Starting phenix.real_space_refine on Fri Mar 14 03:25:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oy3_20221/03_2025/6oy3_20221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oy3_20221/03_2025/6oy3_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_20221/03_2025/6oy3_20221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2025/6oy3_20221.map" model { file = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2025/6oy3_20221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oy3_20221/03_2025/6oy3_20221.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9534 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: {'TYR:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" 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: B Time building chain proxies: 8.63, per 1000 atoms: 0.91 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: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.80 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: 2.37 Time building geometry restraints manager: 3.27 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.600 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 9774 Z= 0.579 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.032 0.003 TRP A 163 HIS 0.003 0.001 HIS A 25 PHE 0.027 0.003 PHE A 187 TYR 0.019 0.002 TYR B 195 ARG 0.005 0.001 ARG A 193 *********************** 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 : 0.958 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: 0.2323 time to fit residues: 47.3296 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 : 1.149 ------------------------------------------------------------------------------- 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 99 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 GLN B 531 ASN B 617 GLN A 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 = 0.3786 r_free = 0.3786 target = 0.156215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.129961 restraints weight = 12403.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.129049 restraints weight = 20028.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130307 restraints weight = 19553.558| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1832 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= 0.200 Angle : 0.649 10.736 13260 Z= 0.333 Chirality : 0.041 0.152 1472 Planarity : 0.005 0.048 1666 Dihedral : 5.766 65.295 1275 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer: Outliers : 2.10 % Allowed : 15.43 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.54 (0.20), residues: 1152 helix: -2.78 (0.15), residues: 804 sheet: -3.31 (0.60), residues: 54 loop : -2.88 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 561 HIS 0.002 0.001 HIS B 611 PHE 0.010 0.001 PHE B 187 TYR 0.020 0.001 TYR B 581 ARG 0.003 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8417 (tp30) cc_final: 0.7909 (tp30) REVERT: B 282 MET cc_start: 0.7867 (mmm) cc_final: 0.7439 (tpp) REVERT: B 531 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8756 (t0) REVERT: B 617 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8822 (tm-30) REVERT: B 636 ARG cc_start: 0.6943 (ttp-110) cc_final: 0.5698 (ttp-170) REVERT: A 106 GLN cc_start: 0.5811 (OUTLIER) cc_final: 0.5101 (pp30) REVERT: A 112 GLU cc_start: 0.8265 (tp30) cc_final: 0.7855 (tp30) REVERT: A 263 TRP cc_start: 0.7589 (p90) cc_final: 0.7196 (p90) REVERT: A 288 GLN cc_start: 0.7339 (mt0) cc_final: 0.7105 (mp10) REVERT: A 300 VAL cc_start: 0.9469 (p) cc_final: 0.9256 (t) REVERT: A 464 GLN cc_start: 0.7608 (tp40) cc_final: 0.7294 (tp40) REVERT: A 503 ASP cc_start: 0.8702 (m-30) cc_final: 0.8111 (t0) REVERT: A 510 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8768 (tm-30) outliers start: 21 outliers final: 11 residues processed: 143 average time/residue: 0.2000 time to fit residues: 40.6797 Evaluate side-chains 129 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 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 69 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 5 optimal weight: 0.3980 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 chunk 4 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 GLN ** 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 = 0.3587 r_free = 0.3587 target = 0.136362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109468 restraints weight = 13508.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.108120 restraints weight = 26124.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109171 restraints weight = 25216.261| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9774 Z= 0.287 Angle : 0.659 11.644 13260 Z= 0.331 Chirality : 0.043 0.157 1472 Planarity : 0.004 0.054 1666 Dihedral : 5.711 76.837 1274 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.12 % Favored : 94.70 % Rotamer: Outliers : 2.71 % Allowed : 17.94 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.23), residues: 1152 helix: -2.03 (0.17), residues: 810 sheet: -3.37 (0.62), residues: 52 loop : -2.54 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 263 HIS 0.002 0.001 HIS B 611 PHE 0.011 0.001 PHE B 187 TYR 0.012 0.001 TYR A 234 ARG 0.002 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8474 (tp30) cc_final: 0.7938 (tp30) REVERT: B 282 MET cc_start: 0.7949 (mmm) cc_final: 0.7501 (tpp) REVERT: B 617 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8911 (tm-30) REVERT: B 636 ARG cc_start: 0.6975 (ttp-110) cc_final: 0.5660 (ttp-170) REVERT: A 112 GLU cc_start: 0.8323 (tp30) cc_final: 0.7983 (tp30) REVERT: A 187 PHE cc_start: 0.9217 (OUTLIER) cc_final: 0.8442 (t80) REVERT: A 263 TRP cc_start: 0.7465 (p90) cc_final: 0.7110 (p90) REVERT: A 288 GLN cc_start: 0.7199 (mt0) cc_final: 0.6915 (mp10) REVERT: A 300 VAL cc_start: 0.9486 (p) cc_final: 0.9258 (t) REVERT: A 464 GLN cc_start: 0.7788 (tp40) cc_final: 0.7451 (tp40) REVERT: A 503 ASP cc_start: 0.8855 (m-30) cc_final: 0.8126 (t0) REVERT: A 510 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8770 (tm-30) outliers start: 27 outliers final: 18 residues processed: 137 average time/residue: 0.2016 time to fit residues: 39.6777 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 1.066 ------------------------------------------------------------------------------- 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 394 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 508 VAL 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 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 Chi-restraints excluded: chain A residue 616 VAL Chi-restraints excluded: chain A residue 647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3615 r_free = 0.3615 target = 0.139144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111611 restraints weight = 13242.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109325 restraints weight = 21760.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110487 restraints weight = 21968.585| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.164 Angle : 0.573 12.413 13260 Z= 0.282 Chirality : 0.039 0.139 1472 Planarity : 0.004 0.042 1666 Dihedral : 5.419 86.320 1274 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.53 % Rotamer: Outliers : 1.80 % Allowed : 20.14 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.24), residues: 1152 helix: -1.57 (0.18), residues: 810 sheet: -3.00 (0.66), residues: 56 loop : -2.20 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 600 HIS 0.002 0.000 HIS A 366 PHE 0.006 0.001 PHE A 76 TYR 0.011 0.001 TYR B 26 ARG 0.006 0.000 ARG B 697 *********************** 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 138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8375 (tp30) cc_final: 0.7873 (tp30) REVERT: B 282 MET cc_start: 0.7692 (mmm) cc_final: 0.7267 (tpp) REVERT: B 568 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 636 ARG cc_start: 0.6909 (ttp-110) cc_final: 0.5655 (ttp-170) REVERT: A 112 GLU cc_start: 0.8198 (tp30) cc_final: 0.7880 (tp30) REVERT: A 187 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8528 (t80) REVERT: A 288 GLN cc_start: 0.7147 (mt0) cc_final: 0.6891 (mp10) REVERT: A 300 VAL cc_start: 0.9441 (p) cc_final: 0.9218 (t) REVERT: A 464 GLN cc_start: 0.7895 (tp40) cc_final: 0.7532 (tp40) outliers start: 18 outliers final: 10 residues processed: 134 average time/residue: 0.2189 time to fit residues: 41.2036 Evaluate side-chains 118 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR 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 240 VAL Chi-restraints excluded: chain A residue 244 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 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 66 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.136115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108476 restraints weight = 13348.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.107092 restraints weight = 24023.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.108157 restraints weight = 24171.957| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9774 Z= 0.236 Angle : 0.610 10.886 13260 Z= 0.302 Chirality : 0.041 0.136 1472 Planarity : 0.004 0.042 1666 Dihedral : 4.325 15.869 1270 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 3.11 % Allowed : 21.14 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.24), residues: 1152 helix: -1.35 (0.18), residues: 804 sheet: -3.24 (0.63), residues: 52 loop : -2.27 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 600 HIS 0.003 0.001 HIS A 58 PHE 0.019 0.001 PHE B 22 TYR 0.011 0.001 TYR B 195 ARG 0.004 0.000 ARG B 697 *********************** 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 137 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8473 (tp30) cc_final: 0.7935 (tp30) REVERT: B 282 MET cc_start: 0.7764 (mmm) cc_final: 0.7340 (tpp) REVERT: B 568 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8163 (mm) REVERT: B 636 ARG cc_start: 0.6940 (ttp-110) cc_final: 0.5661 (ttp-170) REVERT: A 112 GLU cc_start: 0.8361 (tp30) cc_final: 0.8061 (tp30) REVERT: A 187 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8457 (t80) REVERT: A 290 LEU cc_start: 0.7659 (tp) cc_final: 0.7449 (tp) outliers start: 31 outliers final: 23 residues processed: 129 average time/residue: 0.1989 time to fit residues: 37.0097 Evaluate side-chains 128 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 545 ILE 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 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 244 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 0.0980 chunk 77 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3567 r_free = 0.3567 target = 0.134832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106824 restraints weight = 13569.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.104773 restraints weight = 25861.