Starting phenix.real_space_refine on Mon Sep 14 06:09:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r6q_24286/09_2026/7r6q_24286.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r6q_24286/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7r6q_24286/09_2026/7r6q_24286.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r6q_24286/09_2026/7r6q_24286.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r6q_24286/09_2026/7r6q_24286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r6q_24286/09_2026/7r6q_24286.map" model { file = "/net/cci-nas-00/data/ceres_data/7r6q_24286/09_2026/7r6q_24286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r6q_24286/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 5.60, per 1000 atoms: 0.19 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: 2.52 Conformation dependent library (CDL) restraints added in 929.6 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: 3.48 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: 6.38 Time building geometry restraints manager: 3.43 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=" C3' C 6 59 " pdb=" O3' C 6 59 " ideal model delta sigma weight residual 1.415 1.443 -0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" O3' G 1 251 " pdb=" P U 1 252 " ideal model delta sigma weight residual 1.607 1.592 0.015 1.20e-02 6.94e+03 1.53e+00 ... (remaining 30464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 40903 1.68 - 3.35: 1764 3.35 - 5.03: 435 5.03 - 6.71: 26 6.71 - 8.38: 5 Bond angle restraints: 43133 Sorted by residual: angle pdb=" C3' C 6 59 " pdb=" O3' C 6 59 " pdb=" P U 6 60 " ideal model delta sigma weight residual 119.70 124.92 -5.22 1.20e+00 6.94e-01 1.89e+01 angle pdb=" C3' C 11551 " pdb=" O3' C 11551 " pdb=" P G 11552 " ideal model delta sigma weight residual 119.70 124.20 -4.50 1.20e+00 6.94e-01 1.41e+01 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' A 6 222 " pdb=" O3' A 6 222 " pdb=" P U 6 223 " ideal model delta sigma weight residual 119.70 123.45 -3.75 1.20e+00 6.94e-01 9.77e+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 ... (remaining 43128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 16507 34.57 - 69.13: 1064 69.13 - 103.70: 127 103.70 - 138.26: 1 138.26 - 172.83: 3 Dihedral angle restraints: 17702 sinusoidal: 10587 harmonic: 7115 Sorted by residual: dihedral pdb=" C4' A 1 109 " pdb=" C3' A 1 109 " pdb=" C2' A 1 109 " pdb=" C1' A 1 109 " ideal model delta sinusoidal sigma weight residual 36.35 -37.39 73.73 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' C 11574 " pdb=" C3' C 11574 " pdb=" C2' C 11574 " pdb=" C1' C 11574 " ideal model delta sinusoidal sigma weight residual 36.34 -37.35 73.70 1 3.10e+00 1.04e-01 7.19e+02 dihedral pdb=" C4' A 11571 " pdb=" C3' A 11571 " pdb=" C2' A 11571 " pdb=" C1' A 11571 " ideal model delta sinusoidal sigma weight residual 36.34 -37.32 73.67 1 3.10e+00 1.04e-01 7.18e+02 ... (remaining 17699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4176 0.069 - 0.138: 322 0.138 - 0.207: 40 0.207 - 0.275: 580 0.275 - 0.344: 57 Chirality restraints: 5175 Sorted by residual: chirality pdb=" P U 6 60 " pdb=" OP1 U 6 60 " pdb=" OP2 U 6 60 " pdb=" O5' U 6 60 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" P U 6 223 " pdb=" OP1 U 6 223 " pdb=" OP2 U 6 223 " pdb=" O5' U 6 223 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" P C 1 166 " pdb=" OP1 C 1 166 " pdb=" OP2 C 1 166 " pdb=" O5' C 1 166 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.48e+00 ... (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: 7.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.260 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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= 0.146 Angle : 0.794 8.385 43133 Z= 0.351 Chirality : 0.093 0.344 5175 Planarity : 0.004 0.046 3851 Dihedral : 19.239 172.828 13070 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/Z covalent geometry : bond 0.00309 / 0.15 (30469) covalent geometry : angle 0.79426 / 0.35 (43133) hydrogen bonds : bond 0.14275 / 7.49 ( 1158) hydrogen bonds : angle 5.27815 / 2.10 ( 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 : 0.958 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: 0.8215 time to fit residues: 223.7158 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 : 0.925 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 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: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 189 ASN D 251 ASN K 224 ASN K 295 GLN K 330 ASN o 160 HIS t 34 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 = 0.3560 r_free = 0.3560 target = 