Starting phenix.real_space_refine on Sun Apr 7 18:05:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/04_2024/6sgz_10191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/04_2024/6sgz_10191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/04_2024/6sgz_10191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/04_2024/6sgz_10191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/04_2024/6sgz_10191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sgz_10191/04_2024/6sgz_10191.pdb" } resolution = 3.9 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= 0.004 sd= 0.119 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: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 7171 2.51 5 N 1997 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 20": "OD1" <-> "OD2" Residue "E ARG 23": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E ASP 114": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 375": "NH1" <-> "NH2" Residue "E ARG 406": "NH1" <-> "NH2" Residue "E ASP 455": "OD1" <-> "OD2" Residue "E PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 36": "NH1" <-> "NH2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 107": "NH1" <-> "NH2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H ARG 406": "NH1" <-> "NH2" Residue "J ARG 10": "NH1" <-> "NH2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J GLU 127": "OE1" <-> "OE2" Residue "J GLU 132": "OE1" <-> "OE2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J ARG 148": "NH1" <-> "NH2" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "J ARG 162": "NH1" <-> "NH2" Residue "J ARG 191": "NH1" <-> "NH2" Residue "J ASP 202": "OD1" <-> "OD2" Residue "J ASP 208": "OD1" <-> "OD2" Residue "J TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 291": "OE1" <-> "OE2" Residue "J ASP 324": "OD1" <-> "OD2" Residue "J ARG 369": "NH1" <-> "NH2" Residue "D ARG 4": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11177 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 3120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3120 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 24, 'TRANS': 410} Chain breaks: 2 Chain: "H" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3168 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 27, 'TRANS': 414} Chain breaks: 3 Chain: "I" Number of atoms: 461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 461 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2603 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 26, 'TRANS': 301} Chain breaks: 4 Chain: "D" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1825 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 16, 'TRANS': 224} Chain breaks: 7 Time building chain proxies: 6.18, per 1000 atoms: 0.55 Number of scatterers: 11177 At special positions: 0 Unit cell: (132.938, 116.985, 101.033, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1980 8.00 N 1997 7.00 C 7171 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: 4.54 Conformation dependent library (CDL) restraints added in 2.0 seconds 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 6 sheets defined 58.9% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'E' and resid 34 through 47 removed outlier: 3.660A pdb=" N ILE E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Proline residue: E 40 - end of helix Processing helix chain 'E' and resid 82 through 87 removed outlier: 3.631A pdb=" N GLY E 87 " --> pdb=" O LEU E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 119 Processing helix chain 'E' and resid 127 through 158 removed outlier: 3.748A pdb=" N HIS E 131 " --> pdb=" O TRP E 127 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE E 132 " --> pdb=" O GLY E 128 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA E 133 " --> pdb=" O PRO E 129 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG E 134 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 181 removed outlier: 4.230A pdb=" N GLN E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.522A pdb=" N ALA E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 233 removed outlier: 3.562A pdb=" N ALA E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 264 removed outlier: 3.656A pdb=" N PHE E 244 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 255 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 removed outlier: 4.157A pdb=" N CYS E 273 " --> pdb=" O ASP E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 293 removed outlier: 3.610A pdb=" N TRP E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 296 No H-bonds generated for 'chain 'E' and resid 294 through 296' Processing helix chain 'E' and resid 319 through 350 removed outlier: 3.715A pdb=" N ARG E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER E 346 " --> pdb=" O GLY E 342 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 349 " --> pdb=" O GLY E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 373 removed outlier: 3.819A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 364 " --> pdb=" O TRP E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 378 removed outlier: 4.203A pdb=" N TRP E 377 " --> pdb=" O ARG E 373 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 373 through 378' Processing helix chain 'E' and resid 379 through 404 removed outlier: 4.833A pdb=" N SER E 390 " --> pdb=" O LEU E 386 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 430 Processing helix chain 'E' and resid 440 through 456 removed outlier: 4.309A pdb=" N ALA E 456 " --> pdb=" O THR E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 467 removed outlier: 4.313A pdb=" N VAL