Starting phenix.real_space_refine on Tue Feb 20 22:05:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6q_24286/02_2024/7r6q_24286.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6q_24286/02_2024/7r6q_24286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6q_24286/02_2024/7r6q_24286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6q_24286/02_2024/7r6q_24286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6q_24286/02_2024/7r6q_24286.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r6q_24286/02_2024/7r6q_24286.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "n TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29033 Number of models: 1 Model: "" Number of chains: 19 Chain: "6" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 21, 'rna3p_pur': 29, 'rna3p_pyr': 26} Link IDs: {'rna2p': 32, 'rna3p': 54} Chain breaks: 1 Chain: "D" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3486 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 1 Chain: "G" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1560 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain breaks: 1 Chain: "K" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2291 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 2 Chain: "n" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3467 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 401} Chain breaks: 3 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "t" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2328 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 10, 'TRANS': 279} Chain breaks: 1 Chain: "X" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain breaks: 1 Chain: "m" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1513 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 20, 'TRANS': 159} Chain: "1" Number of atoms: 6301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 6301 Classifications: {'RNA': 295} Modifications used: {'rna2p_pur': 35, 'rna2p_pyr': 37, 'rna3p_pur': 126, 'rna3p_pyr': 97} Link IDs: {'rna2p': 72, 'rna3p': 222} Chain breaks: 8 Chain: "v" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 475 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "2" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1206 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 22, 'rna3p_pyr': 26} Link IDs: {'rna2p': 8, 'rna3p': 48} Chain: "N" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1131 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "h" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 151 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain breaks: 1 Chain: "Z" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "g" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 284 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain breaks: 3 Chain: "w" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 574 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain breaks: 1 Chain: "i" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 468 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain breaks: 1 Chain: "L" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 263 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain breaks: 1 Time building chain proxies: 15.39, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 13.51 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 10.44 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: 11.89 Time building geometry restraints manager: 14.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6223 1.33 - 1.45: 8440 1.45 - 1.57: 14855 1.57 - 1.69: 866 1.69 - 1.81: 85 Bond restraints: 30469 Sorted by residual: bond pdb=" CA GLN t 269 " pdb=" C GLN t 269 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.26e-02 6.30e+03 4.07e+00 bond pdb=" CG LEU n 139 " pdb=" CD1 LEU n 139 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.96e+00 bond pdb=" C ASN K 338 " pdb=" N PRO K 339 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.38e+00 bond pdb=" O5' A 1 266 " pdb=" C5' A 1 266 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 2.05e+00 bond pdb=" O5' U 6 225 " pdb=" C5' U 6 225 " ideal model delta sigma weight residual 1.424 1.444 -0.020 1.50e-02 4.44e+03 1.78e+00 ... (remaining 30464 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.20: 2868 106.20 - 113.16: 17044 113.16 - 120.11: 11000 120.11 - 127.07: 11138 127.07 - 134.02: 1083 Bond angle restraints: 43133 Sorted by residual: angle pdb=" C PRO n 245 " pdb=" N PRO n 246 " pdb=" CA PRO n 246 " ideal model delta sigma weight residual 119.76 123.02 -3.26 1.03e+00 9.43e-01 1.00e+01 angle pdb=" C3' C 6 59 " pdb=" O3' C 6 59 " pdb=" P U 6 60 " ideal model delta sigma weight residual 120.20 124.92 -4.72 1.50e+00 4.44e-01 9.89e+00 angle pdb=" O3' C 11551 " pdb=" C3' C 11551 " pdb=" C2' C 11551 " ideal model delta sigma weight residual 113.70 118.32 -4.62 1.50e+00 4.44e-01 9.47e+00 angle pdb=" CB MET m 322 " pdb=" CG MET m 322 " pdb=" SD MET m 322 " ideal model delta sigma weight residual 112.70 104.32 8.38 3.00e+00 1.11e-01 7.81e+00 angle pdb=" N GLY t 137 " pdb=" CA GLY t 137 " pdb=" C GLY t 137 " ideal model delta sigma weight residual 115.61 110.83 4.78 1.74e+00 3.30e-01 7.55e+00 ... (remaining 43128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 17979 35.90 - 71.80: 1130 71.80 - 107.70: 107 107.70 - 143.60: 6 143.60 - 179.49: 10 Dihedral angle restraints: 19232 sinusoidal: 12117 harmonic: 7115 Sorted by residual: dihedral pdb=" O4' C 6 59 " pdb=" C1' C 6 59 " pdb=" N1 C 6 59 " pdb=" C2 C 6 59 " ideal model delta sinusoidal sigma weight residual 232.00 52.51 179.