0.126235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107023 restraints weight = 42763.783| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.13 r_work: 0.3122 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30469 Z= 0.225 Angle : 1.329 25.795 43133 Z= 0.522 Chirality : 0.126 1.332 5175 Planarity : 0.005 0.046 3851 Dihedral : 18.034 176.774 7894 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.17 % Allowed : 7.61 % Favored : 91.22 % 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: 0.29 (0.17), residues: 2357 helix: 0.96 (0.16), residues: 1139 sheet: -0.16 (0.31), residues: 249 loop : -0.54 (0.20), residues: 969 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG t 297 TYR 0.013 0.001 TYR G 97 PHE 0.025 0.001 PHE o 102 TRP 0.009 0.001 TRP N 120 HIS 0.007 0.001 HIS o 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.22 (30469) covalent geometry : angle 1.32876 / 0.52 (43133) hydrogen bonds : bond 0.05717 / 3.02 ( 1158) hydrogen bonds : angle 4.05133 / 1.63 ( 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 202 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.956 Fit side-chains REVERT: D 162 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7113 (mpt) REVERT: D 225 MET cc_start: 0.8164 (mtp) cc_final: 0.7849 (mtp) REVERT: D 251 ASN cc_start: 0.6439 (m-40) cc_final: 0.5322 (OUTLIER) REVERT: o 198 ASP cc_start: 0.8423 (t70) cc_final: 0.7859 (OUTLIER) REVERT: t 170 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: t 301 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5948 (p90) REVERT: X 21 LYS cc_start: 0.8619 (mtmt) cc_final: 0.8171 (mmtm) REVERT: Z 52 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7653 (ttpp) REVERT: w 451 LYS cc_start: 0.8187 (mptt) cc_final: 0.7919 (mmpt) REVERT: L 104 ARG cc_start: 0.7151 (ptp90) cc_final: 0.5378 (ppt170) outliers start: 25 outliers final: 11 residues processed: 191 average time/residue: 0.8626 time to fit residues: 187.8201 Evaluate side-chains 167 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 207 GLU 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 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: 1.9990 chunk 142 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... t 300 GLN ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.128771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.109993 restraints weight = 42546.429| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.09 r_work: 0.3183 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30469 Z= 0.160 Angle : 0.992 19.539 43133 Z= 0.402 Chirality : 0.089 0.828 5175 Planarity : 0.004 0.044 3851 Dihedral : 18.395 178.655 7892 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.45 % Allowed : 10.41 % Favored : 88.14 % 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: 0.51 (0.18), residues: 2357 helix: 1.19 (0.16), residues: 1137 sheet: -0.03 (0.31), residues: 247 loop : -0.51 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 371 TYR 0.010 0.001 TYR D 447 PHE 0.018 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/Z covalent geometry : bond 0.00340 / 0.16 (30469) covalent geometry : angle 0.99169 / 0.40 (43133) hydrogen bonds : bond 0.05096 / 2.67 ( 1158) hydrogen bonds : angle 3.81923 / 1.53 ( 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: 31 poor density : 176 time to evaluate : 0.959 Fit side-chains REVERT: D 251 ASN cc_start: 0.6840 (m-40) cc_final: 0.5416 (p0) REVERT: G 49 TYR cc_start: 0.8101 (p90) cc_final: 0.7630 (p90) REVERT: n 138 MET cc_start: 0.9095 (tpp) cc_final: 0.8796 (tpp) REVERT: n 393 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7949 (mpp) REVERT: o 195 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8018 (tp40) REVERT: o 198 ASP cc_start: 0.8443 (t70) cc_final: 0.7866 (OUTLIER) REVERT: t 49 ARG cc_start: 0.7750 (ptp-110) cc_final: 0.7461 (mtm110) REVERT: t 301 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5768 (p90) REVERT: X 21 LYS cc_start: 0.8548 (mtmt) cc_final: 0.8050 (mmtm) REVERT: v 186 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: Z 52 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7562 (ttpp) REVERT: L 104 ARG cc_start: 0.7299 (ptp90) cc_final: 0.5454 (ppt170) outliers start: 31 outliers final: 12 residues processed: 195 average time/residue: 0.8005 time to fit residues: 179.4730 Evaluate side-chains 170 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 n residue 77 LEU Chi-restraints excluded: chain n residue 393 MET Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 231 ASP 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: 2.9990 chunk 152 optimal weight: 0.5980 chunk 241 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 