Starting phenix.real_space_refine on Sun Mar 10 23:46:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/03_2024/6z3y_11066.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/03_2024/6z3y_11066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/03_2024/6z3y_11066.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/03_2024/6z3y_11066.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/03_2024/6z3y_11066.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3y_11066/03_2024/6z3y_11066.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 46 5.16 5 C 4137 2.51 5 N 933 2.21 5 O 1015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 45": "NH1" <-> "NH2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 239": "OE1" <-> "OE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B GLU 454": "OE1" <-> "OE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6131 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3069 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 11, 'TRANS': 374} Chain breaks: 5 Chain: "A" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3062 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 10, 'TRANS': 374} Chain breaks: 5 Time building chain proxies: 3.71, per 1000 atoms: 0.61 Number of scatterers: 6131 At special positions: 0 Unit cell: (76.775, 87.15, 106.862, 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 46 16.00 O 1015 8.00 N 933 7.00 C 4137 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 83.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'B' and resid 25 through 44 removed outlier: 4.148A pdb=" N LEU B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 32 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.473A pdb=" N ILE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.664A pdb=" N MET B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE B 129 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.606A pdb=" N PHE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 137 " --> pdb=" O ILE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.593A pdb=" N ALA B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 167 removed outlier: 3.604A pdb=" N PHE B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 188 removed outlier: 3.798A pdb=" N GLY B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 185 " --> pdb=" O MET B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 212 Processing helix chain 'B' and resid 216 through 227 removed outlier: 3.730A pdb=" N HIS B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 256 removed outlier: 4.125A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALA B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 303 removed outlier: 4.235A pdb=" N SER B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 292 " --> pdb=" O MET B 288 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 removed outlier: 3.882A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 307' Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.910A pdb=" N GLU B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.627A pdb=" N HIS B 347 " --> pdb=" O VAL B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 370 removed outlier: 4.041A pdb=" N ARG B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 386 removed outlier: 4.162A pdb=" N VAL B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 384 " --> pdb=" O MET B 380 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.508A pdb=" N ALA B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 405 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA B 409 " --> pdb=" O PHE B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 4.156A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 443 through 450 removed outlier: 4.236A pdb=" N ALA B 447 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 479 removed outlier: 3.859A pdb=" N MET B 461 " --> pdb=" O PRO B 457 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 464 " --> pdb=" O MET B 460 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N PHE B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY B 477 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 4.410A pdb=" N LEU B 487 " --> pdb=" O MET B 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.682A pdb=" N LEU A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.616A pdb=" N TYR A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.664A pdb=" N MET A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE A 129 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.805A pdb=" N ASN A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 158 through 165 Processing helix chain 'A' and resid 165 through 189 removed outlier: 3.923A pdb=" N GLY A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 212 removed outlier: 3.713A pdb=" N CYS A 204 " --> pdb=" O HIS A 200 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 254 removed outlier: 3.618A