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 6 223 " pdb=" C1' U 6 223 " pdb=" N1 U 6 223 " pdb=" C2 U 6 223 " ideal model delta sinusoidal sigma weight residual 232.00 53.33 178.67 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 11569 " pdb=" C1' U 11569 " pdb=" N1 U 11569 " pdb=" C2 U 11569 " ideal model delta sinusoidal sigma weight residual -128.00 48.52 -176.52 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 19229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4561 0.054 - 0.109: 527 0.109 - 0.163: 80 0.163 - 0.218: 6 0.218 - 0.272: 1 Chirality restraints: 5175 Sorted by residual: chirality pdb=" CA ASN K 338 " pdb=" N ASN K 338 " pdb=" C ASN K 338 " pdb=" CB ASN K 338 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE t 103 " pdb=" N ILE t 103 " pdb=" C ILE t 103 " pdb=" CB ILE t 103 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" C3' A 1 266 " pdb=" C4' A 1 266 " pdb=" O3' A 1 266 " pdb=" C2' A 1 266 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 5172 not shown) Planarity restraints: 3851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 11807 " -0.030 2.00e-02 2.50e+03 1.25e-02 4.71e+00 pdb=" N9 G 11807 " 0.028 2.00e-02 2.50e+03 pdb=" C8 G 11807 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G 11807 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G 11807 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 11807 " -0.004 2.00e-02 2.50e+03 pdb=" O6 G 11807 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G 11807 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 11807 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 11807 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 11807 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 11807 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 11646 " -0.029 2.00e-02 2.50e+03 1.25e-02 4.70e+00 pdb=" N9 G 11646 " 0.031 2.00e-02 2.50e+03 pdb=" C8 G 11646 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 11646 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 11646 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 11646 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 11646 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G 11646 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 11646 " 0.000 2.00e-02 2.50e+03 pdb=" N2 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 11646 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G 11646 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 296 " -0.028 2.00e-02 2.50e+03 1.27e-02 4.41e+00 pdb=" N9 A 1 296 " 0.030 2.00e-02 2.50e+03 pdb=" C8 A 1 296 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 1 296 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 1 296 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 1 296 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 1 296 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 296 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 296 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 1 296 " 0.003 2.00e-02 2.50e+03 ... (remaining 3848 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2407 2.74 - 3.28: 26708 3.28 - 3.82: 50940 3.82 - 4.36: 64240 4.36 - 4.90: 97833 Nonbonded interactions: 242128 Sorted by model distance: nonbonded pdb=" OP2 G 2 103 " pdb=" O2' A 2 105 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR D 395 " pdb=" OD1 ASN D 397 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP K 184 " pdb=" OG SER K 208 " model vdw 2.207 2.440 nonbonded pdb=" OP2 G 1 297 " pdb=" N2 G 1 297 " model vdw 2.229 2.520 nonbonded pdb=" OP2 G 1 148 " pdb=" OH TYR N 4 " model vdw 2.230 2.440 ... (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 ========== 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 17.030 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 82.940 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30469 Z= 0.167 Angle : 0.515 8.385 43133 Z= 0.278 Chirality : 0.036 0.272 5175 Planarity : 0.004 0.046 3851 Dihedral : 19.636 179.495 14600 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP N 28 HIS 0.005 0.001 HIS D 375 PHE 0.023 0.001 PHE o 102 TYR 0.017 0.001 TYR G 97 ARG 0.005 0.000 ARG D 328 *********************** 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 fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 2.788 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: 0.7128 (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: 1.7226 time to fit residues: 470.8197 Evaluate side-chains 168 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 233 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 141 optimal weight: 0.0570 chunk 112 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 132 optimal weight: 0.5980 chunk 161 optimal weight: 4.9990 chunk 251 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN D 251 ASN K 224 ASN K 295 GLN o 125 ASN t 