Starting phenix.real_space_refine on Fri Apr 5 22:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/04_2024/6z3z_11067.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/04_2024/6z3z_11067.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/04_2024/6z3z_11067.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/04_2024/6z3z_11067.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/04_2024/6z3z_11067.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z3z_11067/04_2024/6z3z_11067.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4121 2.51 5 N 931 2.21 5 O 1019 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 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "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 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "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 "B TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 203": "OD1" <-> "OD2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 451": "NH1" <-> "NH2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6115 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3061 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 10, 'TRANS': 374} Chain breaks: 5 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3054 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 9, 'TRANS': 374} Chain breaks: 5 Time building chain proxies: 3.90, per 1000 atoms: 0.64 Number of scatterers: 6115 At special positions: 0 Unit cell: (77.8125, 87.15, 102.713, 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 44 16.00 O 1019 8.00 N 931 7.00 C 4121 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 seconds 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 82.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'B' and resid 25 through 44 removed outlier: 3.629A pdb=" N LEU B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.596A pdb=" N VAL B 57 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 66 removed outlier: 3.862A pdb=" N LEU B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 60 through 66' Processing helix chain 'B' and resid 125 through 129 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.674A pdb=" N HIS B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 165 Processing helix chain 'B' and resid 165 through 188 removed outlier: 4.086A pdb=" N GLY B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 178 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 179 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 185 " --> pdb=" O MET B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 256 removed outlier: 4.317A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 253 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 303 removed outlier: 3.622A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.760A pdb=" N PHE B 324 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 327 " --> pdb=" O ALA B 323 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU B 328 " --> pdb=" O PHE B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 341 removed outlier: 3.571A pdb=" N LEU B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 3.589A pdb=" N ALA B 346 " --> pdb=" O GLY B 342 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASN B 351 " --> pdb=" O HIS B 347 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU B 353 " --> pdb=" O THR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 371 removed outlier: 4.270A pdb=" N ARG B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 385 removed outlier: 4.085A pdb=" N VAL B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N MET B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 384 " --> pdb=" O MET B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 410 removed outlier: 3.992A pdb=" N PHE B 405 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 removed outlier: 3.827A pdb=" N GLY B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 431 removed outlier: 3.843A pdb=" N PHE B 431 " --> pdb=" O PRO B 428 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 4.246A pdb=" N MET B 436 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER B 438 " --> pdb=" O MET B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 450 removed outlier: 3.837A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 450 " --> pdb=" O PHE B 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 