Starting phenix.real_space_refine on Wed Mar 4 00:25:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oy3_20221/03_2026/6oy3_20221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oy3_20221/03_2026/6oy3_20221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2026/6oy3_20221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2026/6oy3_20221.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2026/6oy3_20221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2026/6oy3_20221.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 38 5.16 5 C 6234 2.51 5 N 1594 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 594, 4765 Classifications: {'peptide': 594} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 23, 'TRANS': 570} Chain breaks: 8 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: A Time building chain proxies: 3.37, per 1000 atoms: 0.35 Number of scatterers: 9534 At special positions: 0 Unit cell: (140.301, 78.9192, 100.841, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 38 16.00 O 1664 8.00 N 1594 7.00 C 6234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 276.9 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 64.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 36 through 51 removed outlier: 3.813A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 88 removed outlier: 3.590A pdb=" N ALA B 83 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 removed outlier: 3.699A pdb=" N LEU B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE B 119 " --> pdb=" O ARG B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 163 removed outlier: 3.892A pdb=" N LYS B 157 " --> pdb=" O HIS B 153 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.806A pdb=" N ILE B 174 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 197 removed outlier: 3.515A pdb=" N ARG B 193 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.513A pdb=" N ALA B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA B 209 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 246 removed outlier: 3.690A pdb=" N GLY B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 228 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL B 240 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 289 removed outlier: 3.766A pdb=" N LYS B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 318 removed outlier: 3.815A pdb=" N VAL B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 302 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 307 " --> pdb=" O GLY B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 358 removed outlier: 3.708A pdb=" N LEU B 336 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.775A pdb=" N GLY B 345 " --> pdb=" O PRO B 341 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 347 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 382 removed outlier: 3.524A pdb=" N ILE B 371 " --> pdb=" O ASP B 367 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 392 removed outlier: 3.667A pdb=" N VAL B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 4.464A pdb=" N PHE B 438 " --> pdb=" O SER B 434 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.614A pdb=" N ALA B 450 " --> pdb=" O ILE B 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.588A pdb=" N LYS B 465 " --> pdb=" O GLN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.826A pdb=" N GLN B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 514 removed outlier: 4.523A pdb=" N ASP B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE B 511 " --> pdb=" O MET B 507 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B 512 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR B 513 " --> pdb=" O MET B 509 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 514 " --> pdb=" O GLN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 534 through 546 removed outlier: 4.253A pdb=" N ALA B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA B 544 " --> pdb=" O ALA B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.803A pdb=" N LEU B 568 " --> pdb=" O ALA B 564 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER B 569 " --> pdb=" O LEU B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 583 removed outlier: 4.109A pdb=" N SER B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 581 " --> pdb=" O SER B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 620 removed outlier: 4.779A pdb=" N LEU B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 626 removed outlier: 5.181A pdb=" N LEU B 624 " --> pdb=" O ARG B 621 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 625 " --> pdb=" O PHE B 622 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 626 " --> pdb=" O VAL B 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 626' Processing helix chain 'B' and resid 629 through 648 removed outlier: 3.695A pdb=" N GLN B 633 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 634 " --> pdb=" O PRO B 630 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 647 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 715 removed outlier: 3.550A pdb=" N ILE B 712 " --> pdb=" O GLY B 708 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 51 removed outlier: 3.813A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 88 removed outlier: 3.591A pdb=" N ALA A 83 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 124 removed outlier: 3.699A pdb=" N LEU A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 163 removed outlier: 3.892A pdb=" N LYS A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 182 removed outlier: 3.807A pdb=" N ILE A 174 " --> pdb=" O GLU A 170 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 removed outlier: 3.515A pdb=" N ARG A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 212 removed outlier: 3.513A pdb=" N ALA A 204 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 246 removed outlier: 3.690A pdb=" N GLY A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 228 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TRP A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 289 removed outlier: 3.765A pdb=" N LYS A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 318 removed outlier: 3.815A pdb=" N VAL A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 303 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 307 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 358 removed outlier: 3.708A pdb=" N LEU A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 338 " --> pdb=" O ILE A 334 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Proline residue: A 341 - end of helix removed outlier: 3.775A pdb=" N GLY A 345 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 347 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 382 removed outlier: 3.523A pdb=" N ILE A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 392 removed outlier: 3.667A pdb=" N VAL A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 removed outlier: 4.464A pdb=" N PHE A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.615A pdb=" N ALA A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.587A pdb=" N LYS A 465 " --> pdb=" O GLN A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 493 removed outlier: 3.826A pdb=" N GLN A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 removed outlier: 4.523A pdb=" N ASP A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE A 511 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 534 through 546 removed outlier: 4.253A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.804A pdb=" N LEU A 568 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 4.109A pdb=" N SER A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 581 " --> pdb=" O SER A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 620 removed outlier: 4.779A pdb=" N LEU A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 removed outlier: 5.181A pdb=" N LEU A 624 " --> pdb=" O ARG A 621 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 625 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A 626 " --> pdb=" O VAL A 623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 626' Processing helix chain 'A' and resid 629 through 648 removed outlier: 3.694A pdb=" N GLN A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 634 " --> pdb=" O PRO A 630 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 715 removed outlier: 3.550A pdb=" N ILE A 712 " --> pdb=" O GLY A 708 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 24 removed outlier: 3.666A pdb=" N PHE B 22 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL B 68 " --> pdb=" O PHE B 22 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 69 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 3.666A pdb=" N PHE A 22 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 68 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 69 " --> pdb=" O ALA A 53 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1182 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: 1.19 