34 GLN v 210 GLN i 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30469 Z= 0.147 Angle : 0.483 8.557 43133 Z= 0.249 Chirality : 0.035 0.174 5175 Planarity : 0.004 0.049 3851 Dihedral : 21.085 179.843 9424 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.03 % Allowed : 7.70 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2357 helix: 1.12 (0.16), residues: 1134 sheet: -0.04 (0.31), residues: 249 loop : -0.52 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 PHE 0.018 0.001 PHE o 102 TYR 0.011 0.001 TYR G 55 ARG 0.005 0.000 ARG t 297 *********************** 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 203 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 2.584 Fit side-chains REVERT: D 162 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6670 (mpt) REVERT: D 251 ASN cc_start: 0.6219 (m-40) cc_final: 0.5538 (OUTLIER) REVERT: G 49 TYR cc_start: 0.8049 (p90) cc_final: 0.7833 (p90) REVERT: o 198 ASP cc_start: 0.7542 (t70) cc_final: 0.7128 (OUTLIER) REVERT: t 301 PHE cc_start: 0.5995 (OUTLIER) cc_final: 0.5602 (p90) outliers start: 22 outliers final: 9 residues processed: 191 average time/residue: 1.6121 time to fit residues: 354.1810 Evaluate side-chains 166 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 157 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 MET 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 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain v residue 207 ILE 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 139 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 209 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 251 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 202 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 295 GLN t 300 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 30469 Z= 0.142 Angle : 0.466 9.824 43133 Z= 0.239 Chirality : 0.035 0.200 5175 Planarity : 0.004 0.048 3851 Dihedral : 20.944 179.764 9422 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.77 % Allowed : 10.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2357 helix: 1.40 (0.16), residues: 1132 sheet: 0.15 (0.31), residues: 252 loop : -0.52 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 120 HIS 0.004 0.001 HIS n 83 PHE 0.019 0.001 PHE o 102 TYR 0.010 0.001 TYR D 447 ARG 0.011 0.000 ARG D 371 *********************** 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 218 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 2.597 Fit side-chains REVERT: G 49 TYR cc_start: 0.8018 (p90) cc_final: 0.7810 (p90) REVERT: G 97 TYR cc_start: 0.8995 (m-80) cc_final: 0.8786 (m-80) REVERT: K 326 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7210 (pp) REVERT: n 1 MET cc_start: 0.6611 (mpt) cc_final: 0.6272 (mpt) REVERT: n 138 MET cc_start: 0.8855 (tpp) cc_final: 0.8498 (tpp) REVERT: o 195 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7584 (tp40) REVERT: o 198 ASP cc_start: 0.7628 (t70) cc_final: 0.7189 (OUTLIER) REVERT: t 301 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.5595 (p90) REVERT: m 369 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8118 (mm-40) REVERT: v 186 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: w 451 LYS cc_start: 0.8044 (mptt) cc_final: 0.7805 (mmpt) REVERT: L 104 ARG cc_start: 0.7599 (pmm150) cc_final: 0.5301 (ppt170) outliers start: 38 outliers final: 11 residues processed: 198 average time/residue: 1.7169 time to fit residues: 391.0360 Evaluate side-chains 174 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 207 GLU 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 o residue 195 GLN Chi-restraints excluded: chain t residue 260 SER Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain m residue 369 GLN Chi-restraints excluded: chain v residue 186 GLU Chi-restraints excluded: chain v residue 207 ILE Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain 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 248 optimal weight: 0.0670 chunk 189 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 169 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 295 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30469 Z= 0.173 Angle : 0.480 10.097 43133 Z= 0.244 Chirality : 0.035 0.198 5175 Planarity : 0.004 0.045 3851 Dihedral : 20.890 179.011 9422 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.15 % Allowed : 11.67 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2357 helix: 1.46 (0.16), residues: 1135 sheet: 0.38 (0.31), residues: 248 loop : -0.52 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.005 0.001 HIS n 83 PHE 0.017 0.001 PHE D 96 TYR 0.011 0.001 TYR G 55 ARG 0.009 0.000 ARG t 297 *********************** 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 219 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 2.956 Fit side-chains REVERT: D 251 ASN cc_start: 0.7066 (m-40) cc_final: 0.5590 (OUTLIER) REVERT: G 171 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8499 (tmtm) REVERT: K 141 PHE cc_start: 0.7825 (t80) cc_final: 0.7505 (t80) REVERT: n 138 MET cc_start: 0.8965 (tpp) cc_final: 0.8634 (tpp) REVERT: o 195 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7571 (tp40) REVERT: o 198 ASP cc_start: 0.7646 (t70) cc_final: 0.7200 (OUTLIER) REVERT: t 301 