450' Processing helix chain 'B' and resid 458 through 474 removed outlier: 3.965A pdb=" N SER B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.567A pdb=" N GLY B 478 " --> pdb=" O TRP B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 Processing helix chain 'A' and resid 25 through 44 removed outlier: 3.504A pdb=" N PHE A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 4.449A pdb=" N GLY A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.555A pdb=" N THR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 128' Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.792A pdb=" N ASN A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.537A pdb=" N ILE A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.611A pdb=" N TYR A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.515A pdb=" N ILE A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A 178 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.693A pdb=" N PHE A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 229 through 257 removed outlier: 3.806A pdb=" N GLU A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 241 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 303 removed outlier: 3.930A pdb=" N SER A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.891A pdb=" N THR A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLY A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) removed outlier: 3.786A 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 343 through 348 removed outlier: 3.764A pdb=" N HIS A 347 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 4.543A pdb=" N ARG A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 385 removed outlier: 4.137A pdb=" N TYR A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N MET A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 385 " --> pdb=" O GLY A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.766A pdb=" N ILE A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 408 removed outlier: 3.629A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A 405 " --> pdb=" O PHE A 401 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'A' and resid 432 through 437 removed outlier: 3.830A pdb=" N MET A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 432 through 437' Processing helix chain 'A' and resid 444 through 450 removed outlier: 4.193A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 479 removed outlier: 3.593A pdb=" N LEU A 468 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 removed outlier: 4.182A pdb=" N GLU A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 1026 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: 1.54 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1758 1.34 - 1.46: 1130 1.46 - 1.57: 3318 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 6282 Sorted by residual: bond pdb=" N ARG A 408 " pdb=" CA ARG A 408 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.60e+00 bond pdb=" N ARG B 441 " pdb=" CA ARG B 441 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.32e+00 bond pdb=" N PHE B 129 " pdb=" CA PHE B 129 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.92e+00 bond pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.32e-02 5.74e+03 5.13e+00 bond pdb=" N ASP B 130 " pdb=" CA ASP B 130 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.41e-02 5.03e+03 5.09e+00 ... (remaining 6277 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.37: 127 106.37 - 113.28: 3266 113.28 - 120.18: 2424 120.18 - 127.09: 2639 127.09 - 133.99: 50 Bond angle restraints: 8506 Sorted by residual: angle pdb=" N MET B 127 " pdb=" CA MET B 127 " pdb=" C MET B 127 " ideal model delta sigma weight residual 112.87 108.14 4.73 1.20e+00 6.94e-01 1.56e+01 angle pdb=" C VAL B 228 " pdb=" N ASP B 229 " pdb=" CA ASP B 229 " ideal model delta sigma weight residual 121.80 129.62 -7.82 2.44e+00 1.68e-01 1.03e+01 angle pdb=" CA GLU B 132 " pdb=" C GLU B 132 " pdb=" O GLU B 132 " ideal model delta sigma weight residual 120.90 117.52 3.38 1.07e+00 8.73e-01 9.97e+00 angle pdb=" CA ARG B 441 " pdb=" C ARG B 441 " pdb=" O ARG B 441 " ideal model delta sigma weight residual 120.65 116.93 3.72 1.23e+00 6.61e-01 9.17e+00 angle pdb=" CB ARG B 441 " pdb=" CG ARG B 441 " pdb=" CD ARG B 441 " ideal model delta sigma weight residual 111.30 117.76 -6.46 2.30e+00 