pdb=" N LEU A 235 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 238 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASP A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 271 through 303 removed outlier: 4.494A pdb=" N VAL A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 331 removed outlier: 3.655A pdb=" N PHE A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 341 Processing helix chain 'A' and resid 342 through 348 removed outlier: 3.971A pdb=" N ALA A 346 " --> pdb=" O GLY A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 4.008A pdb=" N ARG A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 4.477A pdb=" N TYR A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N MET A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 381 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 382 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.532A pdb=" N ILE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 411 removed outlier: 3.893A pdb=" N PHE A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 422 removed outlier: 3.509A pdb=" N LEU A 415 " --> pdb=" O ASN A 411 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.815A pdb=" N MET A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.854A pdb=" N ALA A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 479 removed outlier: 3.737A pdb=" N THR A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 488 352 hydrogen bonds defined for protein. 1050 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: 1.65 Time building geometry restraints manager: 2.40 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: 1786 1.34 - 1.46: 1696 1.46 - 1.58: 2738 1.58 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 6300 Sorted by residual: bond pdb=" N ILE B 133 " pdb=" CA ILE B 133 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.78e+00 bond pdb=" N VAL B 137 " pdb=" CA VAL B 137 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.41e-02 5.03e+03 7.59e+00 bond pdb=" N ASN B 136 " pdb=" CA ASN B 136 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 bond pdb=" N GLU B 132 " pdb=" CA GLU B 132 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.82e+00 bond pdb=" N PHE B 134 " pdb=" CA PHE B 134 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.69e+00 ... (remaining 6295 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 145 106.80 - 113.60: 3359 113.60 - 120.40: 2505 120.40 - 127.20: 2473 127.20 - 133.99: 54 Bond angle restraints: 8536 Sorted by residual: angle pdb=" CA GLU A 239 " pdb=" C GLU A 239 " pdb=" O GLU A 239 " ideal model delta sigma weight residual 120.55 117.31 3.24 1.06e+00 8.90e-01 9.33e+00 angle pdb=" O ILE B 133 " pdb=" C ILE B 133 " pdb=" N PHE B 134 " ideal model delta sigma weight residual 121.87 124.67 -2.80 9.70e-01 1.06e+00 8.31e+00 angle pdb=" CA GLU B 239 " pdb=" C GLU B 239 " pdb=" O GLU B 239 " ideal model delta sigma weight residual 120.42 117.44 2.98 1.06e+00 8.90e-01 7.92e+00 angle pdb=" C ARG A 451 " pdb=" N ASP A 452 " pdb=" CA ASP A 452 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.28e+00 angle pdb=" CA ASN B 136 " pdb=" C ASN B 136 " pdb=" O ASN B 136 " ideal model delta sigma weight residual 120.55 117.92 2.63 1.06e+00 8.90e-01 6.17e+00 ... (remaining 8531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 3335 17.41 - 34.82: 179 34.82 - 52.23: 37 52.23 - 69.64: 3 69.64 - 87.05: 6 Dihedral angle restraints: 3560 sinusoidal: 1337 harmonic: 2223 Sorted by residual: dihedral pdb=" CA PHE B 129 " pdb=" C PHE B 129 " pdb=" N ASP B 130 " pdb=" CA ASP B 130 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA PHE A 129 " pdb=" C PHE A 129 " pdb=" N ASP A 130 " pdb=" CA ASP A 130 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP B 452 " pdb=" C ASP B 452 " pdb=" N THR B 453 " pdb=" CA THR B 453 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 3557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 596 0.031 - 0.062: 307 0.062 - 0.093: 71 0.093 - 0.124: 15 0.124 - 0.155: 2 Chirality restraints: 991 Sorted by residual: chirality pdb=" CA GLU A 239 " pdb=" N GLU A 239 " pdb=" C GLU A 239 " pdb=" CB GLU A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE B 133 " pdb=" N ILE B 133 " pdb=" C ILE B 133 " pdb=" CB ILE B 133 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA ASP A 229 " pdb=" N ASP A 229 " pdb=" C ASP A 229 " pdb=" CB ASP A 229 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 988 not shown) Planarity restraints: 1030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 139 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO B 140 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 140 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 139 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 140 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 140 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 140 