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5513 (p90) REVERT: m 298 LYS cc_start: 0.7409 (mppt) cc_final: 0.7032 (mptp) REVERT: m 369 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8165 (mm-40) REVERT: v 186 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: L 104 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.5342 (ppt170) outliers start: 46 outliers final: 22 residues processed: 199 average time/residue: 1.5812 time to fit residues: 362.5347 Evaluate side-chains 187 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 2.371 ------------------------------------------------------------------------------- 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 488 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain n residue 421 VAL Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 260 SER Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain X residue 29 SER Chi-restraints excluded: chain m residue 369 GLN Chi-restraints excluded: chain 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 h residue 100 VAL Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 222 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 228 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 288 GLN G 59 GLN K 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30469 Z= 0.291 Angle : 0.555 9.778 43133 Z= 0.283 Chirality : 0.039 0.206 5175 Planarity : 0.004 0.047 3851 Dihedral : 20.891 176.606 9422 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.03 % Allowed : 12.04 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2357 helix: 1.28 (0.16), residues: 1143 sheet: 0.28 (0.31), residues: 243 loop : -0.58 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 120 HIS 0.007 0.001 HIS D 320 PHE 0.022 0.002 PHE o 102 TYR 0.017 0.002 TYR G 97 ARG 0.010 0.001 ARG t 297 *********************** 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 232 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 167 time to evaluate : 2.540 Fit side-chains REVERT: D 249 PHE cc_start: 0.6337 (OUTLIER) cc_final: 0.5894 (p90) REVERT: D 251 ASN cc_start: 0.7109 (m-40) cc_final: 0.5656 (OUTLIER) REVERT: G 171 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8601 (tmtm) REVERT: K 141 PHE cc_start: 0.7982 (t80) cc_final: 0.7629 (t80) REVERT: K 326 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7374 (pp) REVERT: n 138 MET cc_start: 0.9014 (tpp) cc_final: 0.8667 (tpp) REVERT: n 404 MET cc_start: 0.7132 (mpp) cc_final: 0.6643 (mpp) REVERT: o 165 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7094 (ptp90) REVERT: o 198 ASP cc_start: 0.7631 (t70) cc_final: 0.7182 (OUTLIER) REVERT: t 301 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.5828 (p90) REVERT: m 369 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8245 (mm-40) REVERT: v 186 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: N 67 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8266 (mtm180) REVERT: h 107 LYS cc_start: 0.7666 (mptt) cc_final: 0.7437 (mppt) REVERT: L 85 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7427 (pp) REVERT: L 104 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.5392 (ppt170) outliers start: 65 outliers final: 26 residues processed: 210 average time/residue: 1.5611 time to fit residues: 378.2294 Evaluate side-chains 195 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 161 time to evaluate : 2.926 ------------------------------------------------------------------------------- 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 249 PHE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 66 SER 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 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 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU 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 m residue 369 GLN 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 w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 90 optimal weight: 0.9980 chunk 241 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN G 59 GLN K 295 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30469 Z= 0.204 Angle : 0.513 9.586 43133 Z= 0.262 Chirality : 0.037 0.200 5175 Planarity : 0.004 0.063 3851 Dihedral : 20.890 177.495 9422 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.75 % Allowed : 12.89 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.18), residues: 2357 helix: 1.39 (0.16), residues: 1141 sheet: 0.29 (0.32), residues: 243 loop : -0.56 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 120 HIS 0.006 0.001 HIS n 83 PHE 0.016 0.001 PHE D 96 TYR 0.018 0.001 TYR G 97 ARG 0.012 0.000 ARG t 297 *********************** 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 222 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 163 time to evaluate : 2.878 Fit side-chains REVERT: D 219 ASN cc_start: 0.6345 (t0) cc_final: 0.6123 (t0) REVERT: D 225 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7809 (mpp) REVERT: D 236 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: D 251 ASN cc_start: 0.7052 (m-40) cc_final: 0.5632 (OUTLIER) REVERT: G 171 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8576 (tmtm) REVERT: K 141 PHE cc_start: 0.7936 (t80) cc_final: 0.7603 (t80) REVERT: K 326 