256 optimal weight: 0.8980 chunk 272 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 164 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 266 GLN o 125 ASN t 51 ASN 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 = 0.3641 r_free = 0.3641 target = 0.131915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113311 restraints weight = 42222.548| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.11 r_work: 0.3220 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30469 Z= 0.137 Angle : 0.895 13.709 43133 Z= 0.364 Chirality : 0.078 0.704 5175 Planarity : 0.004 0.044 3851 Dihedral : 18.301 174.505 7892 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.19 % Allowed : 11.44 % Favored : 86.37 % 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: 0.75 (0.18), residues: 2357 helix: 1.42 (0.16), residues: 1131 sheet: 0.25 (0.32), residues: 242 loop : -0.47 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG t 297 TYR 0.010 0.001 TYR D 447 PHE 0.018 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/Z covalent geometry : bond 0.00291 / 0.14 (30469) covalent geometry : angle 0.89477 / 0.36 (43133) hydrogen bonds : bond 0.04563 / 2.39 ( 1158) hydrogen bonds : angle 3.62405 / 1.45 ( 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 239 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 192 time to evaluate : 0.946 Fit side-chains REVERT: D 251 ASN cc_start: 0.6745 (m-40) cc_final: 0.5405 (p0) REVERT: G 171 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8778 (tmtm) REVERT: K 141 PHE cc_start: 0.8161 (t80) cc_final: 0.7760 (t80) REVERT: K 326 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7116 (pp) REVERT: n 138 MET cc_start: 0.9059 (tpp) cc_final: 0.8778 (tpp) REVERT: o 158 MET cc_start: 0.9179 (mmt) cc_final: 0.7902 (mmt) REVERT: o 195 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: o 198 ASP cc_start: 0.8440 (t70) cc_final: 0.7872 (OUTLIER) REVERT: t 301 PHE cc_start: 0.6360 (OUTLIER) cc_final: 0.5776 (p90) REVERT: X 21 LYS cc_start: 0.8583 (mtmt) cc_final: 0.8115 (mmtm) REVERT: v 186 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: w 472 ASP cc_start: 0.8699 (m-30) cc_final: 0.7918 (t0) REVERT: w 481 ASP cc_start: 0.8041 (p0) cc_final: 0.7601 (p0) REVERT: L 104 ARG cc_start: 0.7381 (ptp90) cc_final: 0.5381 (ppt170) outliers start: 47 outliers final: 18 residues processed: 220 average time/residue: 0.7839 time to fit residues: 199.2629 Evaluate side-chains 190 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 355 ILE Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 203 VAL 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 43 GLU Chi-restraints excluded: chain t residue 171 THR Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 111 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 142 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 152 optimal weight: 0.0270 chunk 153 optimal weight: 0.0370 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 166 optimal weight: 0.5980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 295 GLN n 430 GLN ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 356 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.116652 restraints weight = 42096.474| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.08 r_work: 0.3286 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30469 Z= 0.117 Angle : 0.832 11.630 43133 Z= 0.339 Chirality : 0.072 0.632 5175 Planarity : 0.004 0.042 3851 Dihedral : 18.185 179.570 7892 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.68 % Allowed : 12.51 % Favored : 85.81 % 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: 1.61 (0.16), residues: 1128 sheet: 0.42 (0.32), residues: 244 loop : -0.49 (0.20), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG t 297 TYR 0.011 0.001 TYR G 49 PHE 0.016 0.001 PHE D 96 TRP 0.008 0.001 TRP n 199 HIS 0.002 0.001 HIS D 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (30469) covalent geometry : angle 0.83186 / 0.34 (43133) hydrogen bonds : bond 0.04180 / 2.21 ( 1158) hydrogen bonds : angle 3.52235 / 1.41 ( 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 231 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.945 Fit side-chains REVERT: D 225 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: D 251 ASN cc_start: 0.6805 (m-40) cc_final: 0.5464 (p0) REVERT: K 141 PHE cc_start: 0.8155 (t80) cc_final: 0.7764 (t80) REVERT: K 269 GLN cc_start: 0.8244 (mt0) cc_final: 0.8037 (mt0) REVERT: K 326 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.6999 (pp) REVERT: n 138 MET cc_start: 0.9038 (tpp) cc_final: 0.8694 (tpp) REVERT: n 568 LYS cc_start: 0.8678 (mttt) cc_final: 