1.89e-01 7.88e+00 ... (remaining 8501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3206 17.91 - 35.81: 285 35.81 - 53.72: 43 53.72 - 71.63: 4 71.63 - 89.53: 6 Dihedral angle restraints: 3544 sinusoidal: 1329 harmonic: 2215 Sorted by residual: 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 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CB GLU B 483 " pdb=" CG GLU B 483 " pdb=" CD GLU B 483 " pdb=" OE1 GLU B 483 " ideal model delta sinusoidal sigma weight residual 0.00 -89.53 89.53 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 239 " pdb=" CG GLU B 239 " pdb=" CD GLU B 239 " pdb=" OE1 GLU B 239 " ideal model delta sinusoidal sigma weight residual 0.00 -87.34 87.34 1 3.00e+01 1.11e-03 1.02e+01 ... (remaining 3541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 597 0.030 - 0.059: 292 0.059 - 0.089: 63 0.089 - 0.119: 23 0.119 - 0.148: 6 Chirality restraints: 981 Sorted by residual: chirality pdb=" CA MET B 127 " pdb=" N MET B 127 " pdb=" C MET B 127 " pdb=" CB MET B 127 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA PRO B 131 " pdb=" N PRO B 131 " pdb=" C PRO B 131 " pdb=" CB PRO B 131 " both_signs ideal model delta sigma weight residual False 2.72 2.87 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CB ILE A 450 " pdb=" CA ILE A 450 " pdb=" CG1 ILE A 450 " pdb=" CG2 ILE A 450 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 978 not shown) Planarity restraints: 1032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 308 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO A 309 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 139 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO B 140 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 140 " 0.028 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 TYR A 413 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO A 414 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " -0.021 5.00e-02 4.00e+02 ... (remaining 1029 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 356 2.74 - 3.28: 6872 3.28 - 3.82: 9676 3.82 - 4.36: 11671 4.36 - 4.90: 18847 Nonbonded interactions: 47422 Sorted by model distance: nonbonded pdb=" O LEU A 382 " pdb=" OG1 THR A 386 " model vdw 2.198 2.440 nonbonded pdb=" N GLU B 132 " pdb=" OE1 GLU B 132 " model vdw 2.202 2.520 nonbonded pdb=" O LYS A 42 " pdb=" NH1 ARG A 45 " model vdw 2.257 2.520 nonbonded pdb=" O LEU A 299 " pdb=" OG1 THR A 303 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 455 " pdb=" OE1 GLN A 459 " model vdw 2.283 2.440 ... (remaining 47417 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 488)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.000 Extract box with map and model: 3.160 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.570 Find NCS groups from input model: 0.370 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: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 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 0.051 6282 Z= 0.162 Angle : 0.621 8.408 8506 Z= 0.326 Chirality : 0.037 0.148 981 Planarity : 0.004 0.059 1032 Dihedral : 13.781 89.534 2114 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.31 % Allowed : 0.62 % Favored : 99.08 % 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: -0.26 (0.32), residues: 745 helix: 0.30 (0.23), residues: 529 sheet: None (None), residues: 0 loop : -1.12 (0.45), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 429 HIS 0.003 0.001 HIS A 390 PHE 0.015 0.001 PHE B 377 TYR 0.011 0.001 TYR B 350 ARG 0.013 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 0.706 Fit side-chains REVERT: B 398 LEU cc_start: 0.7378 (pt) cc_final: 0.6945 (tp) REVERT: A 29 PHE cc_start: 0.5911 (m-10) cc_final: 0.5142 (m-10) REVERT: A 41 PHE cc_start: 0.6853 (m-80) cc_final: 0.6631 (m-10) REVERT: A 440 LEU cc_start: 0.7342 (mm) cc_final: 0.6990 (mm) outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.1418 time to fit residues: 35.1195 Evaluate side-chains 136 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6282 Z= 0.213 Angle : 0.687 9.319 8506 Z= 0.349 Chirality : 0.040 0.156 981 Planarity : 0.004 0.054 1032 Dihedral : 4.264 20.043 801 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.08 % Allowed : 12.17 % Favored : 86.75 % 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: -0.13 (0.32), residues: 745 helix: 0.52 (0.22), residues: 