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105880 restraints weight = 22953.307| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9774 Z= 0.290 Angle : 0.652 11.602 13260 Z= 0.320 Chirality : 0.043 0.134 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.449 16.138 1270 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.60 % Favored : 95.23 % Rotamer: Outliers : 3.81 % Allowed : 21.74 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.24), residues: 1152 helix: -1.29 (0.18), residues: 808 sheet: -3.33 (0.66), residues: 48 loop : -2.44 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 263 HIS 0.003 0.001 HIS A 58 PHE 0.026 0.001 PHE B 22 TYR 0.014 0.001 TYR B 195 ARG 0.004 0.000 ARG B 697 *********************** 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 145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 107 time to evaluate : 0.963 Fit side-chains REVERT: B 112 GLU cc_start: 0.8507 (tp30) cc_final: 0.7992 (tp30) REVERT: B 282 MET cc_start: 0.7798 (mmm) cc_final: 0.7367 (tpp) REVERT: B 568 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8377 (mt) REVERT: B 636 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.5689 (ttp-170) REVERT: A 112 GLU cc_start: 0.8469 (tp30) cc_final: 0.8204 (tp30) REVERT: A 187 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8366 (t80) REVERT: A 290 LEU cc_start: 0.7638 (tp) cc_final: 0.7435 (tp) outliers start: 38 outliers final: 30 residues processed: 136 average time/residue: 0.1788 time to fit residues: 35.9322 Evaluate side-chains 131 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 545 ILE 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 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 244 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 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 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 115 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3795 r_free = 0.3795 target = 0.156734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.137641 restraints weight = 12515.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.135757 restraints weight = 21114.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.135565 restraints weight = 22768.354| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9774 Z= 0.156 Angle : 0.579 10.792 13260 Z= 0.281 Chirality : 0.039 0.177 1472 Planarity : 0.004 0.039 1666 Dihedral : 4.107 15.302 1270 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.30 % Favored : 96.53 % Rotamer: Outliers : 2.10 % Allowed : 23.55 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.25), residues: 1152 helix: -0.93 (0.19), residues: 790 sheet: -2.44 (0.73), residues: 44 loop : -2.34 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 600 HIS 0.002 0.000 HIS A 366 PHE 0.016 0.001 PHE B 22 TYR 0.011 0.001 TYR A 195 ARG 0.003 0.000 ARG B 697 *********************** 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 126 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.976 Fit side-chains REVERT: B 112 GLU cc_start: 0.8270 (tp30) cc_final: 0.7800 (tp30) REVERT: B 282 MET cc_start: 0.7744 (mmm) cc_final: 0.7344 (tpp) REVERT: B 403 PHE cc_start: 0.5631 (OUTLIER) cc_final: 0.5265 (t80) REVERT: B 636 ARG cc_start: 0.6981 (ttp-110) cc_final: 0.5791 (ttp-170) REVERT: A 112 GLU cc_start: 0.8181 (tp30) cc_final: 0.7948 (tp30) REVERT: A 187 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8587 (t80) REVERT: A 614 LEU cc_start: 0.8849 (mt) cc_final: 0.8434 (tt) outliers start: 21 outliers final: 18 residues processed: 121 average time/residue: 0.2611 time to fit residues: 47.5376 Evaluate side-chains 124 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 299 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 616 VAL Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 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 380 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 530 VAL 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 104 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3580 r_free = 0.3580 target = 0.135942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109923 restraints weight = 13722.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109885 restraints weight = 27863.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110567 restraints weight = 24077.571| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9774 Z= 0.275 Angle : 0.662 12.335 13260 Z= 0.319 Chirality : 0.042 0.205 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.252 15.359 1270 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.79 % Rotamer: Outliers : 3.21 % Allowed : 23.55 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.24), residues: 1152 helix: -0.92 (0.19), residues: 794 sheet: -2.09 (0.82), residues: 38 loop : -2.52 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 600 HIS 0.002 0.000 HIS B 153 PHE 0.013 0.001 PHE B 22 TYR 0.013 0.001 TYR B 195 ARG 0.002 0.000 ARG B 697 *********************** 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 135 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.117 Fit side-chains REVERT: B 112 GLU cc_start: 0.8460 (tp30) cc_final: 0.7950 (tp30) REVERT: B 282 MET cc_start: 0.7808 (mmm) cc_final: 0.7391 (tpp) REVERT: B 403 PHE cc_start: 0.5955 (OUTLIER) cc_final: 0.5513 (t80) REVERT: B 568 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8177 (mt) REVERT: B 636 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.5785 (ttp-170) REVERT: A 112 GLU cc_start: 0.8363 (tp30) cc_final: 0.8128 (tp30) REVERT: A 187 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8465 (t80) outliers start: 32 outliers final: 23 residues processed: 130 average time/residue: 0.2761 time to fit residues: 55.3193 Evaluate side-chains 125 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 1.540 ------------------------------------------------------------------------------- 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 306 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 517 PHE 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 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 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 530 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 0.0010 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113380 restraints weight = 13123.