Starting phenix.real_space_refine on Mon Aug 5 03:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/08_2024/8xuo_38679.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/08_2024/8xuo_38679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/08_2024/8xuo_38679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/08_2024/8xuo_38679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/08_2024/8xuo_38679.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xuo_38679/08_2024/8xuo_38679.cif" } resolution = 2.84 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= 0.027 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 P 16 5.49 5 S 58 5.16 5 C 7788 2.51 5 N 2102 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "G GLU 334": "OE1" <-> "OE2" Residue "G GLU 433": "OE1" <-> "OE2" Residue "G GLU 572": "OE1" <-> "OE2" Residue "G GLU 582": "OE1" <-> "OE2" Residue "G GLU 608": "OE1" <-> "OE2" Residue "G GLU 634": "OE1" <-> "OE2" Residue "G GLU 767": "OE1" <-> "OE2" Residue "G GLU 770": "OE1" <-> "OE2" Residue "G GLU 776": "OE1" <-> "OE2" Residue "G GLU 799": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6064 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain: "G" Number of atoms: 6064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6064 Classifications: {'peptide': 752} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 715} Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'ADP': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.95, per 1000 atoms: 0.57 Number of scatterers: 12254 At special positions: 0 Unit cell: (106.25, 144.5, 96.05, 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) S 58 16.00 P 16 15.00 O 2290 8.00 N 2102 7.00 C 7788 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.0 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 15 sheets defined 43.8% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.587A pdb=" N ARG A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.754A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.777A pdb=" N HIS A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY A 240 " --> pdb=" O LYS A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 235 through 240' Processing helix chain 'A' and resid 242 through 258 removed outlier: 3.528A pdb=" N GLU A 249 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 277 removed outlier: 3.574A pdb=" N TRP A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.698A pdb=" N ALA A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 327 Processing helix chain 'A' and resid 332 through 347 removed outlier: 4.118A pdb=" N LEU A 337 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 364 Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.542A pdb=" N SER A 376 " --> pdb=" O GLN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 4.043A pdb=" N ASN A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 400 " --> pdb=" O MET A 396 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.710A pdb=" N ALA A 407 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 423 through 434 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 478 through 492 Processing helix chain 'A' and resid 509 through 516 removed outlier: 3.987A pdb=" N THR A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR A 516 " --> pdb=" O GLU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.599A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 580 through 586 removed outlier: 3.841A pdb=" N LEU A 586 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 removed outlier: 4.014A pdb=" N LEU A 609 " --> pdb=" O MET A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 684 removed outlier: 3.578A pdb=" N THR A 684 " --> pdb=" O VAL A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 704 through 710 removed outlier: 3.869A pdb=" N LEU A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 713 No H-bonds generated for 'chain 'A' and resid 711 through 713' Processing helix chain 'A' and resid 737 through 741 Processing helix chain 'A' and resid 759 through 766 removed outlier: 3.675A pdb=" N LEU A 763 " --> pdb=" O ASP A 759 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 766 " --> pdb=" O ILE A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 813 removed outlier: 3.724A pdb=" N PHE A 813 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 837 Processing helix chain 'A' and resid 849 through 869 Processing helix chain 'G' and resid 158 through 168 Processing helix chain 'G' and resid 188 through 198 Processing helix chain 'G' and resid 199 through 206 Processing helix chain 'G' and resid 219 through 232 removed outlier: 3.615A pdb=" N LEU G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE G 231 " --> pdb=" O ILE G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 258 Processing helix chain 'G' and resid 269 through 278 removed outlier: 3.990A pdb=" N ILE G 278 " --> pdb=" O GLU G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 303 removed outlier: 3.672A pdb=" N ALA G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 327 Processing helix chain 'G' and resid 332 through 346 removed outlier: 3.506A pdb=" N VAL G 336 " --> pdb=" O PRO G 332 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU G 337 " --> pdb=" O PRO G 333 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N SER G 338 " --> pdb=" O GLU G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 364 Processing helix chain 'G' and resid 366 through 381 Processing helix chain 'G' and resid 387 through 401 removed outlier: 3.634A pdb=" N ASN G 391 " --> pdb=" O PRO G 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG G 400 " --> pdb=" O MET G 396 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 401 " --> pdb=" O SER G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 412 removed outlier: 3.675A pdb=" N ALA G 407 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 415 No H-bonds generated for 'chain 'G' and resid 413 through 415' Processing helix chain 'G' and resid 423 through 434 Processing helix chain 'G' and resid 443 through 458 Processing helix chain 'G' and resid 478 through 492 Processing helix chain 'G' and resid 509 through 515 removed outlier: 3.764A pdb=" N THR G 515 " --> pdb=" O ARG G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 531 removed outlier: 3.583A pdb=" N THR G 531 " --> pdb=" O ASP G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 557 through 563 Processing helix chain 'G' and resid 580 through 586 removed outlier: 3.629A pdb=" N LEU G 586 " --> pdb=" O PHE G 583 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 608 Processing helix chain 'G' and resid 672 through 676 Processing helix chain 'G' and resid 677 through 684 removed outlier: 3.517A pdb=" N THR G 684 " --> pdb=" O VAL G 680 " (cutoff:3.500A) Processing helix chain 'G' and resid 695 through 701 removed outlier: 4.307A pdb=" N LEU G 699 " --> pdb=" O LYS G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 711 Processing helix chain 'G' and resid 737 through 741 Processing helix chain 'G' and resid 756 through 758 No H-bonds generated for 'chain 'G' and resid 756 through 758' Processing helix chain 'G' and resid 759 through 766 Processing helix chain 'G' and resid 809 through 813 removed outlier: 3.542A pdb=" N PHE G 813 " --> pdb=" O ALA G 810 " (cutoff:3.500A) Processing helix chain 'G' and resid 831 through 837 removed outlier: 3.578A pdb=" N LEU G 834 " --> pdb=" O PRO G 831 " (cutoff:3.500A) Processing helix chain 'G' and resid 849 through 870 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 6.760A pdb=" N THR A 208 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N VAL A 263 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A 210 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASP A 265 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N VAL A 212 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N TYR A 260 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A 290 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL A 262 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR A 292 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 264 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU A 177 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU A 291 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL A 179 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N THR A 293 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N VAL A 181 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 307 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 422 removed outlier: 6.821A pdb=" N ILE A 472 " --> pdb=" O ARG A 466 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ARG A 466 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 474 " --> pdb=" O MET A 464 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.553A pdb=" N LEU A 542 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 541 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU A 572 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 549 " --> pdb=" O ASN A 575 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 498 removed outlier: 3.553A pdb=" N LEU A 542 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 541 " --> pdb=" O ASP A 570 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N GLU A 572 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A 595 " --> pdb=" O VAL A 571 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A 573 " --> pdb=" O SER A 595 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 615 " --> pdb=" O HIS A 638 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 602 removed outlier: 3.715A pdb=" N ILE A 626 " --> pdb=" O LYS A 646 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 690 through 694 removed outlier: 6.456A pdb=" N LEU A 748 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS A 775 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N LEU A 750 " --> pdb=" O LYS A 775 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU A 796 " --> pdb=" O VAL A 820 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE A 822 " --> pdb=" O LEU A 796 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 798 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 819 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N GLN A 846 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 821 " --> pdb=" O GLN A 846 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET A 843 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 755 through 756 removed outlier: 5.380A pdb=" N LEU A 755 " --> pdb=" O SER A 780 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AA9, first strand: chain 