567 sheet: None (None), residues: 0 loop : -1.87 (0.49), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 429 HIS 0.004 0.001 HIS A 433 PHE 0.043 0.002 PHE A 470 TYR 0.016 0.001 TYR A 252 ARG 0.004 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 0.729 Fit side-chains REVERT: B 126 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8423 (tttp) REVERT: B 376 ILE cc_start: 0.6829 (mm) cc_final: 0.6136 (mt) REVERT: A 31 LEU cc_start: 0.9377 (mp) cc_final: 0.9162 (mp) REVERT: A 62 MET cc_start: 0.8369 (tpp) cc_final: 0.8129 (tpp) REVERT: A 188 MET cc_start: 0.7536 (mmp) cc_final: 0.6880 (mmt) REVERT: A 434 MET cc_start: 0.7609 (tpt) cc_final: 0.7385 (tpt) REVERT: A 440 LEU cc_start: 0.7560 (mm) cc_final: 0.7248 (mm) outliers start: 7 outliers final: 6 residues processed: 153 average time/residue: 0.1290 time to fit residues: 27.9798 Evaluate side-chains 144 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 GLN ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6282 Z= 0.195 Angle : 0.645 9.689 8506 Z= 0.322 Chirality : 0.039 0.139 981 Planarity : 0.004 0.056 1032 Dihedral : 4.265 17.465 801 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.16 % Allowed : 16.02 % Favored : 81.82 % 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: 0.08 (0.32), residues: 745 helix: 0.63 (0.22), residues: 571 sheet: None (None), residues: 0 loop : -1.70 (0.52), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 429 HIS 0.004 0.001 HIS A 433 PHE 0.044 0.001 PHE A 470 TYR 0.011 0.001 TYR A 379 ARG 0.003 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 156 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: B 25 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8573 (pp) REVERT: B 31 LEU cc_start: 0.7836 (mp) cc_final: 0.7107 (mp) REVERT: B 126 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8358 (tttt) REVERT: B 376 ILE cc_start: 0.6737 (mm) cc_final: 0.6029 (mt) REVERT: A 321 TRP cc_start: 0.8451 (t60) cc_final: 0.8172 (t60) REVERT: A 440 LEU cc_start: 0.7628 (mm) cc_final: 0.7342 (mm) outliers start: 14 outliers final: 7 residues processed: 161 average time/residue: 0.1326 time to fit residues: 30.2422 Evaluate side-chains 146 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.0040 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6282 Z= 0.170 Angle : 0.630 9.113 8506 Z= 0.313 Chirality : 0.038 0.122 981 Planarity : 0.004 0.058 1032 Dihedral : 4.187 16.821 801 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 3.08 % Allowed : 19.11 % Favored : 77.81 % 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: 0.13 (0.32), residues: 745 helix: 0.60 (0.22), residues: 573 sheet: None (None), residues: 0 loop : -1.43 (0.53), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 321 HIS 0.003 0.001 HIS A 390 PHE 0.039 0.001 PHE A 470 TYR 0.016 0.001 TYR A 379 ARG 0.003 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.700 Fit side-chains REVERT: B 25 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8527 (pp) REVERT: B 31 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7646 (mp) REVERT: B 376 ILE cc_start: 0.6740 (mm) cc_final: 0.5911 (mt) REVERT: A 188 MET cc_start: 0.7867 (mmp) cc_final: 0.7023 (mmt) REVERT: A 321 TRP cc_start: 0.8358 (t60) cc_final: 0.7959 (t60) REVERT: A 440 LEU cc_start: 0.7593 (mm) cc_final: 0.7300 (mm) outliers start: 20 outliers final: 10 residues processed: 161 average time/residue: 0.1237 time to fit residues: 28.7326 Evaluate side-chains 160 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 461 MET Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6282 Z= 0.190 Angle : 0.658 10.339 8506 Z= 0.325 Chirality : 0.039 0.125 981 Planarity : 0.004 0.057 1032 Dihedral : 4.270 17.767 801 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.39 % Allowed : 21.88 % Favored : 74.73 % 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: 0.22 (0.32), residues: 745 helix: 0.65 (0.22), residues: 575 sheet: None (None), residues: 0 loop : -1.36 (0.54), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 474 HIS 0.003 0.001 HIS A 390 PHE 0.045 0.001 PHE A 470 TYR 0.017 0.001 TYR A 379 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8725 (pp) REVERT: B 62 MET cc_start: 0.6471 (tmm) cc_final: 0.6178 (tmm) REVERT: B 376 ILE cc_start: 0.6761 (mm) cc_final: 0.5964 (mt) REVERT: B 387 PHE cc_start: 0.8106 (t80) cc_final: 0.7722 (t80) REVERT: A 395 LEU cc_start: 0.7556 (pt) cc_final: 0.7331 (pp) REVERT: A 434 MET cc_start: 0.7020 (tpt) cc_final: 0.6643 (mmm) REVERT: A 440 LEU cc_start: 0.7638 (mm) cc_final: 0.7369 (mm) outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.1318 time to fit residues: 29.5749 Evaluate side-chains 157 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 467 LEU 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: 5.