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 2057 1.45 - 1.57: 5198 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 9774 Sorted by residual: bond pdb=" N VAL A 508 " pdb=" CA VAL A 508 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.22e-02 6.72e+03 9.00e+00 bond pdb=" N VAL B 580 " pdb=" CA VAL B 580 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.87e+00 bond pdb=" N VAL B 508 " pdb=" CA VAL B 508 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.80e+00 bond pdb=" N ILE A 574 " pdb=" CA ILE A 574 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.79e+00 bond pdb=" N VAL A 580 " pdb=" CA VAL A 580 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.72e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12109 1.85 - 3.70: 999 3.70 - 5.55: 112 5.55 - 7.40: 20 7.40 - 9.25: 20 Bond angle restraints: 13260 Sorted by residual: angle pdb=" N VAL B 185 " pdb=" CA VAL B 185 " pdb=" C VAL B 185 " ideal model delta sigma weight residual 112.35 106.99 5.36 1.41e+00 5.03e-01 1.44e+01 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 112.35 107.03 5.32 1.41e+00 5.03e-01 1.42e+01 angle pdb=" N VAL B 508 " pdb=" CA VAL B 508 " pdb=" C VAL B 508 " ideal model delta sigma weight residual 113.39 107.87 5.52 1.47e+00 4.63e-01 1.41e+01 angle pdb=" N VAL A 508 " pdb=" CA VAL A 508 " pdb=" C VAL A 508 " ideal model delta sigma weight residual 113.39 107.87 5.52 1.47e+00 4.63e-01 1.41e+01 angle pdb=" CA VAL B 455 " pdb=" C VAL B 455 " pdb=" N PRO B 456 " ideal model delta sigma weight residual 120.83 123.06 -2.23 6.10e-01 2.69e+00 1.33e+01 ... (remaining 13255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4893 16.16 - 32.33: 603 32.33 - 48.49: 172 48.49 - 64.66: 28 64.66 - 80.82: 10 Dihedral angle restraints: 5706 sinusoidal: 2240 harmonic: 3466 Sorted by residual: dihedral pdb=" CA VAL A 620 " pdb=" C VAL A 620 " pdb=" N ARG A 621 " pdb=" CA ARG A 621 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA VAL B 620 " pdb=" C VAL B 620 " pdb=" N ARG B 621 " pdb=" CA ARG B 621 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU B 85 " pdb=" C LEU B 85 " pdb=" N GLY B 86 " pdb=" CA GLY B 86 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1087 0.061 - 0.122: 310 0.122 - 0.182: 56 0.182 - 0.243: 13 0.243 - 0.304: 6 Chirality restraints: 1472 Sorted by residual: chirality pdb=" CB VAL B 616 " pdb=" CA VAL B 616 " pdb=" CG1 VAL B 616 " pdb=" CG2 VAL B 616 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB VAL A 616 " pdb=" CA VAL A 616 " pdb=" CG1 VAL A 616 " pdb=" CG2 VAL A 616 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CB VAL B 514 " pdb=" CA VAL B 514 " pdb=" CG1 VAL B 514 " pdb=" CG2 VAL B 514 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1469 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 556 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C ASP B 556 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 556 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 557 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 556 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.55e+00 pdb=" C ASP A 556 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP A 556 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 557 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 292 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.94e+00 pdb=" N PRO B 293 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 293 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 293 " -0.040 5.00e-02 4.00e+02 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2855 2.81 - 3.33: 8518 3.33 - 3.85: 14598 3.85 - 4.38: 16221 4.38 - 4.90: 27566 Nonbonded interactions: 69758 Sorted by model distance: nonbonded pdb=" OH TYR A 188 " pdb=" OD2 ASP A 539 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 188 " pdb=" OD2 ASP B 539 " model vdw 2.285 3.040 nonbonded pdb=" OH TYR B 393 " pdb=" OD1 ASN B 429 " model vdw 2.325 3.040 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASN A 429 " model vdw 2.325 3.040 nonbonded pdb=" O SER B 16 " pdb=" OG SER B 16 " model vdw 2.334 3.040 ... (remaining 69753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.009 0.088 9774 Z= 0.457 Angle : 1.102 9.252 13260 Z= 0.671 Chirality : 0.062 0.304 1472 Planarity : 0.007 0.070 1666 Dihedral : 15.731 80.820 3450 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 0.40 % Allowed : 12.83 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.09 (0.17), residues: 1152 helix: -3.96 (0.12), residues: 770 sheet: -3.71 (0.56), residues: 52 loop : -3.60 (0.26), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 193 TYR 0.019 0.002 TYR B 195 PHE 0.027 0.003 PHE A 187 TRP 0.032 0.003 TRP A 163 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00902 ( 9774) covalent geometry : angle 1.10160 (13260) hydrogen bonds : bond 0.28366 ( 396) hydrogen bonds : angle 9.62416 ( 1182) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8414 (tp30) cc_final: 0.8080 (tp30) REVERT: B 282 MET cc_start: 0.8018 (mmm) cc_final: 0.7500 (tpp) REVERT: B 359 ASN cc_start: 0.8326 (t0) cc_final: 0.8013 (t0) REVERT: B 636 ARG cc_start: 0.6735 (ttp-110) cc_final: 0.5309 (ttp-170) REVERT: B 701 MET cc_start: 0.7965 (tmm) cc_final: 0.7746 (tmm) REVERT: A 112 GLU cc_start: 0.8311 (tp30) cc_final: 0.8079 (tp30) REVERT: A 334 ILE cc_start: 0.8384 (tt) cc_final: 0.8151 (tt) REVERT: A 510 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8736 (tm-30) outliers start: 4 outliers final: 2 residues processed: 147 average time/residue: 0.0966 time to fit residues: 19.7379 Evaluate side-chains 100 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 531 ASN B 617 GLN A 103 GLN A 106 GLN A 510 GLN A 531 ASN A 617 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.138550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108745 restraints weight = 13403.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108134 restraints weight = 23352.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109090 restraints weight = 23060.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109505 restraints weight = 14890.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110143 restraints weight = 13559.620| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9774 Z= 0.144 Angle : 0.651 10.480 13260 Z= 0.335 Chirality : 0.041 0.151 1472 Planarity : 0.005 0.048 1666 Dihedral : 5.795 65.414 1275 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 2.20 % Allowed : 15.13 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.52 (0.20), residues: 1152 helix: -2.76 (0.15), residues: 804 sheet: -3.33 (0.60), residues: 54 loop : -2.88 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.020 0.001 TYR B 581 PHE 0.011 0.001 PHE B 187 TRP 0.020 0.002 TRP B 561 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9774) covalent geometry : angle 0.65092 (13260) hydrogen bonds : bond 0.05086 ( 396) hydrogen bonds : angle 4.79607 ( 1182) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8484 (tp30) cc_final: 0.7924 (tp30) REVERT: B 282 MET cc_start: 0.7886 (mmm) cc_final: 0.7450 (tpp) REVERT: B 348 MET cc_start: 0.8374 (ttp) cc_final: 0.8141 (ttp) REVERT: B 359 ASN cc_start: 0.8326 (t0) cc_final: 0.8096 (t0) REVERT: B 531 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8791 (t0) REVERT: B 617 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8853 (tm-30) REVERT: B 636 ARG cc_start: 0.6920 (ttp-110) cc_final: 0.5637 (ttp-170) REVERT: A 106 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.5108 (pp30) REVERT: A 112 GLU cc_start: 0.8310 (tp30) cc_final: 0.7869 (tp30) REVERT: A 263 TRP cc_start: 0.7538 (p90) cc_final: 0.7127 (p90) REVERT: A 288 GLN cc_start: 0.7202 (mt0) cc_final: 0.6907 (mp10) REVERT: A 464 GLN cc_start: 0.7712 (tp40) cc_final: 0.7382 (tp40) REVERT: A 503 ASP cc_start: 0.8781 (m-30) cc_final: 0.8176 (t0) REVERT: A 510 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8762 (tm-30) outliers start: 22 outliers final: 12 residues processed: 144 average time/residue: 0.0866 time to fit residues: 17.8716 Evaluate side-chains 129 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.108691 restraints weight = 13446.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106857 restraints weight = 25375.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.107991 restraints weight = 24483.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108240 restraints weight = 16351.