Starting phenix.real_space_refine on Thu Feb 13 23:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oy3_20221/02_2025/6oy3_20221.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oy3_20221/02_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_20221/02_2025/6oy3_20221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oy3_20221/02_2025/6oy3_20221.map" model { file = "/net/cci-nas-00/data/ceres_data/6oy3_20221/02_2025/6oy3_20221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oy3_20221/02_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-5592/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: 8.84, per 1000 atoms: 0.93 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: 2.19 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: 0.86 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: 2.40 Time building geometry restraints manager: 2.52 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: 0.05 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: 0.710 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.090 Find NCS groups from input model: 0.160 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- 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 : 1.024 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: 0.2272 time to fit residues: 46.2082 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 : 1.562 ------------------------------------------------------------------------------- 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 = 0.3615 r_free = 0.3615 target = 0.138911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109116 restraints weight = 13223.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.107470 restraints weight = 21945.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108704 restraints weight = 20457.347| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1831 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 10.758 13260 Z= 0.333 Chirality : 0.041 0.152 1472 Planarity : 0.005 0.048 1666 Dihedral : 5.767 65.288 1275 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.54 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 A 58 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 : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8483 (tp30) cc_final: 0.7934 (tp30) REVERT: B 282 MET cc_start: 0.7892 (mmm) cc_final: 0.7454 (tpp) REVERT: B 348 MET cc_start: 0.8377 (ttp) cc_final: 0.8161 (ttp) REVERT: B 359 ASN cc_start: 0.8338 (t0) cc_final: 0.8091 (t0) REVERT: B 531 ASN cc_start: 0.9060 (OUTLIER) cc_final: 0.8758 (t0) REVERT: B 617 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8856 (tm-30) REVERT: B 636 ARG cc_start: 0.6909 (ttp-110) cc_final: 0.5631 (ttp-170) REVERT: A 106 GLN cc_start: 0.5823 (OUTLIER) cc_final: 0.5101 (pp30) REVERT: A 112 GLU cc_start: 0.8317 (tp30) cc_final: 0.7884 (tp30) REVERT: A 263 TRP cc_start: 0.7546 (p90) cc_final: 0.7146 (p90) REVERT: A 288 GLN cc_start: 0.7327 (mt0) cc_final: 0.7019 (mp10) REVERT: A 300 VAL cc_start: 0.9509 (p) cc_final: 0.9309 (t) REVERT: A 464 GLN cc_start: 0.7710 (tp40) cc_final: 0.7376 (tp40) REVERT: A 503 ASP cc_start: 0.8755 (m-30) cc_final: 0.8163 (t0) REVERT: A 510 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8822 (tm-30) outliers start: 21 outliers final: 11 residues processed: 143 average time/residue: 0.2033 time to fit residues: 41.5321 Evaluate side-chains 130 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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: 0.8980 chunk 67 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 0.0270 chunk 25 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 117 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112184 restraints weight = 13244.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109310 restraints weight = 20709.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110643 restraints weight = 21313.624| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2212 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= 0.165 Angle : 0.588 11.056 13260 Z= 0.293 Chirality : 0.039 0.135 1472 Planarity : 0.004 0.053 1666 Dihedral : 5.361 72.407 1274 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.73 % Favored : 96.09 % Rotamer: Outliers : 1.90 % Allowed : 17.43 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.50 (0.23), residues: 1152 helix: -1.98 (0.17), residues: 818 sheet: -3.13 (0.62), residues: 54 loop : -2.52 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 263 HIS 0.002 0.000 HIS B 366 PHE 0.007 0.001 PHE B 187 TYR 0.011 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 148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8311 (tp30) cc_final: 0.7822 (tp30) REVERT: B 187 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8734 (t80) REVERT: B 282 MET cc_start: 0.7678 (mmm) cc_final: 0.7259 (tpp) REVERT: B 359 ASN cc_start: 0.8300 (t0) cc_final: 0.8070 (t0) REVERT: B 617 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8639 (tp40) REVERT: B 636 ARG cc_start: 0.6829 (ttp-110) cc_final: 0.5589 (ttp-170) REVERT: A 112 