Starting phenix.real_space_refine on Fri Sep 11 13:12:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oy3_20221/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.map" model { file = "/net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6oy3_20221/09_2026/6oy3_20221.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.01, per 1000 atoms: 0.32 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: 0.81 Conformation dependent library (CDL) restraints added in 302.6 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: 0.22 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: 1.21 Time building geometry restraints manager: 1.04 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.530 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 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/Z covalent geometry : bond 0.00902 / 0.46 ( 9774) covalent geometry : angle 1.10160 / 0.67 (13260) hydrogen bonds : bond 0.28366 / 19.87 ( 396) hydrogen bonds : angle 9.62416 / 6.57 ( 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 : 0.323 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: 0.7501 (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: 0.8737 (tm-30) outliers start: 4 outliers final: 2 residues processed: 147 average time/residue: 0.0942 time to fit residues: 19.5021 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 : 0.363 ------------------------------------------------------------------------------- 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: 0.1980 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: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN B 531 ASN B 617 GLN A 106 GLN A 510 GLN A 531 ASN A 617 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130308 restraints weight = 12511.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.128867 restraints weight = 20166.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.130266 restraints weight = 18303.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131356 restraints weight = 13896.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.131498 restraints weight = 12454.328| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1849 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= 0.148 Angle : 0.649 11.134 13260 Z= 0.333 Chirality : 0.042 0.144 1472 Planarity : 0.005 0.048 1666 Dihedral : 5.748 65.111 1275 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.83 % Rotamer: Outliers : 2.00 % Allowed : 15.23 % Favored : 82.77 % 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: -4.51 (0.20), residues: 1152 helix: -2.76 (0.15), residues: 806 sheet: -3.30 (0.60), residues: 54 loop : -2.84 (0.30), residues: 292 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 0.010 0.001 PHE B 187 TRP 0.021 0.002 TRP B 561 HIS 0.002 0.001 HIS B 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 9774) covalent geometry : angle 0.64943 / 0.33 (13260) hydrogen bonds : bond 0.05087 / 3.59 ( 396) hydrogen bonds : angle 4.79112 / 3.31 ( 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 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8428 (tp30) cc_final: 0.7900 (tp30) REVERT: B 282 MET cc_start: 0.7869 (mmm) cc_final: 0.7413 (tpp) REVERT: B 348 MET cc_start: 0.8382 (ttp) cc_final: 0.8150 (ttp) REVERT: B 531 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8763 (t0) REVERT: B 617 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8827 (tm-30) REVERT: B 636 ARG cc_start: 0.6905 (ttp-110) cc_final: 0.5643 (ttp-170) REVERT: A 106 GLN cc_start: 0.5800 (OUTLIER) cc_final: 0.5088 (pp30) REVERT: A 112 GLU cc_start: 0.8273 (tp30) cc_final: 0.7848 (tp30) REVERT: A 263 TRP cc_start: 0.7584 (p90) cc_final: 0.7151 (p90) REVERT: A 288 GLN cc_start: 0.7271 (mt0) cc_final: 0.6998 (mp10) REVERT: A 464 GLN cc_start: 0.7656 (tp40) cc_final: 0.7336 (tp40) REVERT: A 503 ASP cc_start: 0.8759 (m-30) cc_final: 0.8091 (t0) REVERT: A 510 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8668 (tm-30) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 0.0832 time to fit residues: 17.2619 Evaluate side-chains 126 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3605 r_free = 0.3605 target = 0.138124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112015 restraints weight = 13349.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110602 restraints weight = 23104.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111713 restraints weight = 23402.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111626 restraints weight = 15174.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111824 restraints weight = 16465.685| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9774 Z= 0.141 Angle : 0.606 11.738 13260 Z= 0.303 Chirality : 0.040 0.142 1472 Planarity : 0.004 0.054 1666 Dihedral : 5.482 73.216 1274 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.99 % Favored : 95.83 % Rotamer: Outliers : 2.51 % Allowed : 17.23 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.55 (0.23), residues: 1152 helix: -2.01 (0.17), residues: 816 sheet: -3.14 (0.61), residues: 54 loop : -2.54 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 249 TYR 0.011 0.001 TYR A 234 PHE 0.015 0.001 PHE B 22 TRP 0.023 0.001 TRP B 263 HIS 0.002 0.000 HIS B 611 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9774) covalent geometry : angle 0.60615 / 0.30 (13260) hydrogen bonds : bond 0.04280 / 3.03 ( 396) hydrogen bonds : angle 4.28957 / 2.97 ( 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 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8354 (tp30) cc_final: 0.7855 (tp30) REVERT: B 187 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8827 (t80) REVERT: B 282 MET cc_start: 0.7878 (mmm) cc_final: 0.7471 (tpp) REVERT: B 359 ASN cc_start: 0.8305 (t0) cc_final: 0.8103 (t0) REVERT: B 617 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8660 (tp40) REVERT: B 636 ARG cc_start: 0.6909 (ttp-110) cc_final: 0.5640 (ttp-170) REVERT: A 112 GLU cc_start: 0.8195 (tp30) cc_final: 0.7821 (tp30) REVERT: A 187 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.8390 (t80) REVERT: A 263 TRP cc_start: 0.7439 (p90) cc_final: 0.7083 (p90) REVERT: A 288 GLN cc_start: 0.7163 (mt0) cc_final: 0.6947 (mp10) REVERT: A 464 GLN cc_start: 0.7736 (tp40) cc_final: 0.7408 (tp40) REVERT: A 503 ASP cc_start: 0.8781 (m-30) cc_final: 0.8146 (t0) REVERT: A 510 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8716 (tm-30) outliers start: 25 outliers final: 14 residues processed: 142 average time/residue: 0.0924 time to fit residues: 18.8545 Evaluate side-chains 129 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 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 394 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 154 SER 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 441 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 62 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 0.0040 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 108 optimal weight: 0.0070 chunk 64 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 531 ASN B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110348 restraints weight = 13441.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108218 restraints weight = 23744.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109406 restraints weight = 21611.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109273 restraints weight = 15953.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109498 restraints weight = 17086.709| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9774 Z= 0.143 Angle : 0.598 12.351 13260 Z= 0.295 Chirality : 0.040 0.135 1472 Planarity : 0.004 0.042 1666 Dihedral : 5.350 81.425 1273 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.51 % Favored : 95.31 % Rotamer: Outliers : 2.81 % Allowed : 19.54 % Favored : 77.66 % 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: -2.94 (0.24), residues: 1152 helix: -1.56 (0.18), residues: 810 sheet: -3.16 (0.62), residues: 54 loop : -2.24 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 697 TYR 0.012 0.001 TYR B 195 PHE 0.016 0.001 PHE B 22 TRP 0.026 0.002 TRP B 263 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 9774) covalent geometry : angle 0.59834 / 0.29 (13260) hydrogen bonds : bond 0.03874 / 2.75 ( 396) hydrogen bonds : angle 4.11011 / 2.84 ( 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 140 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8422 (tp30) cc_final: 0.7871 (tp30) REVERT: B 282 MET cc_start: 0.7673 (mmm) cc_final: 0.7272 (tpp) REVERT: B 359 ASN cc_start: 0.8291 (t0) cc_final: 0.8052 (t0) REVERT: B 568 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 617 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8824 (tm-30) REVERT: B 636 ARG cc_start: 0.6933 (ttp-110) cc_final: 0.5666 (ttp-170) REVERT: A 112 GLU cc_start: 0.8246 (tp30) cc_final: 0.7924 (tp30) REVERT: A 187 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8436 (t80) REVERT: A 288 GLN cc_start: 0.7110 (mt0) cc_final: 0.6861 (mp10) REVERT: A 464 GLN cc_start: 0.7926 (tp40) cc_final: 0.7568 (tp40) REVERT: A 503 ASP cc_start: 0.8905 (m-30) cc_final: 0.8180 (t0) outliers start: 28 outliers final: 15 residues processed: 135 average time/residue: 0.0889 time to fit residues: 17.5284 Evaluate side-chains 124 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 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 441 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3609 r_free = 0.3609 target = 0.138625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110184 restraints weight = 13322.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107074 restraints weight = 21462.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.108269 restraints weight = 20635.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.108013 restraints weight = 15699.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108170 restraints weight = 18805.952| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9774 Z= 0.123 Angle : 0.572 11.767 13260 Z= 0.281 Chirality : 0.039 0.130 1472 Planarity : 0.004 0.040 1666 Dihedral : 4.217 15.389 1270 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % Rotamer: Outliers : 2.51 % Allowed : 20.84 % Favored : 76.65 % 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: -2.69 (0.24), residues: 1152 helix: -1.36 (0.18), residues: 808 sheet: -3.11 (0.63), residues: 54 loop : -2.21 (0.35), residues: 290 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 0.013 0.001 PHE B 22 TRP 0.027 0.001 TRP A 600 HIS 0.003 0.000 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9774) covalent geometry : angle 0.57197 / 0.28 (13260) hydrogen bonds : bond 0.03588 / 2.54 ( 396) hydrogen bonds : angle 3.96006 / 2.75 ( 