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108569 restraints weight = 16126.925| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9774 Z= 0.177 Angle : 0.639 12.240 13260 Z= 0.321 Chirality : 0.042 0.155 1472 Planarity : 0.004 0.055 1666 Dihedral : 5.726 75.952 1275 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.71 % Allowed : 17.84 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.56 (0.23), residues: 1152 helix: -2.02 (0.17), residues: 810 sheet: -3.28 (0.60), residues: 54 loop : -2.52 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.012 0.001 TYR B 195 PHE 0.010 0.001 PHE B 187 TRP 0.028 0.002 TRP B 263 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 9774) covalent geometry : angle 0.63876 (13260) hydrogen bonds : bond 0.04475 ( 396) hydrogen bonds : angle 4.40289 ( 1182) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8443 (tp30) cc_final: 0.7904 (tp30) REVERT: B 187 PHE cc_start: 0.9264 (OUTLIER) cc_final: 0.8901 (t80) REVERT: B 282 MET cc_start: 0.7924 (mmm) cc_final: 0.7502 (tpp) REVERT: B 359 ASN cc_start: 0.8374 (t0) cc_final: 0.8132 (t0) REVERT: B 617 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8807 (tm-30) REVERT: B 636 ARG cc_start: 0.6935 (ttp-110) cc_final: 0.5637 (ttp-170) REVERT: A 112 GLU cc_start: 0.8281 (tp30) cc_final: 0.7944 (tp30) REVERT: A 187 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8421 (t80) REVERT: A 263 TRP cc_start: 0.7450 (p90) cc_final: 0.7084 (p90) REVERT: A 288 GLN cc_start: 0.7169 (mt0) cc_final: 0.6896 (mp10) REVERT: A 290 LEU cc_start: 0.7717 (tp) cc_final: 0.7488 (tp) REVERT: A 464 GLN cc_start: 0.7792 (tp40) cc_final: 0.7453 (tp40) REVERT: A 503 ASP cc_start: 0.8893 (m-30) cc_final: 0.8207 (t0) REVERT: A 510 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8800 (tm-30) outliers start: 27 outliers final: 16 residues processed: 137 average time/residue: 0.0848 time to fit residues: 16.6880 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 97 optimal weight: 0.0050 chunk 106 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN B 617 GLN A 103 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.136438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110052 restraints weight = 13587.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109854 restraints weight = 26277.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110630 restraints weight = 24508.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110622 restraints weight = 17825.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111062 restraints weight = 16395.747| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9774 Z= 0.158 Angle : 0.611 12.274 13260 Z= 0.303 Chirality : 0.041 0.145 1472 Planarity : 0.004 0.044 1666 Dihedral : 5.666 87.552 1275 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 2.81 % Allowed : 19.44 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.24), residues: 1152 helix: -1.59 (0.18), residues: 800 sheet: -3.26 (0.63), residues: 52 loop : -2.27 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 697 TYR 0.012 0.001 TYR B 195 PHE 0.010 0.001 PHE B 187 TRP 0.028 0.002 TRP A 600 HIS 0.002 0.001 HIS B 611 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9774) covalent geometry : angle 0.61113 (13260) hydrogen bonds : bond 0.03993 ( 396) hydrogen bonds : angle 4.19957 ( 1182) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8447 (tp30) cc_final: 0.7898 (tp30) REVERT: B 282 MET cc_start: 0.7681 (mmm) cc_final: 0.7275 (tpp) REVERT: B 359 ASN cc_start: 0.8334 (t0) cc_final: 0.8115 (t0) REVERT: B 617 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8830 (tm-30) REVERT: B 636 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.5718 (ttp-170) REVERT: A 112 GLU cc_start: 0.8274 (tp30) cc_final: 0.7939 (tp30) REVERT: A 187 PHE cc_start: 0.9242 (OUTLIER) cc_final: 0.8409 (t80) REVERT: A 288 GLN cc_start: 0.7175 (mt0) cc_final: 0.6919 (mp10) REVERT: A 290 LEU cc_start: 0.7731 (tp) cc_final: 0.7483 (tp) REVERT: A 464 GLN cc_start: 0.7861 (tp40) cc_final: 0.7518 (tp40) outliers start: 28 outliers final: 19 residues processed: 135 average time/residue: 0.0899 time to fit residues: 17.3316 Evaluate side-chains 125 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 0.0570 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.138180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110482 restraints weight = 13352.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108885 restraints weight = 23516.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110031 restraints weight = 23017.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110062 restraints weight = 15664.