E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 37 removed outlier: 3.727A pdb=" N GLU H 37 " --> pdb=" O PRO H 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 34 through 37' Processing helix chain 'H' and resid 38 through 47 Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 115 through 124 removed outlier: 3.533A pdb=" N PHE H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 159 removed outlier: 3.747A pdb=" N ARG H 134 " --> pdb=" O THR H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 179 removed outlier: 4.014A pdb=" N GLN H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 206 removed outlier: 3.652A pdb=" N LEU H 197 " --> pdb=" O ALA H 193 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) Proline residue: H 199 - end of helix Processing helix chain 'H' and resid 215 through 234 removed outlier: 3.609A pdb=" N GLY H 234 " --> pdb=" O ILE H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 264 removed outlier: 3.902A pdb=" N THR H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA H 260 " --> pdb=" O LEU H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 285 removed outlier: 3.526A pdb=" N ILE H 271 " --> pdb=" O SER H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 294 removed outlier: 3.506A pdb=" N ALA H 294 " --> pdb=" O SER H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 345 Proline residue: H 321 - end of helix removed outlier: 4.093A pdb=" N ARG H 325 " --> pdb=" O PRO H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 350 removed outlier: 3.932A pdb=" N VAL H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 373 removed outlier: 3.583A pdb=" N TRP H 360 " --> pdb=" O SER H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 376 No H-bonds generated for 'chain 'H' and resid 374 through 376' Processing helix chain 'H' and resid 379 through 404 removed outlier: 3.714A pdb=" N HIS H 389 " --> pdb=" O TRP H 385 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N SER H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR H 391 " --> pdb=" O LEU H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 429 removed outlier: 3.702A pdb=" N TRP H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 439 Processing helix chain 'H' and resid 440 through 467 removed outlier: 3.885A pdb=" N ASP H 455 " --> pdb=" O ALA H 451 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE H 459 " --> pdb=" O ASP H 455 " (cutoff:3.500A) Proline residue: H 460 - end of helix Processing helix chain 'H' and resid 468 through 471 Processing helix chain 'I' and resid 34 through 55 Processing helix chain 'I' and resid 62 through 90 Processing helix chain 'J' and resid 93 through 130 removed outlier: 3.546A pdb=" N VAL J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 139 removed outlier: 3.775A pdb=" N ALA J 137 " --> pdb=" O GLU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 4.025A pdb=" N LEU J 190 " --> pdb=" O ALA J 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 212 No H-bonds generated for 'chain 'J' and resid 210 through 212' Processing helix chain 'J' and resid 220 through 237 removed outlier: 4.305A pdb=" N ALA J 226 " --> pdb=" O ASP J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 263 Processing helix chain 'J' and resid 285 through 294 Processing helix chain 'J' and resid 295 through 297 No H-bonds generated for 'chain 'J' and resid 295 through 297' Processing helix chain 'J' and resid 386 through 399 removed outlier: 4.080A pdb=" N ARG J 399 " --> pdb=" O ARG J 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 17 removed outlier: 3.571A pdb=" N LEU D 17 " --> pdb=" O VAL D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 Processing helix chain 'D' and resid 49 through 62 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.922A pdb=" N SER D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 163 Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 265 through 270 Processing sheet with id=AA1, first strand: chain 'E' and resid 67 through 71 removed outlier: 8.700A pdb=" N LEU E 94 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA E 13 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 96 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU E 15 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ALA E 98 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 24 through 30 removed outlier: 8.577A pdb=" N LEU H 94 " --> pdb=" O ARG H 11 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA H 13 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU H 96 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU H 15 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ALA H 98 " --> pdb=" O LEU H 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 23 through 24 removed outlier: 3.823A pdb=" N ILE J 24 " --> pdb=" O LYS J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'J' and resid 157 through 165 removed outlier: 7.152A pdb=" N THR J 205 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG J 162 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA J 203 " --> pdb=" O ARG J 162 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP J 164 " --> pdb=" O ARG J 201 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG J 201 " --> pdb=" O ASP J 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 244 through 249 removed outlier: 6.139A pdb=" N GLY J 245 " --> pdb=" O LEU J 315 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL J 317 " --> pdb=" O GLY J 245 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA J 247 " --> pdb=" O VAL J 317 