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 131 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C PRO B 131 " -0.023 2.00e-02 2.50e+03 pdb=" O PRO B 131 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU B 132 " 0.008 2.00e-02 2.50e+03 ... (remaining 1027 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1681 2.80 - 3.32: 6544 3.32 - 3.85: 9741 3.85 - 4.37: 11818 4.37 - 4.90: 18863 Nonbonded interactions: 48647 Sorted by model distance: nonbonded pdb=" O LEU B 382 " pdb=" OG1 THR B 386 " model vdw 2.269 2.440 nonbonded pdb=" O GLY A 477 " pdb=" OG1 THR A 480 " model vdw 2.281 2.440 nonbonded pdb=" OG SER A 455 " pdb=" OE1 GLN A 459 " model vdw 2.285 2.440 nonbonded pdb=" O TYR A 350 " pdb=" NZ LYS A 358 " model vdw 2.292 2.520 nonbonded pdb=" O TYR B 350 " pdb=" NZ LYS B 358 " model vdw 2.293 2.520 ... (remaining 48642 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 'A' selection = (chain 'B' and (resid 23 through 258 or resid 269 through 489)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.900 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: 3.260 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.150 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6300 Z= 0.133 Angle : 0.523 6.361 8536 Z= 0.292 Chirality : 0.037 0.155 991 Planarity : 0.003 0.054 1030 Dihedral : 11.752 87.051 2122 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.68 % Allowed : 9.65 % Favored : 88.67 % 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: 0.09 (0.32), residues: 747 helix: 0.77 (0.23), residues: 516 sheet: None (None), residues: 0 loop : -1.47 (0.45), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 39 HIS 0.002 0.000 HIS B 390 PHE 0.007 0.001 PHE B 184 TYR 0.009 0.001 TYR A 379 ARG 0.001 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 TYR cc_start: 0.8044 (t80) cc_final: 0.7758 (t80) REVERT: B 458 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7474 (tttt) REVERT: A 33 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8266 (pp) REVERT: A 60 LEU cc_start: 0.8577 (mt) cc_final: 0.8360 (mp) REVERT: A 206 PHE cc_start: 0.8669 (t80) cc_final: 0.8328 (t80) outliers start: 11 outliers final: 1 residues processed: 186 average time/residue: 0.1689 time to fit residues: 41.3291 Evaluate side-chains 129 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 69 optimal weight: 0.1980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6300 Z= 0.238 Angle : 0.780 10.791 8536 Z= 0.383 Chirality : 0.043 0.167 991 Planarity : 0.004 0.052 1030 Dihedral : 4.934 36.343 804 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.60 % Allowed : 15.62 % Favored : 81.78 % 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: -0.44 (0.32), residues: 747 helix: 0.35 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -1.97 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 39 HIS 0.004 0.001 HIS A 145 PHE 0.028 0.002 PHE B 324 TYR 0.023 0.002 TYR A 165 ARG 0.003 0.000 ARG B 441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8645 (tpp) cc_final: 0.8301 (ptt) REVERT: B 368 MET cc_start: 0.8494 (mpp) cc_final: 0.7848 (mpp) REVERT: B 458 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7393 (ttpt) REVERT: A 33 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8408 (pp) REVERT: A 60 LEU cc_start: 0.8602 (mt) cc_final: 0.8358 (mp) REVERT: A 338 VAL cc_start: 0.8463 (t) cc_final: 0.8245 (t) outliers start: 17 outliers final: 10 residues processed: 146 average time/residue: 0.1438 time to fit residues: 28.8631 Evaluate side-chains 131 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 HIS ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6300 Z= 0.205 Angle : 0.688 9.864 8536 Z= 0.344 Chirality : 0.041 0.182 991 Planarity : 0.004 0.054 1030 Dihedral : 5.010 37.710 804 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.76 % Allowed : 19.75 % Favored : 77.49 % 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: -0.57 (0.32), residues: 747 helix: 0.26 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -2.01 (0.50), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 39 HIS 0.003 0.001 HIS A 145 PHE 0.031 0.002 PHE B 470 TYR 0.018 0.001 TYR A 379 ARG 0.002 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8581 (tpp) cc_final: 0.8249 (ptt) REVERT: B 310 MET cc_start: 0.8109 (tpp) cc_final: 0.7785 (tpp) REVERT: B 368 MET cc_start: 0.8412 (mpp) cc_final: 0.8042 (mpp) REVERT: B 435 MET cc_start: 0.7323 (mpp) cc_final: 0.6693 (mtm) REVERT: B 458 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7375 (ttpt) REVERT: A 33 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8383 (pp) REVERT: A 60 LEU cc_start: 0.8586 (mt) cc_final: 0.8334 (mp) REVERT: A 203 ASP cc_start: 0.8053 (m-30) cc_final: 0.7535 (t70) REVERT: A 338 VAL cc_start: 0.8460 (t) cc_final: 0.8232 (t) REVERT: A 363 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7440 (mm-40) REVERT: A 451 ARG cc_start: 0.7680 (mmm160) cc_final: 0.7031 (mmm160) outliers start: 18 outliers final: 12 residues processed: 140 average time/residue: 0.1422 time to fit residues: 27.5541 Evaluate side-chains 131 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6300 Z= 0.244 Angle : 0.700 10.673 8536 Z= 0.351 Chirality : 0.042 0.151 991 Planarity : 0.004 0.057 1030 Dihedral : 5.147 36.463 804 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.98 % Allowed : 20.06 % Favored : 75.96 % 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: -0.79 (0.31), residues: 747 helix: 0.12 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -2.19 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 39 HIS 0.003 0.001 HIS A 145 PHE 0.050 0.002 PHE B 470 TYR 0.022 0.002 TYR B 252 ARG 0.002 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8600 (tpp) cc_final: 0.8161 (ptt) REVERT: B 310 MET cc_start: 0.8074 (tpp) cc_final: 0.7754 (tpp) REVERT: B 368 MET cc_start: 0.8393 (mpp) cc_final: 0.7933 (mpp) REVERT: B 458 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7403 (ttpt) REVERT: A 33 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 374 ASN cc_start: 0.8001 (t0) cc_final: 0.7746 (t0) outliers start: 26 outliers final: 18 residues processed: 144 average time/residue: 0.1420 time to fit residues: 28.5441 Evaluate side-chains 130 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6300 Z= 0.193 Angle : 0.693 12.890 8536 Z= 0.343 Chirality : 0.043 0.245 991 Planarity : 0.004 0.055 1030 Dihedral : 5.083 35.986 804 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 3.98 % Allowed : 21.44 % Favored : 74.58 % 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: -0.72 (0.32), residues: 747 helix: 0.19 (0.22), residues: 557 sheet: None (None), residues: 0 loop : -2.31 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 39 HIS 0.003 0.001 HIS A 145 PHE 0.044 0.001 PHE B 470 TYR 0.023 0.001 TYR B 252 ARG 0.003 0.001 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8585 (tpp) cc_final: 0.8199 (ptt) REVERT: B 310 MET cc_start: 0.7992 (tpp) cc_final: 0.7702 (tpp) REVERT: B 368 MET cc_start: 0.8269 (mpp) cc_final: 0.8063 (mpp) REVERT: B 458 LYS cc_start: 0.7863 (mtmt) cc_final: 0.7380 (ttpt) REVERT: A 33 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8303 (pp) REVERT: A 338 VAL cc_start: 0.8423 (t) cc_final: 0.8163 (t) REVERT: A 365 PHE cc_start: 0.7620 (m-80) cc_final: 0.7247 (m-80) REVERT: A 374 ASN cc_start: 0.8017 (t0) cc_final: 0.7754 (t0) outliers start: 26 outliers final: 17 residues processed: 140 average time/residue: 0.1457 time to fit residues: 28.2681 Evaluate side-chains 130 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6300 Z= 0.184 Angle : 0.697 12.683 8536 Z= 0.343 Chirality : 0.043 0.222 991 Planarity : 0.004 0.059 1030 Dihedral : 5.030 36.279 804 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.59 % Allowed : 21.29 % Favored : 74.12 % 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: -0.68 (0.32), residues: 747 helix: 0.16 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -2.00 (0.51), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 39 HIS 0.002 0.001 HIS A 154 PHE 0.038 0.001 PHE B 470 TYR 0.025 0.001 TYR B 252 ARG 0.005 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8584 (tpp) cc_final: 0.8176 (ptt) REVERT: B 310 MET cc_start: 0.7917 (tpp) cc_final: 0.7689 (tpp) REVERT: B 458 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7329 (ttpt) REVERT: A 33 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8269 (pp) REVERT: A 374 ASN cc_start: 0.8033 (t0) cc_final: 0.7759 (t0) outliers start: 30 outliers final: 15 residues processed: 140 average time/residue: 0.1471 time to fit residues: 28.9539 Evaluate side-chains 128 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 461 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6300 Z= 0.192 Angle : 0.706 10.552 8536 Z= 0.348 Chirality : 0.043 0.236 991 Planarity : 0.004 0.056 1030 Dihedral : 5.030 35.714 804 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 3.37 % Allowed : 22.66 % Favored : 73.97 % 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: -0.56 (0.32), residues: 747 helix: 0.22 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -1.84 (0.51), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 39 HIS 0.003 0.001 HIS A 145 PHE 0.035 0.001 PHE B 470 TYR 0.024 0.001 TYR B 252 ARG 0.006 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8575 (tpp) cc_final: 0.8173 (ptt) REVERT: B 310 MET cc_start: 0.7879 (tpp) cc_final: 0.7676 (tpp) REVERT: B 458 LYS cc_start: 0.7765 (mtmt) cc_final: 0.7306 (ttpt) REVERT: A 33 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8199 (pp) outliers start: 22 outliers final: 13 residues processed: 135 average time/residue: 0.1529 time to fit residues: 28.5397 Evaluate side-chains 125 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6300 Z= 0.201 Angle : 0.758 13.062 8536 Z= 