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7039 (pp) REVERT: n 138 MET cc_start: 0.8984 (tpp) cc_final: 0.8683 (tpp) REVERT: n 393 MET cc_start: 0.7968 (mpp) cc_final: 0.7746 (mtp) REVERT: n 404 MET cc_start: 0.7094 (mpp) cc_final: 0.6551 (mpp) REVERT: o 165 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6874 (ptp90) REVERT: o 195 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7617 (tp40) REVERT: o 198 ASP cc_start: 0.7642 (t70) cc_final: 0.7201 (OUTLIER) REVERT: t 130 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.6723 (mtp85) REVERT: t 301 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5841 (p90) REVERT: m 254 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8755 (mtp) REVERT: m 369 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8215 (mm-40) REVERT: v 186 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: N 67 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8253 (mtm180) REVERT: h 107 LYS cc_start: 0.7725 (mptt) cc_final: 0.7438 (mppt) REVERT: w 450 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5519 (tp) REVERT: L 104 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.5372 (ppt170) outliers start: 59 outliers final: 29 residues processed: 201 average time/residue: 1.6578 time to fit residues: 383.2103 Evaluate side-chains 198 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 225 MET Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 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 72 MET Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain o residue 195 GLN Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 369 GLN 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 w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 258 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 266 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 GLN n 157 ASN L 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30469 Z= 0.316 Angle : 0.571 9.443 43133 Z= 0.291 Chirality : 0.040 0.207 5175 Planarity : 0.005 0.049 3851 Dihedral : 20.878 176.505 9422 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.03 % Favored : 95.93 % Rotamer: Outliers : 2.94 % Allowed : 13.07 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2357 helix: 1.24 (0.16), residues: 1143 sheet: 0.24 (0.32), residues: 243 loop : -0.66 (0.20), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP N 120 HIS 0.007 0.001 HIS D 320 PHE 0.016 0.002 PHE D 96 TYR 0.020 0.002 TYR G 97 ARG 0.012 0.001 ARG t 297 *********************** 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 230 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 167 time to evaluate : 2.723 Fit side-chains REVERT: D 236 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: D 251 ASN cc_start: 0.7100 (m-40) cc_final: 0.5725 (OUTLIER) REVERT: K 141 PHE cc_start: 0.8027 (t80) cc_final: 0.7663 (t80) REVERT: K 326 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7219 (pp) REVERT: n 138 MET cc_start: 0.8997 (tpp) cc_final: 0.8680 (tpp) REVERT: n 404 MET cc_start: 0.7220 (mpp) cc_final: 0.6718 (mpp) REVERT: o 165 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7226 (ptp90) REVERT: o 198 ASP cc_start: 0.7639 (t70) cc_final: 0.7179 (OUTLIER) REVERT: t 130 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6736 (mtp85) REVERT: t 301 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5921 (p90) REVERT: m 369 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8319 (mm110) REVERT: v 186 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7442 (tm-30) REVERT: N 67 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8292 (mtm180) REVERT: h 107 LYS cc_start: 0.7627 (mptt) cc_final: 0.7308 (mppt) REVERT: w 450 ILE cc_start: 0.6348 (OUTLIER) cc_final: 0.5573 (tp) REVERT: L 85 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7476 (pp) REVERT: L 104 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.5426 (ppt170) outliers start: 63 outliers final: 32 residues processed: 210 average time/residue: 1.6701 time to fit residues: 403.7618 Evaluate side-chains 198 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 2.598 ------------------------------------------------------------------------------- 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 236 GLU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 143 GLN Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain m residue 369 GLN 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 124 ASP 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 w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 165 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 80 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN G 59 GLN K 295 GLN L 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30469 Z= 0.207 Angle : 0.517 9.685 43133 Z= 0.264 Chirality : 0.037 0.202 5175 Planarity : 0.004 0.046 3851 Dihedral : 20.871 177.710 9422 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.56 % Rotamer: Outliers : 2.52 % Allowed : 14.10 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2357 helix: 1.39 (0.16), residues: 1141 sheet: 0.26 (0.32), residues: 243 loop : -0.59 (0.20), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 120 HIS 0.005 0.001 HIS n 83 PHE 0.016 0.001 