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU J 314 " --> pdb=" O THR J 338 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ILE J 340 " --> pdb=" O LEU J 314 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL J 316 " --> pdb=" O ILE J 340 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ARG J 342 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU J 318 " --> pdb=" O ARG J 342 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU J 360 " --> pdb=" O ARG J 214 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR J 216 " --> pdb=" O LEU J 360 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL J 362 " --> pdb=" O THR J 216 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE J 218 " --> pdb=" O VAL J 362 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 167 through 168 removed outlier: 3.844A pdb=" N LYS D 106 " --> pdb=" O THR D 125 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3727 1.34 - 1.46: 2139 1.46 - 1.58: 5473 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 11389 Sorted by residual: bond pdb=" CA ARG J 357 " pdb=" CB ARG J 357 " ideal model delta sigma weight residual 1.522 1.532 -0.010 8.90e-03 1.26e+04 1.26e+00 bond pdb=" CA VAL H 99 " pdb=" C VAL H 99 " ideal model delta sigma weight residual 1.526 1.535 -0.009 7.90e-03 1.60e+04 1.25e+00 bond pdb=" CB ASP E 378 " pdb=" CG ASP E 378 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.14e+00 bond pdb=" CB ASN E 354 " pdb=" CG ASN E 354 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.10e+00 bond pdb=" CA THR D 103 " pdb=" CB THR D 103 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.61e-02 3.86e+03 1.10e+00 ... (remaining 11384 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.07: 375 106.07 - 113.08: 6635 113.08 - 120.10: 3688 120.10 - 127.11: 4717 127.11 - 134.13: 183 Bond angle restraints: 15598 Sorted by residual: angle pdb=" N GLY J 256 " pdb=" CA GLY J 256 " pdb=" C GLY J 256 " ideal model delta sigma weight residual 115.42 111.22 4.20 1.27e+00 6.20e-01 1.09e+01 angle pdb=" CA TYR D 96 " pdb=" C TYR D 96 " pdb=" N LEU D 97 " ideal model delta sigma weight residual 118.27 123.38 -5.11 1.59e+00 3.96e-01 1.03e+01 angle pdb=" CA LEU D 278 " pdb=" CB LEU D 278 " pdb=" CG LEU D 278 " ideal model delta sigma weight residual 116.30 127.32 -11.02 3.50e+00 8.16e-02 9.91e+00 angle pdb=" N THR J 344 " pdb=" CA THR J 344 " pdb=" C THR J 344 " ideal model delta sigma weight residual 114.04 110.15 3.89 1.24e+00 6.50e-01 9.84e+00 angle pdb=" CA GLY J 256 " pdb=" C GLY J 256 " pdb=" N ASP J 257 " ideal model delta sigma weight residual 118.52 114.71 3.81 1.22e+00 6.72e-01 9.77e+00 ... (remaining 15593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6208 17.86 - 35.72: 497 35.72 - 53.58: 87 53.58 - 71.44: 16 71.44 - 89.30: 6 Dihedral angle restraints: 6814 sinusoidal: 2511 harmonic: 4303 Sorted by residual: dihedral pdb=" CA ALA J 323 " pdb=" C ALA J 323 " pdb=" N ASP J 324 " pdb=" CA ASP J 324 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LEU J 297 " pdb=" C LEU J 297 " pdb=" N ALA J 298 " pdb=" CA ALA J 298 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA VAL E 99 " pdb=" C VAL E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 6811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1248 0.032 - 0.065: 472 0.065 - 0.097: 152 0.097 - 0.129: 58 0.129 - 0.161: 11 Chirality restraints: 1941 Sorted by residual: chirality pdb=" CA TRP J 231 " pdb=" N TRP J 231 " pdb=" C TRP J 231 " pdb=" CB TRP J 231 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA THR D 103 " pdb=" N THR D 103 " pdb=" C THR D 103 " pdb=" CB THR D 103 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CB THR D 103 " pdb=" CA THR D 103 " pdb=" OG1 THR D 103 " pdb=" CG2 THR D 103 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 1938 not shown) Planarity restraints: 1969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 165 " -0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO J 166 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO J 166 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO J 166 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 298 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO E 299 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 299 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 299 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL J 269 " 0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO J 270 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 270 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 270 " 0.026 5.00e-02 4.00e+02 ... (remaining 1966 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1297 2.74 - 3.28: 12184 3.28 - 3.82: 18136 3.82 - 4.36: 20059 4.36 - 4.90: 33731 Nonbonded interactions: 85407 Sorted by model distance: nonbonded pdb=" O VAL H 347 " pdb=" OG SER H 351 " model vdw 2.203 2.440 nonbonded pdb=" O ALA J 233 " pdb=" OG1 THR J 237 " model vdw 2.222 2.440 nonbonded pdb=" O ASN J 348 " pdb=" NH1 ARG J 349 " model vdw 2.228 2.520 nonbonded pdb=" O TRP J 128 " pdb=" NH2 ARG J 144 " model vdw 2.234 2.520 nonbonded pdb=" OD2 ASP J 240 " pdb=" OG SER J 402 " model vdw 2.243 2.440 ... (remaining 85402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'E' and (resid 8 through 16 or resid 21 through 47 or resid 65 through 21 \ 1 or resid 214 through 471)) selection = (chain 'H' and (resid 8 through 299 or resid 315 through 471)) } 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=0.91 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.910 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 30.360 