'G' and resid 208 through 213 removed outlier: 6.794A pdb=" N THR G 208 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL G 263 " --> pdb=" O THR G 208 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE G 210 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP G 265 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL G 212 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N TYR G 260 " --> pdb=" O PRO G 286 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N HIS G 175 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL G 289 " --> pdb=" O HIS G 175 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU G 177 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU G 291 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL G 179 " --> pdb=" O LEU G 291 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR G 293 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL G 181 " --> pdb=" O THR G 293 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS G 307 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 421 through 422 removed outlier: 6.612A pdb=" N GLU G 465 " --> pdb=" O LYS G 473 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N CYS G 475 " --> pdb=" O VAL G 463 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL G 463 " --> pdb=" O CYS G 475 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU G 477 " --> pdb=" O VAL G 461 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL G 461 " --> pdb=" O LEU G 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 497 through 498 removed outlier: 3.515A pdb=" N LEU G 542 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE G 541 " --> pdb=" O ASP G 570 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLU G 572 " --> pdb=" O PHE G 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 497 through 498 removed outlier: 3.515A pdb=" N LEU G 542 " --> pdb=" O LEU G 519 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE G 541 " --> pdb=" O ASP G 570 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLU G 572 " --> pdb=" O PHE G 541 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER G 595 " --> pdb=" O VAL G 571 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER G 573 " --> pdb=" O SER G 595 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE G 594 " --> pdb=" O ILE G 616 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 601 through 602 removed outlier: 7.366A pdb=" N LEU G 624 " --> pdb=" O LYS G 646 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 667 through 671 removed outlier: 4.314A pdb=" N THR G 667 " --> pdb=" O LYS G 689 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY G 691 " --> pdb=" O THR G 667 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N SER G 669 " --> pdb=" O GLY G 691 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG G 693 " --> pdb=" O SER G 669 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE G 671 " --> pdb=" O ARG G 693 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU G 748 " --> pdb=" O LYS G 773 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N LYS G 775 " --> pdb=" O LEU G 748 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU G 750 " --> pdb=" O LYS G 775 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU G 772 " --> pdb=" O TRP G 797 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N GLU G 799 " --> pdb=" O LEU G 772 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N MET G 774 " --> pdb=" O GLU G 799 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU G 819 " --> pdb=" O MET G 844 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLN G 846 " --> pdb=" O LEU G 819 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU G 821 " --> pdb=" O GLN G 846 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET G 843 " --> pdb=" O SER G 879 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 783 through 785 removed outlier: 6.941A pdb=" N TRP G 784 " --> pdb=" O LYS G 807 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 445 hydrogen bonds defined for protein. 1224 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: 4.20 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2011 1.32 - 1.44: 3167 1.44 - 1.57: 7236 1.57 - 1.69: 18 1.69 - 1.82: 86 Bond restraints: 12518 Sorted by residual: bond pdb=" N VAL A 830 " pdb=" CA VAL A 830 " ideal model delta sigma weight residual 1.457 1.490 -0.033 9.00e-03 1.23e+04 1.36e+01 bond pdb=" N ILE A 431 " pdb=" CA ILE A 431 " ideal model delta sigma weight residual 1.461 1.503 -0.043 1.19e-02 7.06e+03 1.28e+01 bond pdb=" N LEU A 429 " pdb=" CA LEU A 429 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C ARG A 428 " pdb=" O ARG A 428 " ideal model delta sigma weight residual 1.237 1.196 0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" C PRO A 422 " pdb=" O PRO A 422 " ideal model delta sigma weight residual 1.233 1.193 0.040 1.23e-02 6.61e+03 1.08e+01 ... (remaining 12513 not shown) Histogram of bond angle deviations from ideal: 95.67 - 103.77: 176 103.77 - 111.86: 6131 111.86 - 119.95: 5068 119.95 - 128.04: 5439 128.04 - 136.14: 138 Bond angle restraints: 16952 Sorted by residual: angle pdb=" O TRP A 430 " pdb=" C TRP A 430 " pdb=" N ILE A 431 " ideal model delta sigma weight residual 122.09 116.21 5.88 1.08e+00 8.57e-01 2.96e+01 angle pdb=" N GLU A 433 " pdb=" CA GLU A 433 " pdb=" C