GLU cc_start: 0.8170 (tp30) cc_final: 0.7805 (tp30) REVERT: A 187 PHE cc_start: 0.9113 (OUTLIER) cc_final: 0.8478 (t80) REVERT: A 263 TRP cc_start: 0.7416 (p90) cc_final: 0.7060 (p90) REVERT: A 288 GLN cc_start: 0.7226 (mt0) cc_final: 0.6956 (mp10) REVERT: A 300 VAL cc_start: 0.9461 (p) cc_final: 0.9247 (t) REVERT: A 464 GLN cc_start: 0.7833 (tp40) cc_final: 0.7488 (tp40) REVERT: A 503 ASP cc_start: 0.8808 (m-30) cc_final: 0.8223 (t0) outliers start: 19 outliers final: 10 residues processed: 144 average time/residue: 0.2195 time to fit residues: 44.3975 Evaluate side-chains 130 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 103 GLN B 531 ASN B 617 GLN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.137941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110282 restraints weight = 13332.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107686 restraints weight = 23036.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108884 restraints weight = 21461.156| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9774 Z= 0.216 Angle : 0.609 12.017 13260 Z= 0.298 Chirality : 0.041 0.188 1472 Planarity : 0.004 0.043 1666 Dihedral : 4.380 16.087 1270 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.77 % Favored : 95.05 % Rotamer: Outliers : 2.20 % Allowed : 19.04 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.91 (0.24), residues: 1152 helix: -1.47 (0.18), residues: 792 sheet: -3.17 (0.62), residues: 54 loop : -2.44 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 263 HIS 0.003 0.001 HIS B 58 PHE 0.018 0.001 PHE B 22 TYR 0.011 0.001 TYR B 195 ARG 0.005 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 136 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8434 (tp30) cc_final: 0.7886 (tp30) REVERT: B 282 MET cc_start: 0.7675 (mmm) cc_final: 0.7279 (tpp) REVERT: B 359 ASN cc_start: 0.8314 (t0) cc_final: 0.8072 (t0) REVERT: B 568 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8191 (mm) REVERT: B 617 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8843 (tm-30) REVERT: B 636 ARG cc_start: 0.6951 (ttp-110) cc_final: 0.5665 (ttp-170) REVERT: A 112 GLU cc_start: 0.8234 (tp30) cc_final: 0.7911 (tp30) REVERT: A 187 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8488 (t80) REVERT: A 288 GLN cc_start: 0.7207 (mt0) cc_final: 0.6936 (mp10) REVERT: A 290 LEU cc_start: 0.7763 (tp) cc_final: 0.7500 (tp) REVERT: A 464 GLN cc_start: 0.7899 (tp40) cc_final: 0.7551 (tp40) REVERT: A 503 ASP cc_start: 0.8864 (m-30) cc_final: 0.8141 (t0) outliers start: 22 outliers final: 14 residues processed: 133 average time/residue: 0.2073 time to fit residues: 39.4709 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108987 restraints weight = 13257.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105827 restraints weight = 21010.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107158 restraints weight = 21342.347| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9774 Z= 0.222 Angle : 0.596 13.292 13260 Z= 0.293 Chirality : 0.040 0.129 1472 Planarity : 0.004 0.041 1666 Dihedral : 4.288 15.751 1270 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer: Outliers : 3.01 % Allowed : 20.14 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.69 (0.24), residues: 1152 helix: -1.28 (0.18), residues: 794 sheet: -3.10 (0.62), residues: 54 loop : -2.44 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 600 HIS 0.003 0.001 HIS B 58 PHE 0.022 0.001 PHE B 517 TYR 0.012 0.001 TYR B 195 ARG 0.003 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 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8434 (tp30) cc_final: 0.7856 (tp30) REVERT: B 282 MET cc_start: 0.7729 (mmm) cc_final: 0.7326 (tpp) REVERT: B 359 ASN cc_start: 0.8321 (t0) cc_final: 0.8069 (t0) REVERT: B 568 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8425 (mt) REVERT: B 636 ARG cc_start: 0.6898 (ttp-110) cc_final: 0.5602 (ttp-170) REVERT: A 112 GLU cc_start: 0.8320 (tp30) cc_final: 0.8018 (tp30) REVERT: A 187 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.8509 (t80) REVERT: A 503 ASP cc_start: 0.8852 (m-30) cc_final: 0.8075 (t0) outliers start: 30 outliers final: 19 residues processed: 134 average time/residue: 0.2157 time to fit residues: 41.2178 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 : 1.119 ------------------------------------------------------------------------------- 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 299 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 187 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** A 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109365 restraints weight = 13375.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107939 restraints weight = 24679.