PHE D 249 TYR 0.014 0.001 TYR G 97 ARG 0.012 0.000 ARG t 49 *********************** 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 215 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 161 time to evaluate : 2.631 Fit side-chains REVERT: D 236 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6945 (pm20) REVERT: D 251 ASN cc_start: 0.7146 (m-40) cc_final: 0.5771 (p0) REVERT: G 171 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8528 (tmtm) REVERT: G 246 MET cc_start: 0.6209 (mtt) cc_final: 0.5736 (tpp) REVERT: K 141 PHE cc_start: 0.7975 (t80) cc_final: 0.7649 (t80) REVERT: K 326 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7213 (pp) REVERT: n 138 MET cc_start: 0.8971 (tpp) cc_final: 0.8692 (tpp) REVERT: n 404 MET cc_start: 0.7170 (mpp) cc_final: 0.6779 (mpp) REVERT: o 165 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6936 (ptp90) REVERT: o 198 ASP cc_start: 0.7638 (t70) cc_final: 0.7190 (OUTLIER) REVERT: t 130 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6711 (mtp85) REVERT: t 170 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: t 301 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5904 (p90) REVERT: m 369 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8199 (mm-40) REVERT: v 186 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: N 67 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8285 (mtm180) REVERT: h 107 LYS cc_start: 0.7633 (mptt) cc_final: 0.7302 (mppt) REVERT: w 450 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5413 (tp) REVERT: L 85 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7457 (pp) REVERT: L 104 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.5364 (ppt170) outliers start: 54 outliers final: 30 residues processed: 200 average time/residue: 1.6471 time to fit residues: 378.4208 Evaluate side-chains 199 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 157 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 236 GLU Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 322 VAL Chi-restraints excluded: chain K residue 326 LEU 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 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 175 VAL Chi-restraints excluded: chain t residue 231 ASP Chi-restraints excluded: chain t residue 301 PHE Chi-restraints excluded: chain m residue 369 GLN 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 124 ASP 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 Z residue 66 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 242 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN G 59 GLN m 356 ASN L 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30469 Z= 0.257 Angle : 0.543 9.585 43133 Z= 0.276 Chirality : 0.038 0.206 5175 Planarity : 0.004 0.048 3851 Dihedral : 20.860 176.444 9422 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.56 % Favored : 96.39 % Rotamer: Outliers : 2.57 % Allowed : 14.43 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2357 helix: 1.34 (0.16), residues: 1140 sheet: 0.25 (0.32), residues: 243 loop : -0.62 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.006 0.001 HIS n 83 PHE 0.015 0.001 PHE D 96 TYR 0.018 0.002 TYR G 97 ARG 0.013 0.000 ARG t 297 *********************** 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 217 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 162 time to evaluate : 2.796 Fit side-chains REVERT: D 236 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7028 (pm20) REVERT: D 251 ASN cc_start: 0.7196 (m-40) cc_final: 0.5755 (OUTLIER) REVERT: G 171 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8515 (tmtm) REVERT: K 141 PHE cc_start: 0.8014 (t80) cc_final: 0.7681 (t80) REVERT: K 326 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7203 (pp) REVERT: n 138 MET cc_start: 0.9021 (tpp) cc_final: 0.8752 (tpp) REVERT: n 404 MET cc_start: 0.7271 (mpp) cc_final: 0.6874 (mpp) REVERT: o 165 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7366 (ptp90) REVERT: o 198 ASP cc_start: 0.7649 (t70) cc_final: 0.7194 (OUTLIER) REVERT: t 130 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6730 (mtp85) REVERT: t 170 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7559 (mt-10) REVERT: t 301 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5937 (p90) REVERT: m 369 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8215 (mm-40) REVERT: v 186 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7431 (tm-30) REVERT: N 67 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8252 (mtm180) REVERT: h 107 LYS cc_start: 0.7648 (mptt) cc_final: 0.7301 (mppt) REVERT: w 450 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5400 (tp) REVERT: w 453 LYS cc_start: 0.5587 (tttp) cc_final: 0.5286 (ttmt) REVERT: L 85 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7465 (pp) REVERT: L 104 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.5376 (ppt170) outliers start: 55 outliers final: 36 residues processed: 202 average time/residue: 1.6290 time to fit residues: 380.0839 Evaluate side-chains 203 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 156 time to evaluate : 2.795 ------------------------------------------------------------------------------- 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 236 