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 0.036 11389 Z= 0.233 Angle : 0.696 11.017 15598 Z= 0.390 Chirality : 0.041 0.161 1941 Planarity : 0.005 0.062 1969 Dihedral : 13.522 89.299 4010 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.32 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.16 (0.18), residues: 1463 helix: -1.82 (0.15), residues: 797 sheet: -3.10 (0.35), residues: 134 loop : -4.05 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 231 HIS 0.004 0.001 HIS J 163 PHE 0.007 0.001 PHE D 226 TYR 0.012 0.001 TYR D 96 ARG 0.004 0.000 ARG J 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 GLU cc_start: 0.8638 (tp30) cc_final: 0.8426 (tp30) REVERT: E 110 GLU cc_start: 0.8405 (pp20) cc_final: 0.8090 (pp20) REVERT: E 216 ASN cc_start: 0.8605 (m-40) cc_final: 0.8404 (m-40) REVERT: E 232 MET cc_start: 0.8452 (ttp) cc_final: 0.8107 (ttt) REVERT: E 288 GLN cc_start: 0.9225 (mp10) cc_final: 0.8462 (mp10) REVERT: E 292 MET cc_start: 0.8723 (mmm) cc_final: 0.8312 (mmm) REVERT: E 391 TYR cc_start: 0.8768 (t80) cc_final: 0.8548 (t80) REVERT: E 407 TYR cc_start: 0.7966 (m-80) cc_final: 0.7576 (m-80) REVERT: E 430 ASN cc_start: 0.7922 (t0) cc_final: 0.7648 (t0) REVERT: E 445 ARG cc_start: 0.8663 (mmp80) cc_final: 0.8427 (tpt-90) REVERT: H 123 ARG cc_start: 0.8636 (mmt180) cc_final: 0.8018 (mmt180) REVERT: I 45 MET cc_start: 0.8739 (mmm) cc_final: 0.8007 (tpp) REVERT: I 58 ARG cc_start: 0.8418 (mtm180) cc_final: 0.7960 (mtt-85) REVERT: I 59 MET cc_start: 0.8950 (mmm) cc_final: 0.8730 (tpp) REVERT: I 62 ASP cc_start: 0.8557 (p0) cc_final: 0.8345 (p0) REVERT: J 168 ASP cc_start: 0.8570 (p0) cc_final: 0.8189 (p0) REVERT: J 376 GLN cc_start: 0.8720 (mp10) cc_final: 0.8425 (mp10) REVERT: D 59 MET cc_start: 0.7481 (mmt) cc_final: 0.7255 (ttt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.2533 time to fit residues: 79.9767 Evaluate side-chains 167 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 8.9990 chunk 112 optimal weight: 0.2980 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN H 331 GLN J 187 HIS ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN D 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11389 Z= 0.303 Angle : 0.710 9.652 15598 Z= 0.353 Chirality : 0.042 0.179 1941 Planarity : 0.005 0.062 1969 Dihedral : 4.897 26.797 1614 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.39 % Favored : 89.54 % Rotamer: Outliers : 2.44 % Allowed : 16.58 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.38 (0.21), residues: 1463 helix: -0.18 (0.18), residues: 807 sheet: -2.55 (0.38), residues: 134 loop : -3.59 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 231 HIS 0.004 0.001 HIS J 239 PHE 0.007 0.001 PHE H 119 TYR 0.022 0.002 TYR D 96 ARG 0.005 0.000 ARG J 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 GLU cc_start: 0.8629 (tp30) cc_final: 0.8417 (tp30) REVERT: E 216 ASN cc_start: 0.8671 (m-40) cc_final: 0.8262 (m-40) REVERT: E 232 MET cc_start: 0.8538 (ttp) cc_final: 0.8204 (ttt) REVERT: E 292 MET cc_start: 0.8672 (mmm) cc_final: 0.8286 (mmm) REVERT: E 391 TYR cc_start: 0.8761 (t80) cc_final: 0.8547 (t80) REVERT: E 407 TYR cc_start: 0.8001 (m-80) cc_final: 0.7736 (m-80) REVERT: E 443 MET cc_start: 0.7619 (mtm) cc_final: 0.7391 (mtm) REVERT: E 445 ARG cc_start: 0.8597 (mmp80) cc_final: 0.8377 (tpt-90) REVERT: H 23 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8159 (ppt90) REVERT: H 123 ARG cc_start: 0.8566 (mmt180) cc_final: 0.8006 (mmt180) REVERT: H 407 TYR cc_start: 0.8398 (m-80) cc_final: 0.7849 (m-80) REVERT: I 45 MET cc_start: 0.8796 (mmm) cc_final: 0.8078 (tpp) REVERT: I 58 ARG cc_start: 0.8502 (mtm180) cc_final: 0.7970 (mtt-85) REVERT: I 59 MET cc_start: 0.8870 (mmm) cc_final: 0.8645 (tpp) REVERT: I 62 ASP cc_start: 0.8542 (p0) cc_final: 0.8145 (p0) REVERT: I 77 ILE cc_start: 0.9164 (mm) cc_final: 0.8905 (tt) REVERT: J 121 GLU cc_start: 0.8339 (tp30) cc_final: 0.7906 (tp30) REVERT: J 158 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9447 (mp) REVERT: J 168 ASP cc_start: 0.8453 (p0) cc_final: 0.8048 (p0) outliers start: 28 outliers final: 19 residues processed: 204 average time/residue: 0.2255 time to fit residues: 65.9014 Evaluate side-chains 182 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 331 GLN Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 222 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 145 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 GLN J 234 GLN ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11389 Z= 0.279 Angle : 0.686 9.660 15598 Z= 0.342 Chirality : 0.042 0.174 1941 Planarity : 0.005 0.061 1969 Dihedral : 4.872 26.560 1614 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.53 % Favored : 89.41 % Rotamer: Outliers : 3.75 % Allowed : 20.59 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.71 (0.22), residues: 1463 helix: 0.42 (0.18), residues: 805 sheet: -2.25 (0.39), residues: 134 loop : -3.37 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 231 HIS 0.003 0.001 HIS J 239 PHE 0.005 0.001 PHE D 226 TYR 0.013 0.002 TYR D 96 ARG 0.003 0.000 ARG J 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 175 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 GLU cc_start: 0.8606 (tp30) cc_final: 0.8388 (tp30) REVERT: E 216 ASN cc_start: 0.8675 (m-40) cc_final: 0.8430 (m-40) REVERT: E 232 MET cc_start: 0.8546 (ttp) cc_final: 0.8207 (ttt) REVERT: E 292 MET cc_start: 0.8659 (mmm) cc_final: 0.8284 (mmm) REVERT: E 387 LEU cc_start: 0.9322 (mt) cc_final: 0.9118 (mp) REVERT: E 391 TYR cc_start: 0.8743 (t80) cc_final: 0.8531 (t80) REVERT: E 407 TYR