0.8438 (mtpt) REVERT: o 198 ASP cc_start: 0.8391 (t70) cc_final: 0.7804 (OUTLIER) REVERT: t 301 PHE cc_start: 0.6399 (OUTLIER) cc_final: 0.5852 (p90) REVERT: X 21 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8164 (mmtm) REVERT: v 186 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: w 451 LYS cc_start: 0.7767 (mmtm) cc_final: 0.7547 (mmpt) REVERT: w 472 ASP cc_start: 0.8668 (m-30) cc_final: 0.7881 (t0) REVERT: w 481 ASP cc_start: 0.7984 (p0) cc_final: 0.7588 (p0) REVERT: L 104 ARG cc_start: 0.7362 (ptp90) cc_final: 0.5077 (ppt170) outliers start: 36 outliers final: 13 residues processed: 218 average time/residue: 0.7866 time to fit residues: 197.6230 Evaluate side-chains 198 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 MET 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 72 MET Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 75 ILE Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 128 LYS Chi-restraints excluded: chain h residue 100 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 142 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 75 optimal weight: 0.0470 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 GLN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 GLN n 430 GLN o 199 ASN m 356 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.130738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111365 restraints weight = 42083.783| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.09 r_work: 0.3204 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30469 Z= 0.156 Angle : 0.880 13.603 43133 Z= 0.360 Chirality : 0.076 0.710 5175 Planarity : 0.004 0.045 3851 Dihedral : 18.181 178.708 7892 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 13.68 % Favored : 84.55 % 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: 0.92 (0.18), residues: 2357 helix: 1.59 (0.16), residues: 1140 sheet: 0.45 (0.32), residues: 243 loop : -0.47 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG t 297 TYR 0.019 0.001 TYR K 292 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/Z covalent geometry : bond 0.00341 / 0.16 (30469) covalent geometry : angle 0.87993 / 0.36 (43133) hydrogen bonds : bond 0.04617 / 2.42 ( 1158) hydrogen bonds : angle 3.55518 / 1.42 ( 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 220 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.955 Fit side-chains REVERT: D 225 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: D 251 ASN cc_start: 0.6559 (m-40) cc_final: 0.5193 (p0) REVERT: K 141 PHE cc_start: 0.8238 (t80) cc_final: 0.7846 (t80) REVERT: K 326 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7151 (pp) REVERT: n 138 MET cc_start: 0.9152 (tpp) cc_final: 0.8850 (tpp) REVERT: n 559 MET cc_start: 0.8032 (mtp) cc_final: 0.7662 (mtm) REVERT: o 158 MET cc_start: 0.9294 (mmt) cc_final: 0.7678 (mmt) REVERT: o 198 ASP cc_start: 0.8465 (t70) cc_final: 0.7896 (t0) REVERT: t 301 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.5883 (p90) REVERT: X 21 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8283 (mmtm) REVERT: m 356 ASN cc_start: 0.8418 (m-40) cc_final: 0.8217 (m110) REVERT: v 186 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: w 451 LYS cc_start: 0.7745 (mmtm) cc_final: 0.7484 (mmmm) REVERT: w 472 ASP cc_start: 0.8712 (m-30) cc_final: 0.7930 (t0) REVERT: w 481 ASP cc_start: 0.8026 (p0) cc_final: 0.7588 (p0) REVERT: L 85 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7302 (pp) REVERT: L 104 ARG cc_start: 0.7552 (ptp90) cc_final: 0.5123 (ppt170) outliers start: 38 outliers final: 20 residues processed: 208 average time/residue: 0.7839 time to fit residues: 188.3897 Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain G residue 203 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 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 o residue 173 ILE Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 231 ASP 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 X residue 31 THR Chi-restraints excluded: chain X residue 111 ASN 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 L residue 85 LEU Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 176 optimal weight: 0.9980 chunk 242 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 231 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 GLN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110107 restraints weight = 42278.081| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.10 r_work: 0.3186 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30469 Z= 0.168 Angle : 0.894 13.850 43133 Z= 0.366 Chirality : 0.078 0.761 5175 Planarity : 0.004 0.044 3851 Dihedral : 18.255 179.167 7892 