GLU A 433 " ideal model delta sigma weight residual 111.28 105.43 5.85 1.09e+00 8.42e-01 2.88e+01 angle pdb=" N PRO G 648 " pdb=" CA PRO G 648 " pdb=" C PRO G 648 " ideal model delta sigma weight residual 111.14 103.39 7.75 1.56e+00 4.11e-01 2.47e+01 angle pdb=" CA TRP A 430 " pdb=" C TRP A 430 " pdb=" N ILE A 431 " ideal model delta sigma weight residual 117.17 122.73 -5.56 1.18e+00 7.18e-01 2.22e+01 angle pdb=" CA LEU A 426 " pdb=" C LEU A 426 " pdb=" O LEU A 426 " ideal model delta sigma weight residual 120.55 115.60 4.95 1.06e+00 8.90e-01 2.18e+01 ... (remaining 16947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 7326 35.53 - 71.07: 319 71.07 - 106.60: 36 106.60 - 142.14: 14 142.14 - 177.67: 5 Dihedral angle restraints: 7700 sinusoidal: 3292 harmonic: 4408 Sorted by residual: dihedral pdb=" C5' ADP A 901 " pdb=" O5' ADP A 901 " pdb=" PA ADP A 901 " pdb=" O2A ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 117.67 -177.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual 300.00 122.98 177.02 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP G 901 " pdb=" O3A ADP G 901 " pdb=" PB ADP G 901 " pdb=" PA ADP G 901 " ideal model delta sinusoidal sigma weight residual -60.00 84.01 -144.02 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 7697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 1885 1.004 - 2.007: 0 2.007 - 3.011: 0 3.011 - 4.014: 0 4.014 - 5.018: 7 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C2 IHP A 902 " pdb=" C1 IHP A 902 " pdb=" C3 IHP A 902 " pdb=" O12 IHP A 902 " both_signs ideal model delta sigma weight residual False -2.52 2.50 -5.02 2.00e-01 2.50e+01 6.29e+02 chirality pdb=" C2 IHP G 902 " pdb=" C1 IHP G 902 " pdb=" C3 IHP G 902 " pdb=" O12 IHP G 902 " both_signs ideal model delta sigma weight residual False -2.52 2.49 -5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C5 IHP A 902 " pdb=" C4 IHP A 902 " pdb=" C6 IHP A 902 " pdb=" O15 IHP A 902 " both_signs ideal model delta sigma weight residual False -2.42 2.56 -4.98 2.00e-01 2.50e+01 6.20e+02 ... (remaining 1889 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 833 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ALA G 833 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA G 833 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU G 834 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 825 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASP G 825 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP G 825 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN G 826 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 645 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C ALA G 645 " 0.049 2.00e-02 2.50e+03 pdb=" O ALA G 645 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS G 646 " -0.017 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 119 2.56 - 3.14: 10144 3.14 - 3.73: 18814 3.73 - 4.31: 25832 4.31 - 4.90: 42921 Nonbonded interactions: 97830 Sorted by model distance: nonbonded pdb=" O LYS A 712 " pdb=" NZ LYS A 712 " model vdw 1.970 3.120 nonbonded pdb=" O LYS A 758 " pdb=" NZ LYS A 758 " model vdw 2.103 3.120 nonbonded pdb=" O LYS G 712 " pdb=" NZ LYS G 712 " model vdw 2.112 3.120 nonbonded pdb=" N GLU G 504 " pdb=" OE1 GLU G 504 " model vdw 2.176 3.120 nonbonded pdb=" N GLU G 785 " pdb=" OE1 GLU G 785 " model vdw 2.209 3.120 ... (remaining 97825 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 34.010 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.004 0.045 12518 Z= 0.271 Angle : 0.832 10.425 16952 Z= 0.464 Chirality : 0.301 5.018 1892 Planarity : 0.005 0.058 2134 Dihedral : 20.563 177.671 4828 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 2.71 % Allowed : 26.98 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1500 helix: 0.70 (0.22), residues: 520 sheet: 0.31 (0.36), residues: 216 loop : -0.31 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 754 HIS 0.006 0.001 HIS G 638 PHE 0.021 0.001 PHE G 779 TYR 0.016 0.001 TYR A 591 ARG 0.006 0.001 ARG G 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 144 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 MET cc_start: 0.7209 (ttt) cc_final: 0.6935 (ttp) REVERT: G 606 MET cc_start: 0.5930 (tpt) cc_final: 0.5705 (tpt) outliers start: 37 outliers final: 27 residues processed: 179 average time/residue: 0.8945 time to fit residues: 179.4404 Evaluate side-chains 146 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 242 CYS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 404 ASP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 591 TYR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 780 SER Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain G residue 242 CYS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 356 ILE Chi-restraints excluded: chain G residue 360 LEU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 591 TYR Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 613 GLN Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 635 ARG Chi-restraints excluded: chain G residue 697 SER Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 804 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.0270 chunk 113 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 380 HIS A 642 ASN A 666 GLN A 710 ASN G 451 ASN G 522 HIS G 537 HIS G 640 HIS G 710 