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109067 restraints weight = 23814.217| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9774 Z= 0.226 Angle : 0.609 12.344 13260 Z= 0.295 Chirality : 0.041 0.122 1472 Planarity : 0.004 0.040 1666 Dihedral : 4.224 15.843 1270 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.69 % Favored : 95.14 % Rotamer: Outliers : 2.71 % Allowed : 21.54 % 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: -2.51 (0.24), residues: 1152 helix: -1.13 (0.19), residues: 796 sheet: -2.85 (0.65), residues: 58 loop : -2.45 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 600 HIS 0.003 0.000 HIS A 58 PHE 0.018 0.001 PHE B 517 TYR 0.012 0.001 TYR B 195 ARG 0.003 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 135 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.067 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8445 (tp30) cc_final: 0.7909 (tp30) REVERT: B 282 MET cc_start: 0.7744 (mmm) cc_final: 0.7347 (tpp) REVERT: B 359 ASN cc_start: 0.8341 (t0) cc_final: 0.8065 (t0) REVERT: B 568 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8201 (mt) REVERT: B 636 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.5687 (ttp-170) REVERT: A 112 GLU cc_start: 0.8351 (tp30) cc_final: 0.8095 (tp30) REVERT: A 187 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8476 (t80) REVERT: A 374 GLN cc_start: 0.7435 (mt0) cc_final: 0.7079 (mt0) outliers start: 27 outliers final: 22 residues processed: 130 average time/residue: 0.2063 time to fit residues: 38.5813 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 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 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: 7.9990 chunk 73 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 0.0470 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 28 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.136136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109392 restraints weight = 13446.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.104488 restraints weight = 15844.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.105320 restraints weight = 17755.759| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2750 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= 0.259 Angle : 0.626 11.915 13260 Z= 0.306 Chirality : 0.041 0.133 1472 Planarity : 0.004 0.040 1666 Dihedral : 4.265 16.201 1270 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.95 % Favored : 94.88 % Rotamer: Outliers : 3.21 % Allowed : 22.04 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.46 (0.24), residues: 1152 helix: -1.04 (0.19), residues: 798 sheet: -3.17 (0.60), residues: 54 loop : -2.55 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 600 HIS 0.003 0.001 HIS A 58 PHE 0.016 0.001 PHE B 517 TYR 0.013 0.001 TYR B 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 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 107 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8477 (tp30) cc_final: 0.7917 (tp30) REVERT: B 282 MET cc_start: 0.7731 (mmm) cc_final: 0.7321 (tpp) REVERT: B 359 ASN cc_start: 0.8335 (t0) cc_final: 0.7956 (t0) REVERT: B 568 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8250 (mt) REVERT: B 636 ARG cc_start: 0.6884 (ttp-110) cc_final: 0.5556 (ttp-170) REVERT: A 112 GLU cc_start: 0.8442 (tp30) cc_final: 0.8190 (tp30) REVERT: A 187 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8426 (t80) outliers start: 32 outliers final: 26 residues processed: 132 average time/residue: 0.2008 time to fit residues: 38.5628 Evaluate side-chains 132 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 104 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 99 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.138953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.112720 restraints weight = 13355.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112401 restraints weight = 26126.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113362 restraints weight = 23793.385| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2913 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= 0.158 Angle : 0.571 11.467 13260 Z= 0.275 Chirality : 0.039 0.130 1472 Planarity : 0.003 0.040 1666 Dihedral : 4.006 15.012 1270 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.92 % Rotamer: Outliers : 2.61 % Allowed : 22.65 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.04 (0.25), residues: 1152 helix: -0.82 (0.19), residues: 804 sheet: -2.53 (0.71), residues: 44 loop : -2.24 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 600 HIS 0.002 0.000 HIS A 58 PHE 0.015 0.001 PHE B 517 TYR 0.012 0.001 TYR A 195 ARG 0.003 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 134 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8325 (tp30) cc_final: 0.7820 (tp30) REVERT: B 282 MET cc_start: 0.7775 (mmm) cc_final: 0.7380 (tpp) REVERT: B 359 ASN cc_start: 0.8265 (t0) cc_final: 0.8032 (t0) REVERT: B 568 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7733 (mt) REVERT: B 636 ARG cc_start: 0.7012 (ttp-110) cc_final: 0.5777 (ttp-170) REVERT: A 112 GLU cc_start: 0.8285 (tp30) cc_final: 0.8050 (tp30) REVERT: A 187 PHE cc_start: 0.9301 (OUTLIER) cc_final: 0.8557 (t80) REVERT: A 614 LEU cc_start: 0.8854 (mt) cc_final: 0.8439 (tt) outliers start: 26 outliers final: 20 residues processed: 129 average time/residue: 0.2192 time to fit residues: 39.9793 Evaluate side-chains 127 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3607 r_free = 0.3607 target = 0.138449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110459 restraints weight = 13212.