cc_start: 0.8007 (m-80) cc_final: 0.7756 (m-80) REVERT: E 445 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8349 (ttt180) REVERT: H 23 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8196 (ppt90) REVERT: H 123 ARG cc_start: 0.8493 (mmt180) cc_final: 0.8241 (mmt180) REVERT: H 407 TYR cc_start: 0.8391 (m-80) cc_final: 0.7855 (m-80) REVERT: I 45 MET cc_start: 0.8789 (mmm) cc_final: 0.8070 (tpp) REVERT: I 58 ARG cc_start: 0.8514 (mtm180) cc_final: 0.7994 (mtt-85) REVERT: I 59 MET cc_start: 0.8859 (mmm) cc_final: 0.8629 (tpp) REVERT: I 62 ASP cc_start: 0.8525 (p0) cc_final: 0.8143 (p0) REVERT: I 77 ILE cc_start: 0.9185 (mm) cc_final: 0.8935 (tt) REVERT: J 121 GLU cc_start: 0.8337 (tp30) cc_final: 0.7957 (tp30) REVERT: J 168 ASP cc_start: 0.8357 (p0) cc_final: 0.8105 (p0) REVERT: J 172 LYS cc_start: 0.9396 (tmmt) cc_final: 0.8955 (tmmt) REVERT: J 262 LYS cc_start: 0.8536 (mttm) cc_final: 0.7989 (tttt) outliers start: 43 outliers final: 28 residues processed: 206 average time/residue: 0.2264 time to fit residues: 66.9927 Evaluate side-chains 196 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 128 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 351 GLN ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11389 Z= 0.267 Angle : 0.681 10.510 15598 Z= 0.336 Chirality : 0.041 0.172 1941 Planarity : 0.005 0.059 1969 Dihedral : 4.786 25.790 1614 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.32 % Favored : 89.61 % Rotamer: Outliers : 4.71 % Allowed : 22.25 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.37 (0.22), residues: 1463 helix: 0.63 (0.19), residues: 812 sheet: -2.06 (0.39), residues: 137 loop : -3.18 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 231 HIS 0.003 0.001 HIS E 389 PHE 0.006 0.001 PHE J 155 TYR 0.023 0.002 TYR J 281 ARG 0.003 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 174 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 37 GLU cc_start: 0.8594 (tp30) cc_final: 0.8381 (tp30) REVERT: E 216 ASN cc_start: 0.8692 (m-40) cc_final: 0.7988 (m-40) REVERT: E 232 MET cc_start: 0.8546 (ttp) cc_final: 0.8207 (ttt) REVERT: E 292 MET cc_start: 0.8653 (mmm) cc_final: 0.8248 (mmm) REVERT: E 387 LEU cc_start: 0.9281 (mt) cc_final: 0.9058 (mp) REVERT: E 391 TYR cc_start: 0.8704 (t80) cc_final: 0.8499 (t80) REVERT: E 407 TYR cc_start: 0.8002 (m-80) cc_final: 0.7781 (m-80) REVERT: E 443 MET cc_start: 0.7442 (mtm) cc_final: 0.7047 (ptp) REVERT: E 445 ARG cc_start: 0.8570 (mmp80) cc_final: 0.8340 (ttt180) REVERT: E 462 MET cc_start: 0.7792 (mmm) cc_final: 0.7454 (mmm) REVERT: H 23 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8093 (ppt90) REVERT: H 121 GLU cc_start: 0.8954 (tp30) cc_final: 0.8599 (tm-30) REVERT: H 123 ARG cc_start: 0.8483 (mmt180) cc_final: 0.7969 (mmt180) REVERT: H 407 TYR cc_start: 0.8397 (m-80) cc_final: 0.7829 (m-80) REVERT: H 444 ARG cc_start: 0.8102 (ptp-170) cc_final: 0.6250 (ttt90) REVERT: I 45 MET cc_start: 0.8788 (mmm) cc_final: 0.8027 (tpp) REVERT: I 58 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7999 (mtt-85) REVERT: I 59 MET cc_start: 0.8820 (mmm) cc_final: 0.8601 (tpp) REVERT: I 62 ASP cc_start: 0.8504 (p0) cc_final: 0.8111 (p0) REVERT: J 121 GLU cc_start: 0.8407 (tp30) cc_final: 0.7968 (tp30) REVERT: J 168 ASP cc_start: 0.8322 (p0) cc_final: 0.8064 (p0) REVERT: J 172 LYS cc_start: 0.9395 (tmmt) cc_final: 0.8916 (tmmt) REVERT: J 262 LYS cc_start: 0.8526 (mttm) cc_final: 0.7971 (tttt) outliers start: 54 outliers final: 41 residues processed: 213 average time/residue: 0.2270 time to fit residues: 69.7382 Evaluate side-chains 207 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 36 optimal weight: 0.0010 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 354 ASN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 234 GLN ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11389 Z= 0.324 Angle : 0.707 9.969 15598 Z= 0.352 Chirality : 0.042 0.177 1941 Planarity : 0.005 0.061 1969 Dihedral : 4.866 29.868 1614 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.21 % Favored : 88.72 % Rotamer: Outliers : 5.41 % Allowed : 22.95 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.25 (0.23), residues: 1463 helix: 0.71 (0.19), residues: 812 sheet: -2.00 (0.40), residues: 137 loop : -3.09 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 231 HIS 0.005 0.001 HIS J 266 PHE 0.006 0.001 PHE D 226 TYR 0.011 0.002 TYR D 96 ARG 0.003 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 170 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 37 GLU cc_start: 0.8608 (tp30) cc_final: 0.8405 (tp30) REVERT: E 232 MET cc_start: 0.8548 (ttp) cc_final: 0.8273 (ttt) REVERT: E 292 MET cc_start: 0.8656 (mmm) cc_final: 0.8230 (mmp) REVERT: E 293 TRP cc_start: 0.9328 (OUTLIER) cc_final: 0.9052 (m-90) REVERT: E 387 LEU cc_start: 0.9298 (mt) cc_final: 0.9079 (mp) REVERT: E 391 TYR cc_start: 0.8753 (t80) cc_final: 0.8545 (t80) REVERT: E 407 TYR cc_start: 0.7981 (m-80) cc_final: 0.7767 (m-80) REVERT: E 443 MET cc_start: 0.7485 (mtm) cc_final: 0.6908 (ptp) REVERT: E 445 ARG cc_start: 0.8593 (mmp80) cc_final: 0.8344 (ttt180) REVERT: H 23 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8141 (ppt90) REVERT: H 121 GLU cc_start: 0.8968 (tp30) cc_final: 0.8561 (tm-30) REVERT: H 123 ARG cc_start: 0.8490 (mmt180) cc_final: 0.8256 (mmt180) REVERT: H 361 TYR cc_start: 0.9415 (t80) cc_final: 0.9131 (t80) REVERT: H 407 TYR cc_start: 0.8431 (m-80) cc_final: 0.7893 (m-80) REVERT: I 45 MET cc_start: 0.8776 (mmm) cc_final: 0.8437 (tpp) REVERT: I 58 ARG cc_start: 0.8505 (mtm180) cc_final: 0.8016 (mtt-85) REVERT: I 