpp) cc_final: 0.6813 (mpp) REVERT: o 198 ASP cc_start: 0.8469 (t70) cc_final: 0.7887 (OUTLIER) REVERT: t 257 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8273 (mtm) REVERT: t 301 PHE cc_start: 0.6247 (OUTLIER) cc_final: 0.5813 (p90) REVERT: X 21 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8342 (mmtm) REVERT: m 369 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8550 (mm-40) REVERT: v 186 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: N 67 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8106 (mtm180) REVERT: w 450 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5356 (tp) REVERT: w 686 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7868 (mtp85) REVERT: L 85 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7354 (pp) REVERT: L 104 ARG cc_start: 0.7659 (ptp90) cc_final: 0.5242 (ptm160) outliers start: 37 outliers final: 21 residues processed: 195 average time/residue: 0.8009 time to fit residues: 178.4885 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain m residue 369 GLN Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain w residue 686 ARG Chi-restraints excluded: chain L residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 238 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 157 optimal weight: 0.0270 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN K 295 GLN m 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.123359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103571 restraints weight = 42895.377| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.14 r_work: 0.3076 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30469 Z= 0.127 Angle : 0.497 10.036 43133 Z= 0.253 Chirality : 0.036 0.200 5175 Planarity : 0.004 0.051 3851 Dihedral : 20.857 179.022 9422 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.77 % Allowed : 14.71 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2357 helix: 1.55 (0.16), residues: 1141 sheet: 0.38 (0.32), residues: 243 loop : -0.43 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG t 297 TYR 0.010 0.001 TYR o 94 PHE 0.015 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00279 (30469) covalent geometry : angle 0.49669 (43133) hydrogen bonds : bond 0.04127 ( 1158) hydrogen bonds : angle 3.58222 ( 2910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4714 Ramachandran restraints generated. 2357 Oldfield, 0 Emsley, 2357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.991 Fit side-chains REVERT: D 207 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7030 (pt0) REVERT: D 236 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6470 (pm20) REVERT: D 251 ASN cc_start: 0.6792 (m-40) cc_final: 0.5464 (p0) REVERT: G 246 MET cc_start: 0.6616 (mtt) cc_final: 0.5971 (tmt) REVERT: K 141 PHE cc_start: 0.8275 (t80) cc_final: 0.7903 (t80) REVERT: K 292 TYR cc_start: 0.8431 (t80) cc_final: 0.8205 (t80) REVERT: K 326 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.6768 (pp) REVERT: n 138 MET cc_start: 0.9143 (tpp) cc_final: 0.8861 (tpp) REVERT: n 404 MET cc_start: 0.7282 (mpp) cc_final: 0.6864 (mpp) REVERT: o 198 ASP cc_start: 0.8520 (t70) cc_final: 0.7933 (OUTLIER) REVERT: t 257 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: t 301 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.5859 (p90) REVERT: X 21 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8413 (mmtm) REVERT: m 369 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8559 (mm-40) REVERT: v 186 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: N 67 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8106 (mtm180) REVERT: w 450 ILE cc_start: 0.5962 (OUTLIER) cc_final: 0.5682 (tp) REVERT: w 686 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8006 (mtp85) REVERT: L 85 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7350 (pp) REVERT: L 104 ARG cc_start: 0.7698 (ptp90) cc_final: 0.5207 (ptm160) outliers start: 38 outliers final: 24 residues processed: 191 average time/residue: 0.7896 time to fit residues: 172.7962 Evaluate side-chains 193 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 106 GLU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 257 MET Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain m residue 369 GLN Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain w residue 686 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 72 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 257 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN K 295 GLN m 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104009 restraints weight = 43130.227| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.15 r_work: 0.3086 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.002 0.044 30469 Z= 0.108 Angle : 0.491 9.948 43133 Z= 0.251 Chirality : 0.035 0.197 5175 Planarity : 0.004 0.054 3851 Dihedral : 20.868 179.406 9422 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.77 % Allowed : 14.75 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2357 helix: 1.59 (0.16), residues: 1141 sheet: 0.39 (0.32), residues: 243 loop : -0.42 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG t 297 TYR 0.009 0.001 TYR o 134 PHE 0.015 0.001 PHE D 96 TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 Details of bonding type rmsd covalent geometry : bond 0.00232 (30469) covalent geometry : angle 0.49095 (43133) hydrogen bonds : bond 0.04041 ( 1158) hydrogen bonds : angle 3.58212 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8355.92 seconds wall clock time: 143 minutes 9.57 seconds (8589.57 seconds total)