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.19 % Allowed : 13.73 % Favored : 84.08 % 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: 0.88 (0.18), residues: 2357 helix: 1.54 (0.16), residues: 1140 sheet: 0.44 (0.32), residues: 243 loop : -0.49 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 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 0.005 0.001 HIS n 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (30469) covalent geometry : angle 0.89356 / 0.37 (43133) hydrogen bonds : bond 0.04692 / 2.46 ( 1158) hydrogen bonds : angle 3.59003 / 1.43 ( 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 225 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.929 Fit side-chains REVERT: D 225 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7935 (mpp) REVERT: D 236 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6521 (pm20) REVERT: D 251 ASN cc_start: 0.6560 (m-40) cc_final: 0.5225 (p0) REVERT: G 171 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8789 (tmtm) REVERT: K 141 PHE cc_start: 0.8276 (t80) cc_final: 0.7900 (t80) REVERT: K 292 TYR cc_start: 0.8387 (t80) cc_final: 0.8081 (t80) REVERT: K 326 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7191 (pp) REVERT: n 138 MET cc_start: 0.9154 (tpp) cc_final: 0.8840 (tpp) REVERT: n 404 MET cc_start: 0.7037 (mpp) cc_final: 0.6554 (mpp) REVERT: n 559 MET cc_start: 0.8138 (mtp) cc_final: 0.7782 (mtm) REVERT: o 198 ASP cc_start: 0.8469 (t70) cc_final: 0.7898 (t0) REVERT: t 301 PHE cc_start: 0.6305 (OUTLIER) cc_final: 0.5756 (p90) REVERT: X 21 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8292 (mmtm) REVERT: m 356 ASN cc_start: 0.8452 (m-40) cc_final: 0.8249 (m110) REVERT: v 186 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: w 451 LYS cc_start: 0.7744 (mmtm) cc_final: 0.7506 (mmmm) REVERT: w 472 ASP cc_start: 0.8678 (m-30) cc_final: 0.7915 (t0) REVERT: w 481 ASP cc_start: 0.8068 (p0) cc_final: 0.7622 (p0) REVERT: L 85 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7338 (pp) REVERT: L 104 ARG cc_start: 0.7591 (ptp90) cc_final: 0.5236 (ptm160) outliers start: 47 outliers final: 24 residues processed: 210 average time/residue: 0.7709 time to fit residues: 187.3263 Evaluate side-chains 193 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 203 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 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 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 301 PHE Chi-restraints excluded: chain t residue 314 ILE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 111 ASN 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 128 LYS Chi-restraints excluded: chain h residue 100 VAL 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: 0.5980 chunk 93 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 chunk 13 optimal weight: 0.0470 chunk 23 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 GLN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.131007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.111660 restraints weight = 42372.031| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.10 r_work: 0.3207 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30469 Z= 0.131 Angle : 0.868 13.394 43133 Z= 0.355 Chirality : 0.076 0.695 5175 Planarity : 0.004 0.056 3851 Dihedral : 18.282 178.666 7892 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.82 % Allowed : 14.05 % Favored : 84.13 % 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: 0.98 (0.18), residues: 2357 helix: 1.61 (0.16), residues: 1138 sheet: 0.47 (0.32), residues: 243 loop : -0.41 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG t 297 TYR 0.014 0.001 TYR G 49 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/Z covalent geometry : bond 0.00278 / 0.13 (30469) covalent geometry : angle 0.86775 / 0.36 (43133) hydrogen bonds : bond 0.04500 / 2.36 ( 1158) hydrogen bonds : angle 3.57238 / 1.43 ( 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: 39 poor density : 166 time to evaluate : 0.983 Fit side-chains REVERT: D 236 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: D 251 ASN cc_start: 0.6529 (m-40) cc_final: 0.5239 (p0) REVERT: G 171 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8771 (tmtm) REVERT: G 246 MET cc_start: 0.6573 (mtt) cc_final: 0.5639 (tpp) REVERT: K 141 PHE cc_start: 0.8258 (t80) cc_final: 0.7894 (t80) REVERT: K 326 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7190 (pp) REVERT: n 138 MET cc_start: 0.9138 (tpp) cc_final: 0.8842 (tpp) REVERT: n 404 MET cc_start: 0.7029 (mpp) cc_final: 0.6519 (mpp) REVERT: n 559 MET cc_start: 0.8125 (mtp) cc_final: 0.7822 (mtm) REVERT: o 158 MET cc_start: 