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 0.2980 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6282 Z= 0.185 Angle : 0.655 9.790 8506 Z= 0.324 Chirality : 0.039 0.133 981 Planarity : 0.004 0.057 1032 Dihedral : 4.257 17.292 801 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.08 % Allowed : 22.96 % Favored : 73.96 % 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: 0.20 (0.32), residues: 745 helix: 0.67 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -1.42 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 321 HIS 0.003 0.001 HIS A 390 PHE 0.044 0.001 PHE A 470 TYR 0.015 0.001 TYR A 379 ARG 0.003 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: B 25 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8728 (pp) REVERT: B 62 MET cc_start: 0.6583 (tmm) cc_final: 0.6003 (tmm) REVERT: B 211 MET cc_start: 0.8594 (mmm) cc_final: 0.8293 (mmm) REVERT: B 239 GLU cc_start: 0.8934 (tm-30) cc_final: 0.8685 (tm-30) REVERT: B 376 ILE cc_start: 0.6743 (mm) cc_final: 0.5927 (mt) REVERT: A 321 TRP cc_start: 0.8351 (t60) cc_final: 0.8006 (t60) REVERT: A 434 MET cc_start: 0.6741 (tpt) cc_final: 0.6461 (mmm) REVERT: A 440 LEU cc_start: 0.7695 (mm) cc_final: 0.7379 (mm) outliers start: 20 outliers final: 12 residues processed: 162 average time/residue: 0.1312 time to fit residues: 30.5903 Evaluate side-chains 156 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6282 Z= 0.193 Angle : 0.694 8.690 8506 Z= 0.337 Chirality : 0.040 0.150 981 Planarity : 0.004 0.057 1032 Dihedral : 4.328 17.186 801 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.93 % Allowed : 24.19 % Favored : 72.88 % 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: 0.05 (0.32), residues: 745 helix: 0.56 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -1.53 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 321 HIS 0.004 0.001 HIS A 390 PHE 0.045 0.001 PHE A 470 TYR 0.015 0.001 TYR A 379 ARG 0.002 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: B 62 MET cc_start: 0.6816 (tmm) cc_final: 0.6350 (tmm) REVERT: B 376 ILE cc_start: 0.6713 (mm) cc_final: 0.5996 (mt) REVERT: A 321 TRP cc_start: 0.8358 (t60) cc_final: 0.7986 (t60) REVERT: A 434 MET cc_start: 0.6752 (tpt) cc_final: 0.6510 (mmm) REVERT: A 440 LEU cc_start: 0.7667 (mm) cc_final: 0.7362 (mm) REVERT: A 461 MET cc_start: 0.7129 (ttt) cc_final: 0.6848 (ttt) outliers start: 19 outliers final: 13 residues processed: 158 average time/residue: 0.1369 time to fit residues: 30.8557 Evaluate side-chains 160 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.3980 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6282 Z= 0.192 Angle : 0.727 9.907 8506 Z= 0.352 Chirality : 0.040 0.137 981 Planarity : 0.004 0.057 1032 Dihedral : 4.348 17.430 801 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.93 % Allowed : 24.96 % Favored : 72.11 % 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: 0.18 (0.32), residues: 745 helix: 0.62 (0.22), residues: 574 sheet: None (None), residues: 0 loop : -1.38 (0.53), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 321 HIS 0.003 0.001 HIS A 390 PHE 0.044 0.001 PHE A 470 TYR 0.016 0.001 TYR A 379 ARG 0.003 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: B 62 MET cc_start: 0.6613 (tmm) cc_final: 0.6091 (tmm) REVERT: B 239 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 376 ILE cc_start: 0.6892 (mm) cc_final: 0.6476 (mm) REVERT: B 387 PHE cc_start: 0.8014 (t80) cc_final: 0.7710 (t80) REVERT: A 211 MET cc_start: 0.7465 (mmm) cc_final: 0.7106 (mmm) REVERT: A 434 MET cc_start: 0.6693 (tpt) cc_final: 0.6114 (mmm) REVERT: A 440 LEU cc_start: 0.7824 (mm) cc_final: 0.7516 (mm) outliers start: 19 outliers final: 16 residues processed: 163 average time/residue: 0.1245 time to fit residues: 29.4205 Evaluate side-chains 160 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 378 CYS Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 