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108983 restraints weight = 23167.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110180 restraints weight = 23695.684| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9774 Z= 0.184 Angle : 0.616 13.038 13260 Z= 0.294 Chirality : 0.040 0.160 1472 Planarity : 0.004 0.049 1666 Dihedral : 3.976 14.873 1270 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.82 % Favored : 96.01 % Rotamer: Outliers : 2.51 % Allowed : 23.25 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.94 (0.25), residues: 1152 helix: -0.70 (0.19), residues: 800 sheet: -2.56 (0.71), residues: 44 loop : -2.32 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 246 HIS 0.002 0.000 HIS B 153 PHE 0.016 0.001 PHE B 517 TYR 0.012 0.001 TYR A 195 ARG 0.011 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 135 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.383 Fit side-chains REVERT: B 112 GLU cc_start: 0.8338 (tp30) cc_final: 0.7861 (tp30) REVERT: B 282 MET cc_start: 0.7861 (mmm) cc_final: 0.7483 (tpp) REVERT: B 359 ASN cc_start: 0.8290 (t0) cc_final: 0.8038 (t0) REVERT: B 568 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7513 (tp) REVERT: B 636 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.5750 (ttp-170) REVERT: A 112 GLU cc_start: 0.8312 (tp30) cc_final: 0.8081 (tp30) REVERT: A 187 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8567 (t80) REVERT: A 614 LEU cc_start: 0.8781 (mt) cc_final: 0.8422 (tt) outliers start: 25 outliers final: 22 residues processed: 130 average time/residue: 0.2045 time to fit residues: 38.9823 Evaluate side-chains 130 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 63 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 98 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.0050 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.139074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112481 restraints weight = 13246.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111345 restraints weight = 23693.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112408 restraints weight = 22574.783| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3115 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= 0.174 Angle : 0.617 12.366 13260 Z= 0.294 Chirality : 0.040 0.153 1472 Planarity : 0.004 0.046 1666 Dihedral : 3.896 14.395 1270 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 2.51 % Allowed : 23.15 % 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: -1.69 (0.25), residues: 1152 helix: -0.59 (0.19), residues: 808 sheet: -2.11 (0.79), residues: 38 loop : -2.10 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 246 HIS 0.001 0.000 HIS A 366 PHE 0.016 0.001 PHE B 517 TYR 0.012 0.001 TYR A 195 ARG 0.011 0.000 ARG B 697 ********************** 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 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.8315 (tp30) cc_final: 0.7822 (tp30) REVERT: B 282 MET cc_start: 0.7762 (mmm) cc_final: 0.7391 (tpp) REVERT: B 359 ASN cc_start: 0.8285 (t0) cc_final: 0.8035 (t0) REVERT: B 568 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.7295 (mp) REVERT: B 636 ARG cc_start: 0.7022 (ttp-110) cc_final: 0.5785 (ttp-170) REVERT: A 112 GLU cc_start: 0.8325 (tp30) cc_final: 0.8084 (tp30) REVERT: A 187 PHE cc_start: 0.9322 (OUTLIER) cc_final: 0.8551 (t80) REVERT: A 614 LEU cc_start: 0.8800 (mt) cc_final: 0.8352 (tt) outliers start: 25 outliers final: 23 residues processed: 134 average time/residue: 0.2235 time to fit residues: 41.8796 Evaluate side-chains 131 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 187 PHE Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 403 PHE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 616 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.136315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110719 restraints weight = 13348.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.110122 restraints weight = 25754.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110802 restraints weight = 21329.014| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9774 Z= 0.259 Angle : 0.669 11.867 13260 Z= 0.323 Chirality : 0.042 0.159 1472 Planarity : 0.004 0.045 1666 Dihedral : 4.059 15.101 1270 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.60 % Favored : 95.31 % Rotamer: Outliers : 2.81 % Allowed : 23.05 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.82 (0.25), residues: 1152 helix: -0.62 (0.19), residues: 804 sheet: -3.09 (0.65), residues: 50 loop : -2.09 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 246 HIS 0.002 0.000 HIS B 153 PHE 0.016 0.001 PHE B 517 TYR 0.013 0.001 TYR A 195 ARG 0.010 0.000 ARG B 697 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.85 seconds wall clock time: 45 minutes 47.98 seconds (2747.98 seconds total)