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 136 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8386 (tp30) cc_final: 0.7847 (tp30) REVERT: B 282 MET cc_start: 0.7724 (mmm) cc_final: 0.7312 (tpp) REVERT: B 359 ASN cc_start: 0.8285 (t0) cc_final: 0.8036 (t0) REVERT: B 568 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 617 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8453 (tp40) REVERT: B 636 ARG cc_start: 0.6898 (ttp-110) cc_final: 0.5609 (ttp-170) REVERT: A 112 GLU cc_start: 0.8279 (tp30) cc_final: 0.7986 (tp30) REVERT: A 187 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8553 (t80) outliers start: 25 outliers final: 16 residues processed: 132 average time/residue: 0.0973 time to fit residues: 18.2105 Evaluate side-chains 122 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 299 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 154 SER 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 253 SER 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 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: 2.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.0170 chunk 0 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3623 r_free = 0.3623 target = 0.139806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111850 restraints weight = 13229.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110494 restraints weight = 24801.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111368 restraints weight = 23027.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111236 restraints weight = 16413.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111583 restraints weight = 16082.816| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9774 Z= 0.108 Angle : 0.566 10.777 13260 Z= 0.274 Chirality : 0.039 0.122 1472 Planarity : 0.003 0.038 1666 Dihedral : 4.026 15.014 1270 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer: Outliers : 2.30 % Allowed : 21.14 % Favored : 76.55 % 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: -2.38 (0.25), residues: 1152 helix: -1.10 (0.19), residues: 802 sheet: -3.03 (0.63), residues: 54 loop : -2.16 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 697 TYR 0.011 0.001 TYR A 195 PHE 0.011 0.001 PHE B 22 TRP 0.022 0.001 TRP A 600 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 9774) covalent geometry : angle 0.56570 / 0.27 (13260) hydrogen bonds : bond 0.03315 / 2.34 ( 396) hydrogen bonds : angle 3.80852 / 2.64 ( 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 136 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8369 (tp30) cc_final: 0.7791 (tp30) REVERT: B 282 MET cc_start: 0.7724 (mmm) cc_final: 0.7337 (tpp) REVERT: B 359 ASN cc_start: 0.8309 (t0) cc_final: 0.8073 (t0) REVERT: B 568 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8241 (mt) REVERT: B 614 LEU cc_start: 0.8664 (mt) cc_final: 0.8215 (tt) REVERT: B 617 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8814 (tm-30) REVERT: B 636 ARG cc_start: 0.6970 (ttp-110) cc_final: 0.5674 (ttp-170) REVERT: A 112 GLU cc_start: 0.8236 (tp30) cc_final: 0.7960 (tp30) REVERT: A 187 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8529 (t80) REVERT: A 614 LEU cc_start: 0.8778 (mt) cc_final: 0.8324 (tt) outliers start: 23 outliers final: 19 residues processed: 130 average time/residue: 0.0897 time to fit residues: 17.0036 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 PHE 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 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 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 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 380 MET 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 579 ILE 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: 0.2980 chunk 25 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 18 optimal weight: 0.0070 chunk 115 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3633 r_free = 0.3633 target = 0.140617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.112908 restraints weight = 13249.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111546 restraints weight = 23548.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112617 restraints weight = 22425.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112521 restraints weight = 15245.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112590 restraints weight = 17354.634| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2950 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= 0.104 Angle : 0.577 11.992 13260 Z= 0.276 Chirality : 0.039 0.158 1472 Planarity : 0.003 0.037 1666 Dihedral : 3.913 14.552 1270 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.39 % Favored : 96.44 % Rotamer: Outliers : 2.71 % Allowed : 21.34 % Favored : 75.95 % 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: -2.07 (0.25), residues: 1152 helix: -0.88 (0.19), residues: 802 sheet: -2.33 (0.73), residues: 44 loop : -2.15 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 697 TYR 0.010 0.001 TYR A 195 PHE 0.010 0.001 PHE B 22 TRP 0.032 0.001 TRP B 246 HIS 0.002 0.000 HIS A 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 9774) covalent geometry : angle 0.57655 / 0.28 (13260) hydrogen bonds : bond 0.03120 / 2.20 ( 396) hydrogen bonds : angle 3.68981 / 2.55 ( 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 145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8248 (tp30) cc_final: 0.7705 (tp30) REVERT: B 282 MET cc_start: 0.7732 (mmm) cc_final: 0.7338 (tpp) REVERT: B 359 ASN cc_start: 0.8246 (t0) cc_final: 0.8020 (t0) REVERT: B 568 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8367 (mt) REVERT: B 614 LEU cc_start: 0.8630 (mt) cc_final: 0.8135 (tt) REVERT: B 636 ARG cc_start: 0.6972 (ttp-110) cc_final: 0.5673 (ttp-170) REVERT: A 112 GLU cc_start: 0.8228 (tp30) cc_final: 0.7973 (tp30) REVERT: A 187 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8524 (t80) REVERT: A 614 LEU cc_start: 0.8751 (mt) cc_final: 0.8266 (tt) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.0930 time to fit residues: 18.8156 Evaluate side-chains 132 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 PHE 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 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 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 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 568 LEU 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: 1.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 617 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3563 r_free = 0.3563 target = 0.134421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107513 restraints weight = 13527.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.104838 restraints weight = 22800.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105966 restraints weight = 21560.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.105941 restraints weight = 15452.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106247 restraints weight = 16064.191| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9774 Z= 0.231 Angle : 0.708 13.033 13260 Z= 0.345 Chirality : 0.045 0.151 1472 Planarity : 0.004 0.040 1666 Dihedral : 4.302 16.113 1270 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.18 % Rotamer: Outliers : 2.81 % Allowed : 22.44 % Favored : 74.75 % 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: -2.37 (0.24), residues: 1152 helix: -1.06 (0.18), residues: 810 sheet: -3.04 (0.67), residues: 50 loop : -2.29 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 621 TYR 0.013 0.002 TYR B 195 PHE 0.013 0.002 PHE B 387 TRP 0.020 0.002 TRP B 246 HIS 0.004 0.001 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 ( 9774) covalent geometry : angle 0.70797 / 0.34 (13260) hydrogen bonds : bond 0.03916 / 2.76 ( 396) hydrogen bonds : angle 4.06697 / 2.82 ( 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 136 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 0.421 Fit side-chains REVERT: B 112 GLU cc_start: 0.8471 (tp30) cc_final: 0.7983 (tp30) REVERT: B 282 MET cc_start: 0.7880 (mmm) cc_final: 0.7496 (tpp) REVERT: B 359 ASN cc_start: 0.8386 (t0) cc_final: 0.8094 (t0) REVERT: B 568 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 636 ARG cc_start: 0.7055 (ttp-110) cc_final: 0.5698 (ttp-170) REVERT: A 112 GLU cc_start: 0.8363 (tp30) cc_final: 0.8148 (tp30) REVERT: A 187 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8418 (t80) REVERT: A 290 LEU cc_start: 0.7679 (tp) cc_final: 0.7452 (tp) REVERT: A 711 MET cc_start: 0.7893 (tpp) cc_final: 0.7692 (mmm) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.0886 time to fit residues: 17.1189 Evaluate side-chains 129 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 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 B residue 616 VAL 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 252 SER Chi-restraints excluded: chain A residue 253 SER 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 441 THR 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: 7.9990 chunk 57 optimal weight: 0.7980 chunk 82 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3605 r_free = 0.3605 target = 0.138183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110711 restraints weight = 13217.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109433 restraints weight = 24945.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109994 restraints weight = 24466.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109374 restraints weight = 19413.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110157 restraints weight = 18500.107| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9774 Z= 0.117 Angle : 0.616 11.986 13260 Z= 0.296 Chirality : 0.040 0.141 1472 Planarity : 0.003 0.037 1666 Dihedral : 4.024 14.817 1270 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.12 % Favored : 96.70 % Rotamer: Outliers : 2.10 % Allowed : 23.75 % 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: -2.01 (0.25), residues: 1152 helix: -0.83 (0.19), residues: 816 sheet: -2.53 (0.70), residues: 44 loop : -2.18 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 490 TYR 0.013 0.001 TYR A 439 PHE 0.006 0.001 PHE B 22 TRP 0.021 0.001 TRP A 600 HIS 0.003 0.000 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9774) covalent geometry : angle 0.61553 / 0.30 (13260) hydrogen bonds : bond 0.03361 / 2.38 ( 396) hydrogen bonds : angle 3.79282 / 2.62 ( 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 133 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.245 Fit side-chains REVERT: B 112 GLU cc_start: 0.8403 (tp30) cc_final: 0.7849 (tp30) REVERT: B 282 MET cc_start: 0.7794 (mmm) cc_final: 0.7399 (tpp) REVERT: B 359 ASN cc_start: 0.8285 (t0) cc_final: 0.7986 (t0) REVERT: B 437 MET