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110340 restraints weight = 15791.954| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9774 Z= 0.118 Angle : 0.575 13.523 13260 Z= 0.282 Chirality : 0.039 0.139 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.339 27.428 1271 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.83 % Rotamer: Outliers : 1.90 % Allowed : 21.74 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.24), residues: 1152 helix: -1.36 (0.18), residues: 806 sheet: -3.24 (0.62), residues: 52 loop : -2.30 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 697 TYR 0.011 0.001 TYR B 195 PHE 0.006 0.001 PHE A 76 TRP 0.028 0.001 TRP B 263 HIS 0.003 0.000 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9774) covalent geometry : angle 0.57472 (13260) hydrogen bonds : bond 0.03593 ( 396) hydrogen bonds : angle 3.98721 ( 1182) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8387 (tp30) cc_final: 0.7867 (tp30) REVERT: B 282 MET cc_start: 0.7705 (mmm) cc_final: 0.7314 (tpp) REVERT: B 359 ASN cc_start: 0.8322 (t0) cc_final: 0.8084 (t0) REVERT: B 636 ARG cc_start: 0.6926 (ttp-110) cc_final: 0.5636 (ttp-170) REVERT: A 112 GLU cc_start: 0.8298 (tp30) cc_final: 0.7991 (tp30) REVERT: A 187 PHE cc_start: 0.9251 (OUTLIER) cc_final: 0.8499 (t80) outliers start: 19 outliers final: 14 residues processed: 122 average time/residue: 0.0851 time to fit residues: 14.9272 Evaluate side-chains 115 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.136778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110422 restraints weight = 13451.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110447 restraints weight = 25879.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.111232 restraints weight = 22602.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111545 restraints weight = 15216.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111898 restraints weight = 15134.713| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9774 Z= 0.152 Angle : 0.608 11.619 13260 Z= 0.297 Chirality : 0.041 0.135 1472 Planarity : 0.004 0.040 1666 Dihedral : 4.251 15.597 1270 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.60 % Favored : 95.23 % Rotamer: Outliers : 3.11 % Allowed : 21.74 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.24), residues: 1152 helix: -1.21 (0.18), residues: 806 sheet: -3.26 (0.61), residues: 52 loop : -2.27 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 697 TYR 0.012 0.001 TYR B 195 PHE 0.021 0.001 PHE B 22 TRP 0.029 0.001 TRP A 600 HIS 0.003 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 9774) covalent geometry : angle 0.60829 (13260) hydrogen bonds : bond 0.03639 ( 396) hydrogen bonds : angle 3.98329 ( 1182) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8427 (tp30) cc_final: 0.7895 (tp30) REVERT: B 282 MET cc_start: 0.7745 (mmm) cc_final: 0.7340 (tpp) REVERT: B 359 ASN cc_start: 0.8327 (t0) cc_final: 0.8089 (t0) REVERT: B 568 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8099 (mm) REVERT: B 636 ARG cc_start: 0.7000 (ttp-110) cc_final: 0.5698 (ttp-170) REVERT: A 112 GLU cc_start: 0.8326 (tp30) cc_final: 0.8063 (tp30) REVERT: A 187 PHE cc_start: 0.9298 (OUTLIER) cc_final: 0.8469 (t80) outliers start: 31 outliers final: 24 residues processed: 134 average time/residue: 0.0808 time to fit residues: 15.7876 Evaluate side-chains 126 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** 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 = 0.3610 r_free = 0.3610 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110665 restraints weight = 13374.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107852 restraints weight = 22869.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109062 restraints weight = 21273.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109068 restraints weight = 16589.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109444 restraints weight = 15314.371| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9774 Z= 0.114 Angle : 0.571 12.017 13260 Z= 0.278 Chirality : 0.039 0.137 1472 Planarity : 0.003 0.039 1666 Dihedral : 4.080 14.925 1270 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.56 % Favored : 96.27 % Rotamer: Outliers : 2.61 % Allowed : 21.74 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.25), residues: 1152 helix: -0.99 (0.19), residues: 804 sheet: -2.51 (0.76), residues: 42 loop : -2.31 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 33 TYR 0.012 0.001 TYR A 195 PHE 0.025 0.001 PHE B 22 TRP 0.024 0.001 TRP A 600 HIS 0.002 0.000 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9774) covalent geometry : angle 0.57105 (13260) hydrogen bonds : bond 0.03303 ( 396) hydrogen bonds : angle 3.80781 ( 1182) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8399 (tp30) cc_final: 0.7836 (tp30) REVERT: B 282 MET cc_start: 0.7751 (mmm) cc_final: 0.7353 (tpp) REVERT: B 359 ASN cc_start: 0.8265 (t0) cc_final: 0.7979 (t0) REVERT: B 437 MET cc_start: 0.8931 (mmm) cc_final: 0.8601 (tpp) REVERT: B 636 ARG cc_start: 0.6966 (ttp-110) cc_final: 0.5649 (ttp-170) REVERT: A 112 GLU cc_start: 0.8307 (tp30) cc_final: 0.8020 (tp30) REVERT: A 187 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8520 (t80) REVERT: A 614 LEU cc_start: 0.8749 (mt) cc_final: 0.8352 (tt) outliers start: 26 outliers final: 20 residues processed: 128 average time/residue: 0.0736 time to fit residues: 13.9850 Evaluate side-chains 124 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 98 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** 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 = 0.3754 r_free = 0.3754 target = 0.153018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127195 restraints weight = 12744.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125129 restraints weight = 20923.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126522 restraints weight = 20584.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126491 restraints weight = 14406.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126831 restraints weight = 13946.926| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9774 Z= 0.176 Angle : 0.643 11.909 13260 Z= 0.310 Chirality : 0.042 0.167 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.190 15.547 1270 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 3.71 % Allowed : 21.64 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.24), residues: 1152 helix: -1.01 (0.18), residues: 810 sheet: -3.11 (0.62), residues: 54 loop : -2.29 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 697 TYR 0.013 0.001 TYR B 195 PHE 0.016 0.001 PHE B 22 TRP 0.037 0.002 TRP B 246 HIS 0.002 0.000 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9774) covalent geometry : angle 0.64272 (13260) hydrogen bonds : bond 0.03575 ( 396) hydrogen bonds : angle 3.90788 ( 1182) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.282 Fit side-chains REVERT: B 112 GLU cc_start: 0.8374 (tp30) cc_final: 0.7862 (tp30) REVERT: B 282 MET cc_start: 0.7836 (mmm) cc_final: 0.7457 (tpp) REVERT: B 359 ASN cc_start: 0.8338 (t0) cc_final: 0.8082 (t0) REVERT: B 437 MET cc_start: 0.8872 (mmm) cc_final: 0.8510 (tpp) REVERT: B 636 ARG cc_start: 0.7038 (ttp-110) cc_final: 0.5758 (ttp-170) REVERT: A 112 GLU cc_start: 0.8297 (tp30) cc_final: 0.8063 (tp30) REVERT: A 187 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8453 (t80) outliers start: 37 outliers final: 32 residues processed: 127 average time/residue: 0.0792 time to fit residues: 14.7939 Evaluate side-chains 129 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 218 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** 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 = 0.3585 r_free = 0.3585 target = 0.136401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109584 restraints weight = 13466.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.104535 restraints weight = 15994.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105099 restraints weight = 21332.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.105815 restraints weight = 15783.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.106231 restraints weight = 13690.377| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9774 Z= 0.168 Angle : 0.644 11.419 13260 Z= 0.312 Chirality : 0.042 0.131 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.193 15.557 1270 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.17 % Favored : 95.66 % Rotamer: Outliers : 3.81 % Allowed : 22.14 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.24), residues: 1152 helix: -0.94 (0.19), residues: 812 sheet: -2.54 (0.72), residues: 44 loop : -2.34 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.013 0.001 TYR A 195 PHE 0.008 0.001 PHE A 76 TRP 0.029 0.002 TRP B 246 HIS 0.002 0.000 HIS B 153 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9774) covalent geometry : angle 0.64429 (13260) hydrogen bonds : bond 0.03577 ( 396) hydrogen bonds : angle 3.91611 ( 1182) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.361 Fit side-chains REVERT: B 112 GLU cc_start: 0.8429 (tp30) cc_final: 0.7872 (tp30) REVERT: B 282 MET cc_start: 0.7754 (mmm) cc_final: 0.7365 (tpp) REVERT: B 359 ASN cc_start: 0.8315 (t0) cc_final: 0.7937 (t0) REVERT: B 437 MET cc_start: 0.8879 (mmm) cc_final: 0.8544 (tpp) REVERT: B 636 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.5658 (ttp-170) REVERT: A 112 GLU