59 MET cc_start: 0.8842 (mmm) cc_final: 0.8607 (tpp) REVERT: I 62 ASP cc_start: 0.8526 (p0) cc_final: 0.8162 (p0) REVERT: J 121 GLU cc_start: 0.8434 (tp30) cc_final: 0.8035 (tp30) REVERT: J 168 ASP cc_start: 0.8367 (p0) cc_final: 0.8102 (p0) REVERT: J 172 LYS cc_start: 0.9419 (tmmt) cc_final: 0.8934 (tmmt) REVERT: J 262 LYS cc_start: 0.8524 (mttm) cc_final: 0.7941 (tttt) REVERT: J 288 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8120 (tm-30) outliers start: 62 outliers final: 47 residues processed: 217 average time/residue: 0.2156 time to fit residues: 68.0962 Evaluate side-chains 215 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 165 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 339 VAL Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 258 TRP Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 354 ASN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11389 Z= 0.299 Angle : 0.705 9.780 15598 Z= 0.348 Chirality : 0.042 0.183 1941 Planarity : 0.005 0.061 1969 Dihedral : 4.858 29.046 1614 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.87 % Favored : 89.06 % Rotamer: Outliers : 5.24 % Allowed : 24.17 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.15 (0.23), residues: 1463 helix: 0.80 (0.19), residues: 811 sheet: -1.94 (0.41), residues: 137 loop : -3.06 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 231 HIS 0.005 0.001 HIS J 266 PHE 0.006 0.001 PHE D 48 TYR 0.014 0.002 TYR J 281 ARG 0.003 0.000 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 170 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 37 GLU cc_start: 0.8609 (tp30) cc_final: 0.8405 (tp30) REVERT: E 216 ASN cc_start: 0.8735 (m-40) cc_final: 0.7983 (m-40) REVERT: E 232 MET cc_start: 0.8554 (ttp) cc_final: 0.8280 (ttt) REVERT: E 292 MET cc_start: 0.8636 (mmm) cc_final: 0.8208 (mmp) REVERT: E 293 TRP cc_start: 0.9329 (OUTLIER) cc_final: 0.9068 (m-90) REVERT: E 320 LEU cc_start: 0.9347 (tp) cc_final: 0.9067 (tp) REVERT: E 387 LEU cc_start: 0.9293 (mt) cc_final: 0.9069 (mp) REVERT: E 407 TYR cc_start: 0.7977 (m-80) cc_final: 0.7765 (m-80) REVERT: E 443 MET cc_start: 0.7503 (mtm) cc_final: 0.6915 (ptp) REVERT: E 445 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8344 (ttt180) REVERT: H 23 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8186 (ppt90) REVERT: H 121 GLU cc_start: 0.8964 (tp30) cc_final: 0.8553 (tm-30) REVERT: H 123 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8257 (mmt180) REVERT: H 407 TYR cc_start: 0.8434 (m-80) cc_final: 0.7896 (m-80) REVERT: I 45 MET cc_start: 0.8790 (mmm) cc_final: 0.8095 (tpp) REVERT: I 58 ARG cc_start: 0.8489 (mtm180) cc_final: 0.8027 (mtt-85) REVERT: I 59 MET cc_start: 0.8820 (mmm) cc_final: 0.8526 (tpp) REVERT: I 62 ASP cc_start: 0.8507 (p0) cc_final: 0.8131 (p0) REVERT: J 121 GLU cc_start: 0.8490 (tp30) cc_final: 0.8016 (tp30) REVERT: J 127 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8373 (mm-30) REVERT: J 168 ASP cc_start: 0.8351 (p0) cc_final: 0.8090 (p0) REVERT: J 172 LYS cc_start: 0.9428 (tmmt) cc_final: 0.8944 (tmmt) REVERT: J 262 LYS cc_start: 0.8503 (mttm) cc_final: 0.7928 (tttt) REVERT: J 288 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8117 (tm-30) outliers start: 60 outliers final: 49 residues processed: 215 average time/residue: 0.2091 time to fit residues: 65.6963 Evaluate side-chains 220 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 168 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 405 ASP Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 258 TRP Chi-restraints excluded: chain J residue 268 ASP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 371 GLN D 136 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11389 Z= 0.196 Angle : 0.669 9.891 15598 Z= 0.325 Chirality : 0.041 0.187 1941 Planarity : 0.005 0.057 1969 Dihedral : 4.638 26.322 1614 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.77 % Favored : 90.16 % Rotamer: Outliers : 3.49 % Allowed : 26.61 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.90 (0.23), residues: 1463 helix: 0.98 (0.19), residues: 813 sheet: -1.73 (0.42), residues: 137 loop : -2.95 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 231 HIS 0.003 0.001 HIS J 341 PHE 0.010 0.001 PHE D 48 TYR 0.013 0.002 TYR J 281 ARG 0.003 0.000 ARG J 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8461 (ttp) cc_final: 0.8155 (ttt) REVERT: E 292 MET cc_start: 0.8603 (mmm) cc_final: 0.8220 (mmm) REVERT: E 293 TRP cc_start: 0.9329 (OUTLIER) cc_final: 0.9118 (m-90) REVERT: E 320 LEU cc_start: 0.9326 (tp) cc_final: 0.9034 (tp) REVERT: E 387 LEU cc_start: 0.9212 (mt) cc_final: 0.8979 (mp) REVERT: E 391 TYR cc_start: 0.8549 (t80) cc_final: 0.8183 (t80) REVERT: E 407 TYR cc_start: 0.7966 (m-80) cc_final: 0.7693 (m-80) REVERT: E 445 ARG cc_start: 0.8582 (mmp80) cc_final: 0.8374 (ttt180) REVERT: H 23 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8149 (ppt90) REVERT: H 121 GLU cc_start: 0.8944 (tp30) cc_final: 0.8482 (tm-30) REVERT: H 123 ARG cc_start: 0.8461 (mmt180) cc_final: 0.8180 (mmt180) REVERT: H 361 TYR cc_start: 0.9356 (t80) cc_final: 0.9052 (t80) REVERT: H 407 TYR cc_start: 0.8279 (m-80) cc_final: 0.7799 (m-80) REVERT: H 444 ARG cc_start: 0.8103 (ptp-170) cc_final: 0.6233 (tpt90) REVERT: I 45 MET cc_start: 0.8769 (mmm) cc_final: 0.7975 (tpp) REVERT: I 58 ARG cc_start: 0.8366 (mtm180) cc_final: 0.8031 (mtt-85) REVERT: I 59 MET cc_start: 0.8771 (mmm) cc_final: 0.8555 (tpp) REVERT: I 62 ASP cc_start: 0.8423 (p0) cc_final: 0.8143 (p0) REVERT: J 121 GLU cc_start: 0.8475 (tp30) cc_final: 0.7963 (tp30) REVERT: J 172 LYS cc_start: 