433 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6282 Z= 0.203 Angle : 0.735 10.716 8506 Z= 0.357 Chirality : 0.041 0.134 981 Planarity : 0.004 0.057 1032 Dihedral : 4.409 17.066 801 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.24 % Allowed : 26.04 % Favored : 70.72 % 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: 0.14 (0.32), residues: 745 helix: 0.58 (0.22), residues: 579 sheet: None (None), residues: 0 loop : -1.36 (0.54), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 321 HIS 0.004 0.001 HIS A 390 PHE 0.048 0.001 PHE A 470 TYR 0.017 0.001 TYR A 379 ARG 0.003 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.718 Fit side-chains revert: symmetry clash REVERT: B 31 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.6836 (mp) REVERT: B 62 MET cc_start: 0.6889 (tmm) cc_final: 0.6514 (tmm) REVERT: B 376 ILE cc_start: 0.6856 (mm) cc_final: 0.6465 (mm) REVERT: B 387 PHE cc_start: 0.7996 (t80) cc_final: 0.7706 (t80) REVERT: A 211 MET cc_start: 0.7508 (mmm) cc_final: 0.7205 (mmm) REVERT: A 321 TRP cc_start: 0.8513 (t60) cc_final: 0.8273 (t60) REVERT: A 328 GLU cc_start: 0.7845 (tp30) cc_final: 0.7623 (tp30) REVERT: A 434 MET cc_start: 0.6314 (tpt) cc_final: 0.5962 (mmm) REVERT: A 437 PHE cc_start: 0.7268 (m-80) cc_final: 0.7000 (m-80) REVERT: A 440 LEU cc_start: 0.7870 (mm) cc_final: 0.7577 (mm) outliers start: 21 outliers final: 16 residues processed: 156 average time/residue: 0.1260 time to fit residues: 28.5725 Evaluate side-chains 161 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6282 Z= 0.205 Angle : 0.761 10.749 8506 Z= 0.365 Chirality : 0.041 0.193 981 Planarity : 0.004 0.057 1032 Dihedral : 4.444 17.422 801 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.93 % Allowed : 26.81 % Favored : 70.26 % 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: 0.14 (0.32), residues: 745 helix: 0.58 (0.22), residues: 575 sheet: None (None), residues: 0 loop : -1.35 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 321 HIS 0.003 0.001 HIS A 390 PHE 0.049 0.001 PHE A 470 TYR 0.017 0.001 TYR A 379 ARG 0.003 0.000 ARG A 441 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1490 Ramachandran restraints generated. 745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 31 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.6798 (mp) REVERT: B 239 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 376 ILE cc_start: 0.6837 (mm) cc_final: 0.6435 (mm) REVERT: B 387 PHE cc_start: 0.7989 (t80) cc_final: 0.7705 (t80) REVERT: B 454 GLU cc_start: 0.7657 (tp30) cc_final: 0.7436 (tp30) REVERT: A 211 MET cc_start: 0.7433 (mmm) cc_final: 0.7064 (mmm) REVERT: A 321 TRP cc_start: 0.8511 (t60) cc_final: 0.8275 (t60) REVERT: A 361 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8245 (t) REVERT: A 363 GLN cc_start: 0.7691 (mt0) cc_final: 0.7455 (mt0) REVERT: A 440 LEU cc_start: 0.7943 (mm) cc_final: 0.7641 (mm) outliers start: 19 outliers final: 15 residues processed: 158 average time/residue: 0.1291 time to fit residues: 29.2080 Evaluate side-chains 165 residues out of total 649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 PHE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 244 ASP Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 310 MET Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 467 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.0040 chunk 40 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.119438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.108670 restraints weight = 18427.030| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 4.13 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6282 Z= 0.203 Angle : 0.777 14.443 8506 Z= 0.372 Chirality : 0.041 0.196 981 Planarity : 0.004 0.056 1032 Dihedral : 4.459 17.387 801 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.08 % Allowed : 27.12 % Favored : 69.80 % 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: 0.12 (0.32), residues: 745 helix: 0.58 (0.22), residues: 576 sheet: None (None), residues: 0 loop : -1.41 (0.53), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 321 HIS 0.003 0.001 HIS A 145 PHE 0.049 0.001 PHE A 470 TYR 0.022 0.001 TYR A 379 ARG 0.003 0.000 ARG A 441 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1513.28 seconds wall clock time: 28 minutes 17.62 seconds (1697.62 seconds total)