0.369 Chirality : 0.045 0.237 991 Planarity : 0.004 0.053 1030 Dihedral : 5.137 36.079 804 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 3.98 % Allowed : 22.66 % Favored : 73.35 % 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: -0.64 (0.32), residues: 747 helix: 0.20 (0.22), residues: 553 sheet: None (None), residues: 0 loop : -2.03 (0.52), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 39 HIS 0.003 0.001 HIS A 145 PHE 0.046 0.002 PHE B 470 TYR 0.025 0.001 TYR B 252 ARG 0.006 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8597 (tpp) cc_final: 0.8183 (ptt) REVERT: B 458 LYS cc_start: 0.7730 (mtmt) cc_final: 0.7272 (ttpp) REVERT: A 33 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8202 (pp) REVERT: A 459 GLN cc_start: 0.7358 (tm-30) cc_final: 0.6646 (tm-30) outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 0.1504 time to fit residues: 27.4459 Evaluate side-chains 128 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 20 optimal weight: 0.0060 chunk 61 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.0270 chunk 44 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 369 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6300 Z= 0.193 Angle : 0.752 11.235 8536 Z= 0.366 Chirality : 0.045 0.213 991 Planarity : 0.004 0.052 1030 Dihedral : 5.080 36.228 804 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.06 % Allowed : 23.12 % Favored : 73.81 % 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: -0.56 (0.32), residues: 747 helix: 0.24 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -1.97 (0.52), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 39 HIS 0.004 0.001 HIS B 145 PHE 0.045 0.002 PHE B 470 TYR 0.024 0.001 TYR B 252 ARG 0.007 0.000 ARG A 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8514 (tpp) cc_final: 0.8179 (ptt) REVERT: B 458 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7210 (ttpt) REVERT: A 33 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8045 (pp) REVERT: A 377 PHE cc_start: 0.7703 (m-10) cc_final: 0.7328 (m-10) outliers start: 20 outliers final: 16 residues processed: 128 average time/residue: 0.1479 time to fit residues: 26.2667 Evaluate side-chains 124 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.0020 chunk 60 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6300 Z= 0.204 Angle : 0.766 11.115 8536 Z= 0.375 Chirality : 0.047 0.283 991 Planarity : 0.004 0.050 1030 Dihedral : 5.137 36.352 804 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.37 % Allowed : 23.43 % Favored : 73.20 % 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: -0.67 (0.32), residues: 747 helix: 0.20 (0.22), residues: 557 sheet: None (None), residues: 0 loop : -2.22 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 39 HIS 0.010 0.001 HIS B 145 PHE 0.043 0.002 PHE B 470 TYR 0.024 0.001 TYR B 252 ARG 0.007 0.001 ARG A 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1494 Ramachandran restraints generated. 747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 62 MET cc_start: 0.8527 (tpp) cc_final: 0.8182 (ptt) REVERT: B 458 LYS cc_start: 0.7654 (mtmt) cc_final: 0.7261 (ttpt) REVERT: A 33 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8054 (pp) REVERT: A 377 PHE cc_start: 0.7727 (m-10) cc_final: 0.7340 (m-10) REVERT: A 402 LEU cc_start: 0.9070 (pp) cc_final: 0.8637 (mm) outliers start: 22 outliers final: 20 residues processed: 126 average time/residue: 0.1522 time to fit residues: 26.5290 Evaluate side-chains 127 residues out of total 653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 ILE Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 369 ASN Chi-restraints excluded: chain B residue 379 TYR Chi-restraints excluded: chain B residue 475 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 453 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS B 369 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.094598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.086175 restraints weight = 30318.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.087556 restraints weight = 19536.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088494 restraints weight = 14317.380| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6300 Z= 0.187 Angle : 0.755 11.169 8536 Z= 0.369 Chirality : 0.045 0.257 991 Planarity : 0.004 0.050 1030 Dihedral : 5.069 36.797 804 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.91 % Allowed : 23.12 % Favored : 73.97 % 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: -0.61 (0.32), residues: 747 helix: 0.26 (0.22), residues: 557 sheet: None (None), residues: 0 loop : -2.23 (0.50), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 39 HIS 0.008 0.001 HIS B 145 PHE 0.042 0.001 PHE B 470 TYR 0.022 0.001 TYR B 252 ARG 0.008 0.001 ARG A 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1366.49 seconds wall clock time: 25 minutes 39.39 seconds (1539.39 seconds total)