0.9418 (tmmt) cc_final: 0.8963 (tmmt) REVERT: J 262 LYS cc_start: 0.8490 (mttm) cc_final: 0.7702 (tttt) REVERT: J 291 GLU cc_start: 0.8484 (tp30) cc_final: 0.8219 (tm-30) REVERT: J 397 LEU cc_start: 0.9423 (tp) cc_final: 0.9213 (tp) outliers start: 40 outliers final: 33 residues processed: 229 average time/residue: 0.2300 time to fit residues: 77.6477 Evaluate side-chains 216 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 258 TRP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 129 optimal weight: 0.0020 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 354 ASN ** E 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11389 Z= 0.218 Angle : 0.682 9.383 15598 Z= 0.331 Chirality : 0.041 0.190 1941 Planarity : 0.005 0.058 1969 Dihedral : 4.536 26.024 1614 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.71 % Favored : 90.23 % Rotamer: Outliers : 4.10 % Allowed : 26.96 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.23), residues: 1463 helix: 1.13 (0.19), residues: 807 sheet: -1.37 (0.45), residues: 128 loop : -2.84 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 360 HIS 0.004 0.001 HIS J 266 PHE 0.010 0.001 PHE D 48 TYR 0.017 0.002 TYR D 96 ARG 0.004 0.000 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8458 (ttp) cc_final: 0.8161 (ttt) REVERT: E 292 MET cc_start: 0.8609 (mmm) cc_final: 0.8200 (mmm) REVERT: E 293 TRP cc_start: 0.9333 (OUTLIER) cc_final: 0.9129 (m-90) REVERT: E 320 LEU cc_start: 0.9331 (tp) cc_final: 0.9050 (tp) REVERT: E 387 LEU cc_start: 0.9150 (mt) cc_final: 0.8921 (mp) REVERT: E 391 TYR cc_start: 0.8571 (t80) cc_final: 0.8151 (t80) REVERT: E 407 TYR cc_start: 0.7968 (m-80) cc_final: 0.7662 (m-80) REVERT: E 445 ARG cc_start: 0.8580 (mmp80) cc_final: 0.8362 (ttt-90) REVERT: H 23 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8152 (ppt90) REVERT: H 121 GLU cc_start: 0.8930 (tp30) cc_final: 0.8523 (tm-30) REVERT: H 123 ARG cc_start: 0.8470 (mmt180) cc_final: 0.8005 (mmt180) REVERT: H 407 TYR cc_start: 0.8284 (m-80) cc_final: 0.7781 (m-80) REVERT: H 444 ARG cc_start: 0.8143 (ptp-170) cc_final: 0.6223 (tpt90) REVERT: I 45 MET cc_start: 0.8785 (mmm) cc_final: 0.8125 (tpp) REVERT: I 58 ARG cc_start: 0.8316 (mtm180) cc_final: 0.8034 (mtt-85) REVERT: I 59 MET cc_start: 0.8780 (mmm) cc_final: 0.8506 (tpp) REVERT: I 62 ASP cc_start: 0.8441 (p0) cc_final: 0.8157 (p0) REVERT: J 121 GLU cc_start: 0.8477 (tp30) cc_final: 0.7989 (tp30) REVERT: J 127 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8245 (mm-30) REVERT: J 172 LYS cc_start: 0.9430 (tmmt) cc_final: 0.8995 (tmmt) REVERT: J 262 LYS cc_start: 0.8428 (mttm) cc_final: 0.7635 (tttt) REVERT: J 288 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: J 291 GLU cc_start: 0.8502 (tp30) cc_final: 0.8240 (tm-30) REVERT: D 153 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8681 (ttm170) REVERT: D 170 GLU cc_start: 0.9001 (tp30) cc_final: 0.8556 (mm-30) outliers start: 47 outliers final: 39 residues processed: 225 average time/residue: 0.2094 time to fit residues: 68.8144 Evaluate side-chains 222 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 258 TRP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 288 GLU Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 53 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 0.0050 chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 0.0870 overall best weight: 0.7974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 354 ASN D 131 ASN D 136 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11389 Z= 0.197 Angle : 0.689 9.462 15598 Z= 0.333 Chirality : 0.042 0.229 1941 Planarity : 0.005 0.054 1969 Dihedral : 4.501 24.016 1614 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.50 % Favored : 90.43 % Rotamer: Outliers : 3.84 % Allowed : 27.49 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1463 helix: 1.17 (0.19), residues: 808 sheet: -1.16 (0.46), residues: 128 loop : -2.80 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 360 HIS 0.003 0.001 HIS J 341 PHE 0.010 0.001 PHE I 86 TYR 0.016 0.002 TYR J 352 ARG 0.007 0.000 ARG E 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8497 (ttp) cc_final: 0.8272 (ttt) REVERT: E 292 MET cc_start: 0.8597 (mmm) cc_final: 0.8185 (mmm) REVERT: E 293 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.9100 (m-90) REVERT: E 320 LEU cc_start: 0.9320 (tp) cc_final: 0.9053 (tp) REVERT: E 387 LEU cc_start: 0.9092 (mt) cc_final: 0.8846 (mp) REVERT: E 391 TYR cc_start: 0.8539 (t80) cc_final: 0.8020 (t80) REVERT: E 407 TYR cc_start: 0.7913 (m-80) cc_final: 0.7583 (m-80) REVERT: E 443 MET cc_start: 0.7150 (ptp) cc_final: 0.6641 (pmm) REVERT: H 23 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8081 (ppt90) REVERT: H 121 GLU cc_start: 0.8902 (tp30) cc_final: 0.8440 (tm-30) REVERT: H 123 ARG cc_start: 0.8472 (mmt180) cc_final: 0.8038 (mmt180) REVERT: H 361 TYR cc_start: 0.9296 (t80) cc_final: 0.9034 (t80) REVERT: H 407 TYR cc_start: 0.8229 (m-80) cc_final: 0.7723 (m-80) REVERT: H 444 ARG cc_start: 0.8068 (ptp-170) cc_final: 0.6160 (tpt170) REVERT: I 45 MET cc_start: 0.8775 (mmm) cc_final: 0.8188 (tpp) REVERT: I 58 ARG cc_start: 0.8267 (mtm180) cc_final: 0.8061 (mtt-85) REVERT: I 59 MET cc_start: 0.8730 (mmm) cc_final: 0.8456 (tpp) REVERT: I 62 ASP cc_start: 0.8415 (p0) cc_final: 0.8120 (p0) REVERT: J 121 GLU cc_start: 0.8446 (tp30) cc_final: 0.8000 (tp30) REVERT: J 127 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8214 (mm-30) REVERT: J 172 LYS cc_start: 0.9437 (tmmt) cc_final: 0.9029 (tmmt) REVERT: J 262 LYS cc_start: 0.8355 (mttm) cc_final: 0.7540 (tttt) REVERT: J 291 GLU cc_start: 0.8459 (tp30) cc_final: 0.8209 (tm-30) REVERT: J 385 MET cc_start: 0.8362 (ttp) cc_final: 0.8068 (ttm) REVERT: J 397 LEU cc_start: 0.9383 (tp) cc_final: 0.9155 (tp) REVERT: D 170 GLU cc_start: 0.9058 (tp30) cc_final: 0.8550 (mm-30) outliers start: 44 outliers final: 36 residues processed: 222 average time/residue: 0.2113 time to fit residues: 69.0765 Evaluate side-chains 220 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 182 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 185 VAL Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 258 TRP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 117 optimal weight: 0.0870 chunk 12 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 354 ASN J 341 HIS D 131 ASN D 136 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11389 Z= 0.211 Angle : 0.696 9.314 15598 Z= 0.336 Chirality : 0.042 0.209 1941 Planarity : 0.005 0.056 1969 Dihedral : 4.436 23.344 1614 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.64 % Favored : 90.29 % Rotamer: Outliers : 3.58 % Allowed : 27.84 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1463 helix: 1.22 (0.19), residues: 808 sheet: -1.06 (0.46), residues: 128 loop : -2.76 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 164 HIS 0.005 0.001 HIS H 330 PHE 0.010 0.001 PHE D 48 TYR 0.015 0.001 TYR J 352 ARG 0.006 0.000 ARG E 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2926 Ramachandran restraints generated. 1463 Oldfield, 0 Emsley, 1463 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8532 (ttp) cc_final: 0.8314 (ttt) REVERT: E 292 MET cc_start: 0.8608 (mmm) cc_final: 0.8216 (mmm) REVERT: E 293 TRP cc_start: 0.9306 (OUTLIER) cc_final: 0.9020 (m-90) REVERT: E 320 LEU cc_start: 0.9307 (tp) cc_final: 0.9071 (tp) REVERT: E 361 TYR cc_start: 0.8745 (t80) cc_final: 0.8396 (t80) REVERT: E 387 LEU cc_start: 0.9055 (mt) cc_final: 0.8823 (mp) REVERT: E 391 TYR cc_start: 0.8556 (t80) cc_final: 0.8044 (t80) REVERT: E 407 TYR cc_start: 0.7906 (m-80) cc_final: 0.7585 (m-80) REVERT: E 443 MET cc_start: 0.6787 (ptp) cc_final: 0.6212 (pmm) REVERT: H 23 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.8106 (ppt90) REVERT: H 121 GLU cc_start: 0.8885 (tp30) cc_final: 0.8493 (tm-30) REVERT: H 123 ARG cc_start: 0.8475 (mmt180) cc_final: 0.8044 (mmt180) REVERT: H 361 TYR cc_start: 0.9280 (t80) cc_final: 0.9044 (t80) REVERT: H 407 TYR cc_start: 0.8208 (m-80) cc_final: 0.7715 (m-80) REVERT: H 444 ARG cc_start: 0.8107 (ptp-170) cc_final: 0.6191 (tpt170) REVERT: I 45 MET cc_start: 0.8850 (mmm) cc_final: 0.8196 (tpp) REVERT: I 58 ARG cc_start: 0.8311 (mtm180) cc_final: 0.8101 (mtt-85) REVERT: I 59 MET cc_start: 0.8774 (mmm) cc_final: 0.8491 (tpp) REVERT: I 62 ASP cc_start: 0.8438 (p0) cc_final: 0.8135 (p0) REVERT: J 121 GLU cc_start: 0.8497 (tp30) cc_final: 0.8028 (tp30) REVERT: J 127 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8208 (mm-30) REVERT: J 172 LYS cc_start: 0.9439 (tmmt) cc_final: 0.9042 (tmmt) REVERT: J 262 LYS cc_start: 0.8366 (mttm) cc_final: 0.7552 (tttt) REVERT: J 291 GLU cc_start: 0.8438 (tp30) cc_final: 0.8169 (tm-30) REVERT: D 47 MET cc_start: 0.4186 (mmt) cc_final: 0.3916 (mmt) REVERT: D 149 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8813 (tm-30) REVERT: D 170 GLU cc_start: 0.8992 (tp30) cc_final: 0.8578 (mm-30) outliers start: 41 outliers final: 36 residues processed: 212 average time/residue: 0.1923 time to fit residues: 60.4741 Evaluate side-chains 217 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 179 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 148 THR Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 293 TRP Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 249 VAL Chi-restraints excluded: chain H residue 271 ILE Chi-restraints excluded: chain H residue 315 SER Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 354 ASN Chi-restraints excluded: chain H residue 395 VAL Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 13 THR Chi-restraints excluded: chain J residue 178 ASP Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain J residue 244 LEU Chi-restraints excluded: chain J residue 258 TRP Chi-restraints excluded: chain J residue 269 VAL Chi-restraints excluded: chain J residue 286 THR Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 341 HIS Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 236 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 120 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 43 GLN E 354 ASN ** J 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.083904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.069058 restraints weight = 36215.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.071171 restraints weight = 18100.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.072546 restraints weight = 11318.020| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11389 Z= 0.223 Angle : 0.702 9.563 15598 Z= 0.339 Chirality : 0.042 0.203 1941 Planarity : 0.005 0.056 1969 Dihedral : 4.418 22.654 1614 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.71 % Favored : 90.23 % Rotamer: Outliers : 3.84 % Allowed : 27.49 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.42 (0.23), residues: 1463 helix: 1.28 (0.19), residues: 805 sheet: -0.97 (0.46), residues: 128 loop : -2.66 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 164 HIS 0.007 0.001 HIS H 330 PHE 0.009 0.001 PHE I 86 TYR 0.015 0.001 TYR J 352 ARG 0.006 0.000 ARG E 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.35 seconds wall clock time: 42 minutes 39.20 seconds (2559.20 seconds total)