0.9280 (mmt) cc_final: 0.7728 (mmt) REVERT: o 198 ASP cc_start: 0.8488 (t70) cc_final: 0.7920 (t0) REVERT: t 231 ASP cc_start: 0.8828 (p0) cc_final: 0.8626 (p0) REVERT: t 301 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5746 (p90) REVERT: X 21 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8282 (mmtm) REVERT: v 186 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7850 (tm-30) REVERT: N 67 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8170 (mtm180) REVERT: w 451 LYS cc_start: 0.7671 (mmtm) cc_final: 0.7465 (mmpt) REVERT: L 85 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7333 (pp) REVERT: L 104 ARG cc_start: 0.7548 (ptp90) cc_final: 0.5225 (ptm160) outliers start: 39 outliers final: 24 residues processed: 193 average time/residue: 0.8176 time to fit residues: 181.4896 Evaluate side-chains 186 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 171 LYS 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 244 LEU Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 51 ASN 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 X residue 31 THR Chi-restraints excluded: chain X residue 111 ASN 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 L residue 85 LEU Chi-restraints excluded: chain L residue 103 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 167 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 19 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 145 optimal weight: 0.0970 chunk 82 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 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 = 0.3642 r_free = 0.3642 target = 0.132059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112714 restraints weight = 42275.494| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.10 r_work: 0.3224 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30469 Z= 0.127 Angle : 0.854 12.993 43133 Z= 0.349 Chirality : 0.074 0.682 5175 Planarity : 0.004 0.056 3851 Dihedral : 18.260 177.201 7892 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.73 % Allowed : 14.52 % Favored : 83.75 % 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: 1.00 (0.18), residues: 2357 helix: 1.65 (0.16), residues: 1140 sheet: 0.52 (0.32), residues: 243 loop : -0.44 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG t 297 TYR 0.019 0.001 TYR K 292 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/Z covalent geometry : bond 0.00268 / 0.13 (30469) covalent geometry : angle 0.85350 / 0.35 (43133) hydrogen bonds : bond 0.04407 / 2.32 ( 1158) hydrogen bonds : angle 3.54526 / 1.42 ( 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 204 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.945 Fit side-chains REVERT: D 236 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6609 (pm20) REVERT: D 251 ASN cc_start: 0.6509 (m-40) cc_final: 0.5230 (p0) REVERT: G 246 MET cc_start: 0.6594 (mtt) cc_final: 0.5992 (tmt) REVERT: K 141 PHE cc_start: 0.8262 (t80) cc_final: 0.7909 (t80) REVERT: K 326 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7071 (pp) REVERT: n 138 MET cc_start: 0.9126 (tpp) cc_final: 0.8854 (tpp) REVERT: n 404 MET cc_start: 0.7042 (mpp) cc_final: 0.6519 (mpp) REVERT: n 559 MET cc_start: 0.8130 (mtp) cc_final: 0.7860 (mtm) REVERT: n 568 LYS cc_start: 0.8652 (mttt) cc_final: 0.8448 (mtpt) REVERT: o 158 MET cc_start: 0.9266 (mmt) cc_final: 0.7725 (mmt) REVERT: o 198 ASP cc_start: 0.8488 (t70) cc_final: 0.7919 (t0) REVERT: t 231 ASP cc_start: 0.8808 (p0) cc_final: 0.8606 (p0) REVERT: t 301 PHE cc_start: 0.6260 (OUTLIER) cc_final: 0.5706 (p90) REVERT: X 21 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8286 (mmtm) REVERT: v 186 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: w 449 MET cc_start: 0.5212 (mpp) cc_final: 0.4856 (mmp) REVERT: w 451 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7391 (mmpt) REVERT: L 85 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7323 (pp) REVERT: L 104 ARG cc_start: 0.7528 (ptp90) cc_final: 0.5224 (ptm160) outliers start: 37 outliers final: 23 residues processed: 192 average time/residue: 0.8052 time to fit residues: 178.0472 Evaluate side-chains 189 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 203 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 326 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 75 ILE 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 X residue 31 THR 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 128 LYS Chi-restraints excluded: chain h residue 100 VAL Chi-restraints excluded: chain Z residue 55 LYS 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: 1.9990 chunk 71 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 157 