GLU Chi-restraints excluded: chain D residue 249 PHE Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 66 SER Chi-restraints excluded: chain G residue 171 LYS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 205 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 288 VAL 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 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 130 ARG Chi-restraints excluded: chain t residue 170 GLU Chi-restraints excluded: chain t residue 175 VAL 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 m residue 369 GLN 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 124 ASP 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 Z residue 66 THR Chi-restraints excluded: chain w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 163 optimal weight: 0.4980 chunk 263 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 275 optimal weight: 9.9990 chunk 253 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 134 optimal weight: 0.0170 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN G 59 GLN K 295 GLN m 356 ASN L 103 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30469 Z= 0.155 Angle : 0.501 9.791 43133 Z= 0.256 Chirality : 0.036 0.222 5175 Planarity : 0.004 0.053 3851 Dihedral : 20.864 179.053 9422 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 2.01 % Allowed : 15.22 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2357 helix: 1.51 (0.16), residues: 1140 sheet: 0.32 (0.32), residues: 237 loop : -0.54 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 120 HIS 0.005 0.001 HIS n 83 PHE 0.015 0.001 PHE D 96 TYR 0.012 0.001 TYR G 97 ARG 0.014 0.000 ARG t 297 ********************** 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 207 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 2.489 Fit side-chains REVERT: D 236 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: D 251 ASN cc_start: 0.7237 (m-40) cc_final: 0.5897 (OUTLIER) REVERT: K 141 PHE cc_start: 0.7940 (t80) cc_final: 0.7622 (t80) REVERT: K 326 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7039 (pp) REVERT: n 138 MET cc_start: 0.8953 (tpp) cc_final: 0.8618 (tpp) REVERT: n 404 MET cc_start: 0.7243 (mpp) cc_final: 0.6900 (mpp) REVERT: o 165 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6931 (ptp90) REVERT: o 198 ASP cc_start: 0.7642 (t70) cc_final: 0.7186 (OUTLIER) REVERT: t 130 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6729 (mtp85) REVERT: t 170 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7462 (mt-10) REVERT: t 301 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.5859 (p90) REVERT: m 369 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8274 (mm110) REVERT: m 406 ASN cc_start: 0.8616 (t0) cc_final: 0.8208 (t160) REVERT: v 186 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: N 67 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8225 (mtm180) REVERT: h 107 LYS cc_start: 0.7642 (mptt) cc_final: 0.7296 (mppt) REVERT: w 450 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5534 (tp) REVERT: L 85 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7449 (pp) REVERT: L 104 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.5352 (ppt170) outliers start: 43 outliers final: 27 residues processed: 194 average time/residue: 1.6345 time to fit residues: 364.4672 Evaluate side-chains 196 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 266 GLN Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain G residue 66 SER 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 288 VAL Chi-restraints excluded: chain K residue 326 LEU Chi-restraints excluded: chain n residue 72 MET Chi-restraints excluded: chain n residue 77 LEU Chi-restraints excluded: chain n residue 132 ILE Chi-restraints excluded: chain n residue 151 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 165 ARG Chi-restraints excluded: chain o residue 173 ILE Chi-restraints excluded: chain t residue 43 GLU Chi-restraints excluded: chain t residue 130 ARG 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 m residue 369 GLN 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 w residue 450 ILE Chi-restraints excluded: chain w residue 477 ARG Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 174 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN G 59 GLN m 356 ASN L 103 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.120378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100563 restraints weight = 43101.882| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.16 r_work: 0.3029 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30469 Z= 0.270 Angle : 0.547 10.051 43133 Z= 0.279 Chirality : 0.038 0.208 5175 Planarity : 0.004 0.049 3851 Dihedral : 20.837 176.545 9422 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.19 % Allowed : 15.13 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2357 helix: 1.39 (0.16), residues: 1139 sheet: 0.30 (0.32), residues: 243 loop : -0.58 (0.20), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 120 HIS 0.007 0.001 HIS n 83 PHE 0.015 0.001 PHE D 96 TYR 0.015 0.002 TYR G 97 ARG 0.014 0.000 ARG t 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7563.21 seconds wall clock time: 137 minutes 8.23 seconds (8228.23 seconds total)