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12518 Z= 0.317 Angle : 0.835 13.061 16952 Z= 0.390 Chirality : 0.049 0.488 1892 Planarity : 0.005 0.047 2134 Dihedral : 12.116 179.450 1769 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 6.45 % Allowed : 23.09 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1500 helix: 0.98 (0.22), residues: 520 sheet: 0.54 (0.36), residues: 216 loop : -0.50 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 211 HIS 0.006 0.001 HIS A 638 PHE 0.015 0.002 PHE G 583 TYR 0.024 0.002 TYR G 591 ARG 0.005 0.001 ARG G 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 145 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 190 THR cc_start: 0.8966 (t) cc_final: 0.8744 (m) REVERT: A 219 ARG cc_start: 0.6913 (mtp-110) cc_final: 0.6456 (mtp-110) REVERT: A 420 GLN cc_start: 0.8297 (mm110) cc_final: 0.8092 (mm110) REVERT: A 610 TRP cc_start: 0.3210 (OUTLIER) cc_final: 0.2027 (m-90) REVERT: A 772 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8276 (tt) REVERT: A 777 ASN cc_start: 0.7048 (m-40) cc_final: 0.6755 (t0) REVERT: A 800 ARG cc_start: 0.6530 (tpt-90) cc_final: 0.6060 (tpm170) REVERT: A 843 MET cc_start: 0.7475 (ttt) cc_final: 0.7231 (ttp) REVERT: A 844 MET cc_start: 0.7038 (tmm) cc_final: 0.6779 (tmm) REVERT: G 294 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8117 (ptm160) REVERT: G 579 PHE cc_start: 0.5767 (m-80) cc_final: 0.5299 (m-80) REVERT: G 581 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6494 (ptt180) REVERT: G 687 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.7001 (mp) outliers start: 88 outliers final: 30 residues processed: 214 average time/residue: 1.0840 time to fit residues: 255.0468 Evaluate side-chains 153 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 370 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 581 ARG Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 622 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 804 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 30.0000 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 92 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 GLN A 666 GLN G 380 HIS G 487 GLN G 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 0.036 12518 Z= 0.183 Angle : 0.630 9.746 16952 Z= 0.307 Chirality : 0.043 0.352 1892 Planarity : 0.004 0.046 2134 Dihedral : 10.787 165.040 1737 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.69 % Allowed : 24.63 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1500 helix: 1.34 (0.23), residues: 528 sheet: 0.86 (0.37), residues: 218 loop : -0.42 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 757 HIS 0.003 0.001 HIS A 640 PHE 0.018 0.001 PHE G 779 TYR 0.010 0.001 TYR A 591 ARG 0.005 0.001 ARG A 637 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 140 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 THR cc_start: 0.8881 (t) cc_final: 0.8645 (p) REVERT: A 219 ARG cc_start: 0.6817 (mtp-110) cc_final: 0.6472 (mtp-110) REVERT: A 239 HIS cc_start: 0.7484 (OUTLIER) cc_final: 0.6884 (m90) REVERT: A 777 ASN cc_start: 0.7206 (m-40) cc_final: 0.6898 (m-40) REVERT: A 800 ARG cc_start: 0.6517 (tpt-90) cc_final: 0.6045 (tpm170) REVERT: A 844 MET cc_start: 0.6893 (tmm) cc_final: 0.6654 (tmm) REVERT: G 579 PHE cc_start: 0.5606 (m-80) cc_final: 0.5279 (m-80) REVERT: G 581 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6436 (ptt180) REVERT: G 718 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.5505 (mm-30) REVERT: G 735 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8436 (mp) REVERT: G 785 GLU cc_start: 0.7805 (mp0) cc_final: 0.7589 (mp0) outliers start: 64 outliers final: 21 residues processed: 191 average time/residue: 1.1142 time to fit residues: 233.4242 Evaluate side-chains 144 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 581 ARG Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 643 SER Chi-restraints excluded: chain G residue 671 ILE Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 8.9990 chunk 15 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 386 HIS A 640 HIS A 666 GLN A 710 ASN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN G 638 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.140 12518 Z= 0.447 Angle : 0.827 11.384 16952 Z= 0.410 Chirality : 0.050 0.223 1892 Planarity : 0.006 0.053 2134 Dihedral : 10.049 145.760 1730 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 7.04 % Allowed : 23.53 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.22), residues: 1500 helix: 0.56 (0.22), residues: 532 sheet: 0.12 (0.33), residues: 256 loop : -0.68 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 754 HIS 0.008 0.002 HIS G 638 PHE 0.019 0.003 PHE A 158 TYR 0.039 0.003 TYR A 591 ARG 0.012 0.001 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 149 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 ARG cc_start: 0.6911 (mtp-110) cc_final: 0.6540 (mtp-110) REVERT: A 239 HIS cc_start: 0.7878 (OUTLIER) cc_final: 0.7334 (m90) REVERT: A 270 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: A 274 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: A 610 TRP cc_start: 0.3491 (OUTLIER) cc_final: 0.2161 (m-90) REVERT: A 777 ASN cc_start: 0.7471 (m-40) cc_final: 0.7141 (m-40) REVERT: A 785 GLU cc_start: 0.7457 (tm-30) cc_final: 0.6904 (mp0) REVERT: A 800 ARG cc_start: 