cc_start: 0.8337 (tp30) cc_final: 0.8091 (tp30) REVERT: A 187 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.8452 (t80) REVERT: A 263 TRP cc_start: 0.7588 (p90) cc_final: 0.7274 (p90) REVERT: A 614 LEU cc_start: 0.8693 (mt) cc_final: 0.8320 (tt) REVERT: A 711 MET cc_start: 0.8121 (tpp) cc_final: 0.7390 (tpp) outliers start: 38 outliers final: 34 residues processed: 130 average time/residue: 0.0754 time to fit residues: 14.5346 Evaluate side-chains 135 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 218 TYR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 54 optimal weight: 0.0870 chunk 38 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 0.0060 chunk 67 optimal weight: 0.0370 chunk 110 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** 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 = 0.3645 r_free = 0.3645 target = 0.142040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115483 restraints weight = 13038.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114137 restraints weight = 22810.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114653 restraints weight = 22767.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114692 restraints weight = 15827.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.114818 restraints weight = 16533.361| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9774 Z= 0.099 Angle : 0.586 10.785 13260 Z= 0.281 Chirality : 0.038 0.143 1472 Planarity : 0.003 0.039 1666 Dihedral : 3.824 13.487 1270 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.21 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 24.35 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.25), residues: 1152 helix: -0.58 (0.19), residues: 804 sheet: -2.05 (0.76), residues: 40 loop : -2.17 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 697 TYR 0.010 0.001 TYR B 26 PHE 0.012 0.001 PHE B 517 TRP 0.026 0.002 TRP B 246 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9774) covalent geometry : angle 0.58634 (13260) hydrogen bonds : bond 0.02946 ( 396) hydrogen bonds : angle 3.60194 ( 1182) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8169 (tp30) cc_final: 0.7687 (tp30) REVERT: B 282 MET cc_start: 0.7721 (mmm) cc_final: 0.7198 (tpp) REVERT: B 359 ASN cc_start: 0.8250 (t0) cc_final: 0.8016 (t0) REVERT: B 437 MET cc_start: 0.8876 (mmm) cc_final: 0.8641 (tpp) REVERT: B 614 LEU cc_start: 0.8774 (mt) cc_final: 0.8343 (tt) REVERT: B 636 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.5793 (ttp-170) REVERT: A 112 GLU cc_start: 0.8284 (tp30) cc_final: 0.8034 (tp30) REVERT: A 187 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8563 (t80) REVERT: A 614 LEU cc_start: 0.8705 (mt) cc_final: 0.8234 (tt) REVERT: A 711 MET cc_start: 0.7544 (tpp) cc_final: 0.7333 (tpp) outliers start: 15 outliers final: 13 residues processed: 134 average time/residue: 0.0876 time to fit residues: 16.7596 Evaluate side-chains 125 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 0.9980 chunk 80 optimal weight: 0.0030 chunk 48 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** 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 = 0.3635 r_free = 0.3635 target = 0.141160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113153 restraints weight = 13084.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111091 restraints weight = 23269.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112174 restraints weight = 21644.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111936 restraints weight = 17020.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112154 restraints weight = 15619.395| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9774 Z= 0.102 Angle : 0.591 11.781 13260 Z= 0.281 Chirality : 0.039 0.153 1472 Planarity : 0.003 0.039 1666 Dihedral : 3.740 13.121 1270 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.61 % Rotamer: Outliers : 1.20 % Allowed : 25.05 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.25), residues: 1152 helix: -0.47 (0.19), residues: 810 sheet: -1.95 (0.78), residues: 40 loop : -2.12 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 697 TYR 0.014 0.001 TYR A 439 PHE 0.010 0.001 PHE B 517 TRP 0.024 0.001 TRP B 246 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9774) covalent geometry : angle 0.59144 (13260) hydrogen bonds : bond 0.02922 ( 396) hydrogen bonds : angle 3.56684 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1271.88 seconds wall clock time: 22 minutes 39.77 seconds (1359.77 seconds total)