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112233 restraints weight = 23392.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112728 restraints weight = 22154.843| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9774 Z= 0.150 Angle : 0.592 12.947 13260 Z= 0.283 Chirality : 0.038 0.135 1472 Planarity : 0.003 0.040 1666 Dihedral : 3.931 15.683 1270 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.95 % Favored : 96.88 % Rotamer: Outliers : 2.40 % Allowed : 24.25 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.25), residues: 1152 helix: -0.64 (0.19), residues: 794 sheet: -2.36 (0.74), residues: 44 loop : -2.32 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 600 HIS 0.002 0.000 HIS A 366 PHE 0.009 0.001 PHE B 517 TYR 0.011 0.001 TYR A 195 ARG 0.003 0.000 ARG B 697 *********************** 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 132 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.177 Fit side-chains REVERT: B 112 GLU cc_start: 0.8321 (tp30) cc_final: 0.7847 (tp30) REVERT: B 282 MET cc_start: 0.7755 (mmm) cc_final: 0.7349 (tpp) REVERT: B 403 PHE cc_start: 0.5859 (OUTLIER) cc_final: 0.5380 (t80) REVERT: B 636 ARG cc_start: 0.7042 (ttp-110) cc_final: 0.5783 (ttp-170) REVERT: A 112 GLU cc_start: 0.8246 (tp30) cc_final: 0.8004 (tp30) REVERT: A 187 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8563 (t80) REVERT: A 614 LEU cc_start: 0.8875 (mt) cc_final: 0.8401 (tt) outliers start: 24 outliers final: 18 residues processed: 128 average time/residue: 0.2048 time to fit residues: 39.3639 Evaluate side-chains 124 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 616 VAL 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 428 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 568 LEU 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 63 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112973 restraints weight = 13313.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112312 restraints weight = 21926.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112389 restraints weight = 21687.375| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.181 Angle : 0.627 12.330 13260 Z= 0.298 Chirality : 0.040 0.134 1472 Planarity : 0.003 0.040 1666 Dihedral : 3.913 16.271 1270 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 2.40 % Allowed : 24.25 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.25), residues: 1152 helix: -0.53 (0.19), residues: 790 sheet: -2.01 (0.81), residues: 38 loop : -2.34 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 246 HIS 0.001 0.000 HIS A 153 PHE 0.009 0.001 PHE B 387 TYR 0.012 0.001 TYR A 195 ARG 0.003 0.000 ARG B 178 ********************** 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 137 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 1.056 Fit side-chains REVERT: B 112 GLU cc_start: 0.8296 (tp30) cc_final: 0.7860 (tp30) REVERT: B 282 MET cc_start: 0.7768 (mmm) cc_final: 0.7358 (tpp) REVERT: B 403 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5409 (t80) REVERT: B 636 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.5770 (ttp-170) REVERT: A 112 GLU cc_start: 0.8307 (tp30) cc_final: 0.8063 (tp30) REVERT: A 187 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8544 (t80) REVERT: A 263 TRP cc_start: 0.7571 (p90) cc_final: 0.7316 (p90) REVERT: A 614 LEU cc_start: 0.8891 (mt) cc_final: 0.8435 (tt) outliers start: 24 outliers final: 22 residues processed: 133 average time/residue: 0.2196 time to fit residues: 41.9762 Evaluate side-chains 131 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain B residue 517 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 616 VAL 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 428 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 568 LEU 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 89 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3810 r_free = 0.3810 target = 0.158436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139574 restraints weight = 12455.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.137510 restraints weight = 21692.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.137379 restraints weight = 23167.413| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.184 Angle : 0.629 11.876 13260 Z= 0.299 Chirality : 0.040 0.183 1472 Planarity : 0.003 0.040 1666 Dihedral : 3.862 15.722 1270 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 2.71 % Allowed : 23.95 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.25), residues: 1152 helix: -0.42 (0.19), residues: 790 sheet: -1.96 (0.81), residues: 38 loop : -2.31 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 246 HIS 0.002 0.000 HIS B 153 PHE 0.009 0.001 PHE B 387 TYR 0.012 0.001 TYR B 195 ARG 0.002 0.000 ARG B 697 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2703.10 seconds wall clock time: 49 minutes 19.48 seconds (2959.48 seconds total)