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3625 r_free = 0.3625 target = 0.130789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.111477 restraints weight = 42251.110| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.11 r_work: 0.3202 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30469 Z= 0.147 Angle : 0.867 13.486 43133 Z= 0.355 Chirality : 0.075 0.728 5175 Planarity : 0.004 0.052 3851 Dihedral : 18.233 178.901 7892 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.68 % Allowed : 14.71 % Favored : 83.61 % 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: 0.97 (0.18), residues: 2357 helix: 1.64 (0.16), residues: 1140 sheet: 0.48 (0.32), residues: 243 loop : -0.46 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG t 297 TYR 0.015 0.001 TYR K 292 PHE 0.015 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/Z covalent geometry : bond 0.00319 / 0.15 (30469) covalent geometry : angle 0.86666 / 0.36 (43133) hydrogen bonds : bond 0.04564 / 2.42 ( 1158) hydrogen bonds : angle 3.55512 / 1.42 ( 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 203 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.908 Fit side-chains REVERT: D 236 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6582 (pm20) REVERT: D 251 ASN cc_start: 0.6524 (m-40) cc_final: 0.5205 (p0) REVERT: G 171 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8729 (tmtm) REVERT: G 246 MET cc_start: 0.6591 (mtt) cc_final: 0.5987 (tmt) REVERT: K 141 PHE cc_start: 0.8293 (t80) cc_final: 0.7939 (t80) REVERT: K 326 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.6969 (pp) REVERT: n 138 MET cc_start: 0.9144 (tpp) cc_final: 0.8849 (tpp) REVERT: n 404 MET cc_start: 0.7137 (mpp) cc_final: 0.6616 (mpp) REVERT: n 559 MET cc_start: 0.8152 (mtp) cc_final: 0.7859 (mtm) REVERT: o 158 MET cc_start: 0.9305 (mmt) cc_final: 0.7700 (mmt) REVERT: o 198 ASP cc_start: 0.8465 (t70) cc_final: 0.7889 (t0) REVERT: t 301 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.5694 (p90) REVERT: X 21 LYS cc_start: 0.8690 (mtmt) cc_final: 0.8309 (mmtm) REVERT: m 298 LYS cc_start: 0.7743 (mppt) cc_final: 0.7270 (mptp) REVERT: m 356 ASN cc_start: 0.8394 (m-40) cc_final: 0.8191 (m110) REVERT: v 186 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: N 67 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8167 (mtm180) REVERT: w 451 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7401 (mmmm) REVERT: L 85 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7333 (pp) REVERT: L 104 ARG cc_start: 0.7644 (ptp90) cc_final: 0.5255 (ptm160) outliers start: 36 outliers final: 23 residues processed: 192 average time/residue: 0.8396 time to fit residues: 184.9863 Evaluate side-chains 192 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 171 LYS Chi-restraints excluded: chain G residue 203 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 326 LEU Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 51 ASN Chi-restraints excluded: chain t residue 231 ASP 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 X residue 31 THR 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 Z residue 55 LYS 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 72 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 52 optimal weight: 0.7980 chunk 113 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 228 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 257 optimal weight: 0.9980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 59 GLN ** K 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 GLN o 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.131964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112667 restraints weight = 42434.497| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.10 r_work: 0.3222 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30469 Z= 0.128 Angle : 0.850 13.096 43133 Z= 0.348 Chirality : 0.074 0.686 5175 Planarity : 0.004 0.055 3851 Dihedral : 18.243 177.291 7892 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.59 % Allowed : 14.94 % 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: 1.02 (0.18), residues: 2357 helix: 1.68 (0.16), residues: 1140 sheet: 0.52 (0.33), residues: 237 loop : -0.44 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG t 297 TYR 0.014 0.001 TYR G 49 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/Z covalent geometry : bond 0.00272 / 0.13 (30469) covalent geometry : angle 0.84999 / 0.35 (43133) hydrogen bonds : bond 0.04428 / 2.35 ( 1158) hydrogen bonds : angle 3.54072 / 1.41 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9142.19 seconds wall clock time: 156 minutes 55.91 seconds (9415.91 seconds total)