0.6509 (tpt-90) cc_final: 0.5970 (tpm170) REVERT: A 844 MET cc_start: 0.7062 (tmm) cc_final: 0.6825 (tmt) REVERT: G 239 HIS cc_start: 0.7692 (OUTLIER) cc_final: 0.7195 (m90) REVERT: G 294 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8221 (ptm160) REVERT: G 718 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.5753 (mm-30) REVERT: G 732 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7576 (ptmt) REVERT: G 735 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8493 (tp) REVERT: G 766 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7656 (tt) REVERT: G 823 CYS cc_start: 0.7682 (t) cc_final: 0.7037 (t) outliers start: 96 outliers final: 34 residues processed: 224 average time/residue: 1.0605 time to fit residues: 261.2070 Evaluate side-chains 163 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 735 LEU Chi-restraints excluded: chain G residue 753 THR Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 817 LYS Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 74 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 36 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 666 GLN A 818 HIS G 287 ASN G 613 GLN G 768 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12518 Z= 0.210 Angle : 0.651 8.016 16952 Z= 0.320 Chirality : 0.043 0.247 1892 Planarity : 0.005 0.070 2134 Dihedral : 9.480 144.089 1730 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.11 % Allowed : 27.71 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1500 helix: 1.01 (0.23), residues: 522 sheet: 0.34 (0.34), residues: 256 loop : -0.59 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 631 HIS 0.002 0.001 HIS G 482 PHE 0.028 0.002 PHE G 876 TYR 0.012 0.001 TYR A 591 ARG 0.009 0.001 ARG A 511 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 140 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7223 (m90) REVERT: A 610 TRP cc_start: 0.3273 (OUTLIER) cc_final: 0.1968 (m-90) REVERT: A 777 ASN cc_start: 0.7508 (m-40) cc_final: 0.7181 (m-40) REVERT: A 785 GLU cc_start: 0.7446 (tm-30) cc_final: 0.6971 (mp0) REVERT: A 800 ARG cc_start: 0.6564 (tpt-90) cc_final: 0.5969 (tpm170) REVERT: A 815 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6743 (mtm-85) REVERT: A 844 MET cc_start: 0.7297 (tmm) cc_final: 0.6991 (tmm) REVERT: G 294 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8107 (ptm160) REVERT: G 718 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.5665 (mm-30) REVERT: G 732 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7511 (ptmt) REVERT: G 785 GLU cc_start: 0.7834 (mp0) cc_final: 0.7521 (mp0) REVERT: G 815 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.6713 (mtt90) REVERT: G 823 CYS cc_start: 0.7536 (t) cc_final: 0.7036 (t) outliers start: 56 outliers final: 24 residues processed: 187 average time/residue: 1.0901 time to fit residues: 224.0379 Evaluate side-chains 154 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 718 GLU Chi-restraints excluded: chain G residue 750 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 817 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12518 Z= 0.292 Angle : 0.693 8.061 16952 Z= 0.341 Chirality : 0.045 0.219 1892 Planarity : 0.005 0.081 2134 Dihedral : 9.413 142.907 1730 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.13 % Allowed : 27.20 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1500 helix: 0.85 (0.23), residues: 534 sheet: 0.13 (0.34), residues: 258 loop : -0.74 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 631 HIS 0.004 0.001 HIS G 482 PHE 0.025 0.002 PHE G 876 TYR 0.023 0.002 TYR A 591 ARG 0.007 0.001 ARG G 511 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 141 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7904 (OUTLIER) cc_final: 0.7314 (m90) REVERT: A 610 TRP cc_start: 0.3456 (OUTLIER) cc_final: 0.2083 (m-90) REVERT: A 765 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7868 (mt0) REVERT: A 785 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7149 (mp0) REVERT: A 800 ARG cc_start: 0.6504 (tpt-90) cc_final: 0.6221 (mmm160) REVERT: A 815 ARG cc_start: 0.7663 (mtp85) cc_final: 0.6903 (mtm-85) REVERT: A 844 MET cc_start: 0.7045 (tmm) cc_final: 0.6808 (tmt) REVERT: G 239 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7208 (m90) REVERT: G 294 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8103 (ptm160) REVERT: G 732 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7536 (ptmt) REVERT: G 815 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7165 (mtp85) REVERT: G 823 CYS cc_start: 0.7645 (t) cc_final: 0.7105 (t) outliers start: 70 outliers final: 36 residues processed: 193 average time/residue: 1.0529 time to fit residues: 223.5703 Evaluate side-chains 163 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 256 LYS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 599 ILE Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 779 PHE Chi-restraints excluded: chain G residue 855 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.0020 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 818 HIS G 613 GLN G 865 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12518 Z= 0.196 Angle : 0.645 8.084 16952 Z= 0.316 Chirality : 0.042 0.232 1892 Planarity : 0.005 0.078 2134 Dihedral : 9.133 140.605 1730 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.59 % Allowed : 29.11 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1500 helix: 1.18 (0.23), residues: 522 sheet: 0.16 (0.33), residues: 278 loop : -0.49 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 754 HIS 0.005 0.001 HIS A 768 PHE 0.029 0.001 PHE G 876 TYR 0.011 0.001 TYR G 739 ARG 0.007 0.001 ARG G 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 141 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.4012 (OUTLIER) cc_final: 0.3786 (tm-30) REVERT: A 239 HIS cc_start: 0.7926 (OUTLIER) cc_final: 0.7367 (m90) REVERT: A 610 TRP cc_start: 0.3342 (OUTLIER) cc_final: 0.1987 (m-90) REVERT: A 765 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7856 (mt0) REVERT: A 768 HIS cc_start: 0.7669 (m-70) cc_final: 0.7387 (m-70) REVERT: A 785 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7177 (mp0) REVERT: A 815 ARG cc_start: 0.7484 (mtp85) cc_final: 0.6793 (mtm-85) REVERT: A 844 MET cc_start: 0.6899 (tmm) cc_final: 0.6612 (tmt) REVERT: G 239 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7159 (m90) REVERT: G 294 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8045 (ptm160) REVERT: G 493 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: G 601 ILE cc_start: 0.8014 (mt) cc_final: 0.7741 (mt) REVERT: G 766 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7450 (tt) REVERT: G 815 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.7074 (mtp85) REVERT: G 823 CYS cc_start: 0.7601 (t) cc_final: 0.7113 (t) outliers start: 49 outliers final: 21 residues processed: 178 average time/residue: 1.0239 time to fit residues: 200.9653 Evaluate side-chains 155 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 750 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 126 optimal weight: 0.0970 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 768 HIS A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 12518 Z= 0.338 Angle : 0.745 10.197 16952 Z= 0.367 Chirality : 0.046 0.212 1892 Planarity : 0.006 0.080 2134 Dihedral : 9.337 142.126 1726 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.77 % Allowed : 28.37 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.22), residues: 1500 helix: 0.90 (0.23), residues: 532 sheet: -0.03 (0.33), residues: 278 loop : -0.65 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 757 HIS 0.007 0.001 HIS A 768 PHE 0.026 0.002 PHE G 876 TYR 0.027 0.002 TYR G 591 ARG 0.012 0.001 ARG G 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 130 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7350 (m90) REVERT: A 270 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: A 274 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: A 610 TRP cc_start: 0.3720 (OUTLIER) cc_final: 0.2268 (m-90) REVERT: A 765 GLN cc_start: 0.8255 (mm-40) cc_final: 0.7974 (mt0) REVERT: A 785 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7359 (mp0) REVERT: A 800 ARG cc_start: 0.6755 (mmm160) cc_final: 0.5913 (tpm170) REVERT: A 815 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7077 (mtm-85) REVERT: A 844 MET cc_start: 0.6952 (tmm) cc_final: 0.6719 (tmt) REVERT: G 219 ARG cc_start: 0.6841 (mtt90) cc_final: 0.6487 (mtm-85) REVERT: G 239 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7252 (m90) REVERT: G 294 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8132 (ptm160) REVERT: G 493 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: G 766 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7501 (tt) REVERT: G 815 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7188 (mtp85) REVERT: G 823 CYS cc_start: 0.7718 (t) cc_final: 0.7155 (t) outliers start: 65 outliers final: 32 residues processed: 179 average time/residue: 1.0861 time to fit residues: 214.2691 Evaluate side-chains 160 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 120 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 622 ARG Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 501 LEU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 609 LEU Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 667 THR Chi-restraints excluded: chain G residue 680 VAL Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 699 LEU Chi-restraints excluded: chain G residue 708 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 127 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 chunk 142 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 768 HIS A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN G 858 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12518 Z= 0.232 Angle : 0.684 10.649 16952 Z= 0.337 Chirality : 0.043 0.222 1892 Planarity : 0.005 0.074 2134 Dihedral : 9.144 138.838 1726 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.67 % Allowed : 29.84 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1500 helix: 1.03 (0.23), residues: 522 sheet: 0.02 (0.33), residues: 278 loop : -0.56 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 757 HIS 0.007 0.001 HIS A 768 PHE 0.030 0.002 PHE G 876 TYR 0.015 0.001 TYR A 591 ARG 0.014 0.001 ARG G 622 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 131 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.3839 (tm-30) REVERT: A 239 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7352 (m90) REVERT: A 610 TRP cc_start: 0.3649 (OUTLIER) cc_final: 0.2211 (m-90) REVERT: A 701 ASP cc_start: 0.7064 (t0) cc_final: 0.6250 (p0) REVERT: A 785 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7480 (mp0) REVERT: A 800 ARG cc_start: 0.6741 (mmm160) cc_final: 0.5923 (tpm170) REVERT: A 815 ARG cc_start: 0.7462 (mtp85) cc_final: 0.6838 (mtm-85) REVERT: A 817 LYS cc_start: 0.7427 (mtmm) cc_final: 0.6873 (mtpm) REVERT: G 239 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7182 (m90) REVERT: G 294 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8047 (ptm160) REVERT: G 493 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: G 585 GLN cc_start: 0.6069 (tm-30) cc_final: 0.5094 (mp-120) REVERT: G 688 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6515 (mmpt) REVERT: G 744 LYS cc_start: 0.8139 (tptm) cc_final: 0.7911 (mppt) REVERT: G 751 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7342 (mp) REVERT: G 766 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7463 (tt) REVERT: G 815 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7185 (mtp85) REVERT: G 823 CYS cc_start: 0.7714 (t) cc_final: 0.7185 (t) outliers start: 50 outliers final: 25 residues processed: 172 average time/residue: 1.0617 time to fit residues: 201.3201 Evaluate side-chains 157 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 493 GLU Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 688 LYS Chi-restraints excluded: chain G residue 699 LEU Chi-restraints excluded: chain G residue 751 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 768 HIS A 818 HIS ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 613 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12518 Z= 0.243 Angle : 0.688 9.652 16952 Z= 0.342 Chirality : 0.044 0.209 1892 Planarity : 0.005 0.071 2134 Dihedral : 9.108 138.122 1726 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.30 % Allowed : 30.13 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1500 helix: 0.99 (0.23), residues: 522 sheet: 0.00 (0.33), residues: 278 loop : -0.57 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 757 HIS 0.006 0.001 HIS A 768 PHE 0.030 0.002 PHE G 876 TYR 0.017 0.002 TYR G 591 ARG 0.013 0.001 ARG G 622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 131 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 HIS cc_start: 0.7905 (OUTLIER) cc_final: 0.7348 (m90) REVERT: A 610 TRP cc_start: 0.3737 (OUTLIER) cc_final: 0.2246 (m-90) REVERT: A 701 ASP cc_start: 0.7166 (t0) cc_final: 0.6420 (p0) REVERT: A 785 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7528 (mp0) REVERT: A 815 ARG cc_start: 0.7330 (mtp85) cc_final: 0.6769 (mtm-85) REVERT: A 817 LYS cc_start: 0.7561 (mtmm) cc_final: 0.6995 (mtpm) REVERT: G 239 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.7092 (m90) REVERT: G 294 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8045 (ptm160) REVERT: G 688 LYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6582 (mmtt) REVERT: G 744 LYS cc_start: 0.8111 (tptm) cc_final: 0.7821 (mppt) REVERT: G 751 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7347 (mp) REVERT: G 766 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7487 (tt) REVERT: G 815 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.7177 (mtp85) REVERT: G 823 CYS cc_start: 0.7714 (t) cc_final: 0.7178 (t) outliers start: 45 outliers final: 26 residues processed: 167 average time/residue: 0.8731 time to fit residues: 160.8603 Evaluate side-chains 154 residues out of total 1364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 239 HIS Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 581 ARG Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 610 TRP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 843 MET Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 239 HIS Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 294 ARG Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 525 VAL Chi-restraints excluded: chain G residue 592 VAL Chi-restraints excluded: chain G residue 630 ILE Chi-restraints excluded: chain G residue 687 LEU Chi-restraints excluded: chain G residue 688 LYS Chi-restraints excluded: chain G residue 699 LEU Chi-restraints excluded: chain G residue 750 LEU Chi-restraints excluded: chain G residue 751 LEU Chi-restraints excluded: chain G residue 766 LEU Chi-restraints excluded: chain G residue 779 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 0.0970 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 GLN A 768 HIS A 818 HIS G 174 ASN G 613 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.221380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.181571 restraints weight = 15893.719| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 3.22 r_work: 0.4076 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12518 Z= 0.239 Angle : 0.687 9.247 16952 Z= 0.343 Chirality : 0.044 0.208 1892 Planarity : 0.005 0.069 2134 Dihedral : 9.089 137.213 1726 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.30 % Allowed : 30.65 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.22), residues: 1500 helix: 1.03 (0.23), residues: 522 sheet: 0.01 (0.33), residues: 278 loop : -0.60 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 757 HIS 0.006 0.001 HIS A 768 PHE 0.029 0.002 PHE G 876 TYR 0.016 0.001 TYR G 591 ARG 0.017 0.001 ARG A 746 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4224.65 seconds wall clock time: 75 minutes 14.56 seconds (4514.56 seconds total)