cc_start: 0.8886 (mmm) cc_final: 0.8649 (tpp) REVERT: B 600 TRP cc_start: 0.7241 (t60) cc_final: 0.6825 (t-100) REVERT: B 636 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.5749 (ttp-170) REVERT: A 112 GLU cc_start: 0.8363 (tp30) cc_final: 0.8139 (tp30) REVERT: A 187 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8587 (t80) REVERT: A 614 LEU cc_start: 0.8576 (mt) cc_final: 0.8245 (tt) REVERT: A 711 MET cc_start: 0.7844 (tpp) cc_final: 0.7627 (mmm) outliers start: 21 outliers final: 19 residues processed: 130 average time/residue: 0.0906 time to fit residues: 17.0792 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 : 0.360 ------------------------------------------------------------------------------- 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 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 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 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 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 54 optimal weight: 0.8980 chunk 38 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 80 optimal weight: 0.0070 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3627 r_free = 0.3627 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113756 restraints weight = 13152.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112120 restraints weight = 25815.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113164 restraints weight = 23937.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114123 restraints weight = 16775.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.114030 restraints weight = 16312.758| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3174 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= 0.109 Angle : 0.611 12.011 13260 Z= 0.292 Chirality : 0.039 0.141 1472 Planarity : 0.003 0.037 1666 Dihedral : 3.864 14.010 1270 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.20 % Allowed : 23.55 % Favored : 74.25 % 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: -1.72 (0.25), residues: 1152 helix: -0.61 (0.19), residues: 808 sheet: -2.18 (0.80), residues: 38 loop : -2.10 (0.34), residues: 306 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 0.014 0.001 PHE B 387 TRP 0.024 0.001 TRP A 600 HIS 0.003 0.000 HIS B 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9774) covalent geometry : angle 0.61141 / 0.29 (13260) hydrogen bonds : bond 0.03131 / 2.21 ( 396) hydrogen bonds : angle 3.66609 / 2.54 ( 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 138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.366 Fit side-chains REVERT: B 112 GLU cc_start: 0.8326 (tp30) cc_final: 0.7807 (tp30) REVERT: B 282 MET cc_start: 0.7676 (mmm) cc_final: 0.7294 (tpp) REVERT: B 359 ASN cc_start: 0.8279 (t0) cc_final: 0.7995 (t0) REVERT: B 614 LEU cc_start: 0.8741 (mt) cc_final: 0.8508 (tp) REVERT: B 636 ARG cc_start: 0.6995 (ttp-110) cc_final: 0.5747 (ttp-170) REVERT: B 711 MET cc_start: 0.7750 (tpp) cc_final: 0.7509 (tpp) REVERT: A 112 GLU cc_start: 0.8283 (tp30) cc_final: 0.8048 (tp30) REVERT: A 187 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8610 (t80) REVERT: A 249 ARG cc_start: 0.8037 (tpt-90) cc_final: 0.7808 (ttt90) REVERT: A 263 TRP cc_start: 0.7598 (p90) cc_final: 0.7361 (p90) REVERT: A 614 LEU cc_start: 0.8767 (mt) cc_final: 0.8323 (tt) outliers start: 22 outliers final: 19 residues processed: 134 average time/residue: 0.0896 time to fit residues: 17.5064 Evaluate side-chains 131 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 382 SER 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 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 394 ILE Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 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: 7.9990 chunk 80 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 111 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3624 r_free = 0.3624 target = 0.140093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113411 restraints weight = 13226.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111811 restraints weight = 25051.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112260 restraints weight = 23166.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112560 restraints weight = 15969.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112639 restraints weight = 16409.072| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3259 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= 0.115 Angle : 0.626 11.568 13260 Z= 0.298 Chirality : 0.040 0.143 1472 Planarity : 0.003 0.038 1666 Dihedral : 3.833 16.289 1270 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.44 % Rotamer: Outliers : 2.30 % Allowed : 23.85 % Favored : 73.85 % 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: -1.52 (0.25), residues: 1152 helix: -0.35 (0.19), residues: 782 sheet: -2.15 (0.79), residues: 38 loop : -2.25 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 697 TYR 0.013 0.001 TYR A 439 PHE 0.031 0.001 PHE B 517 TRP 0.022 0.001 TRP A 600 HIS 0.002 0.000 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 9774) covalent geometry : angle 0.62622 / 0.30 (13260) hydrogen bonds : bond 0.03108 / 2.19 ( 396) hydrogen bonds : angle 3.60216 / 2.49 ( 1182) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1391.32 seconds wall clock time: 24 minutes 50.69 seconds (1490.69 seconds total)