Starting phenix.real_space_refine on Tue Aug 26 11:49:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yut_34110/08_2025/7yut_34110.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yut_34110/08_2025/7yut_34110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yut_34110/08_2025/7yut_34110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yut_34110/08_2025/7yut_34110.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yut_34110/08_2025/7yut_34110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yut_34110/08_2025/7yut_34110.map" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 23028 2.51 5 N 6402 2.21 5 O 6894 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 191 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36450 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6075 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Time building chain proxies: 7.04, per 1000 atoms: 0.19 Number of scatterers: 36450 At special positions: 0 Unit cell: (159.9, 194.34, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 6894 8.00 N 6402 7.00 C 23028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 42 sheets defined 46.2% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 3.615A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.795A pdb=" N LEU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 139 removed outlier: 3.579A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 172 through 181 removed outlier: 4.034A pdb=" N ILE A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 236 removed outlier: 3.979A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 removed outlier: 4.731A pdb=" N ASP A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.746A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 removed outlier: 3.537A pdb=" N LYS A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 296 removed outlier: 3.517A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.895A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 412 removed outlier: 3.688A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.751A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 Processing helix chain 'A' and resid 523 through 535 removed outlier: 4.107A pdb=" N THR A 535 " --> pdb=" O ILE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 630 through 647 removed outlier: 3.654A pdb=" N LYS A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 636 " --> pdb=" O VAL A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.840A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 3.511A pdb=" N GLU A 744 " --> pdb=" O GLU A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.920A pdb=" N GLU A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 768 removed outlier: 3.732A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.631A pdb=" N GLY C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.585A pdb=" N LEU C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 136 removed outlier: 3.645A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.810A pdb=" N VAL C 152 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS C 153 " --> pdb=" O GLU C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 149 through 153' Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.774A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 235 removed outlier: 3.752A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 308 through 319 removed outlier: 3.835A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.679A pdb=" N VAL C 335 " --> pdb=" O GLU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 4.088A pdb=" N GLY C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 424 through 427 removed outlier: 3.555A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 424 through 427' Processing helix chain 'C' and resid 434 through 444 removed outlier: 3.968A pdb=" N ALA C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 483 removed outlier: 3.780A pdb=" N ASP C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 515 removed outlier: 3.901A pdb=" N SER C 514 " --> pdb=" O GLN C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 540 through 560 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.617A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 591 removed outlier: 3.516A pdb=" N THR C 590 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU C 591 " --> pdb=" O ALA C 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 587 through 591' Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.966A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 4.109A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 3.944A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 743 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU C 745 " --> pdb=" O GLN C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.889A pdb=" N GLY C 753 " --> pdb=" O GLU C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 769 removed outlier: 3.661A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 40 removed outlier: 3.890A pdb=" N LYS E 31 " --> pdb=" O ARG E 27 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 137 Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 172 through 182 removed outlier: 3.574A pdb=" N LEU E 182 " --> pdb=" O GLU E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 235 removed outlier: 3.579A pdb=" N ARG E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 256 removed outlier: 4.264A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 281 through 296 removed outlier: 3.571A pdb=" N VAL E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 315 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.925A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 386 through 391 Processing helix chain 'E' and resid 403 through 412 removed outlier: 4.125A pdb=" N HIS E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 412 " --> pdb=" O ALA E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 427 Processing helix chain 'E' and resid 434 through 444 removed outlier: 3.732A pdb=" N ALA E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 483 Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 515 Processing helix chain 'E' and resid 523 through 535 removed outlier: 4.090A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 removed outlier: 3.760A pdb=" N GLU E 544 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 579 removed outlier: 4.003A pdb=" N TYR E 577 " --> pdb=" O ASP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 646 removed outlier: 3.810A pdb=" N LYS E 634 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 652 removed outlier: 3.525A pdb=" N TYR E 651 " --> pdb=" O HIS E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 659 removed outlier: 4.144A pdb=" N TYR E 658 " --> pdb=" O GLU E 655 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 691 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.740A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 740 Processing helix chain 'E' and resid 761 through 768 removed outlier: 3.656A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 39 Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.598A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 150 removed outlier: 3.519A pdb=" N GLN D 148 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU D 149 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.696A pdb=" N ALA D 169 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 removed outlier: 3.841A pdb=" N LYS D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 234 removed outlier: 3.712A pdb=" N ARG D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS D 207 " --> pdb=" O PHE D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 251 removed outlier: 3.632A pdb=" N LYS D 251 " --> pdb=" O GLU D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.875A pdb=" N ASP D 271 " --> pdb=" O LEU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.946A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.977A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL D 335 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 386 through 391 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.511A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 443 removed outlier: 4.299A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 removed outlier: 3.502A pdb=" N ASN D 449 " --> pdb=" O GLU D 446 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR D 450 " --> pdb=" O GLN D 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 446 through 450' Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.901A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE D 477 " --> pdb=" O LEU D 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 473 through 477' Processing helix chain 'D' and resid 494 through 506 Processing helix chain 'D' and resid 506 through 515 Processing helix chain 'D' and resid 523 through 534 removed outlier: 3.824A pdb=" N ILE D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.697A pdb=" N TYR D 577 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 591 removed outlier: 4.118A pdb=" N GLU D 591 " --> pdb=" O ALA D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.536A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.648A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 747 through 752 Processing helix chain 'D' and resid 761 through 768 removed outlier: 3.786A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 39 removed outlier: 3.993A pdb=" N ARG F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 138 removed outlier: 3.798A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA F 137 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 168 Processing helix chain 'F' and resid 172 through 182 Processing helix chain 'F' and resid 185 through 235 removed outlier: 3.777A pdb=" N LYS F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 removed outlier: 3.895A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 280 through 294 removed outlier: 4.015A pdb=" N VAL F 285 " --> pdb=" O PRO F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 316 Processing helix chain 'F' and resid 324 through 337 removed outlier: 4.053A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL F 335 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG F 336 " --> pdb=" O TYR F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 372 removed outlier: 3.545A pdb=" N LEU F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 412 Processing helix chain 'F' and resid 423 through 427 removed outlier: 3.800A pdb=" N MET F 427 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 443 removed outlier: 4.101A pdb=" N ALA F 438 " --> pdb=" O ASP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 477 removed outlier: 3.977A pdb=" N THR F 476 " --> pdb=" O THR F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 515 Processing helix chain 'F' and resid 523 through 534 removed outlier: 3.702A pdb=" N ILE F 527 " --> pdb=" O THR F 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 560 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 579 removed outlier: 4.132A pdb=" N TYR F 577 " --> pdb=" O ASP F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 removed outlier: 3.659A pdb=" N LYS F 634 " --> pdb=" O GLY F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 718 through 728 Processing helix chain 'F' and resid 736 through 745 removed outlier: 4.229A pdb=" N ALA F 741 " --> pdb=" O ASP F 738 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 743 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU F 745 " --> pdb=" O GLN F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 3.965A pdb=" N LEU F 751 " --> pdb=" O PRO F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 768 removed outlier: 3.666A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 39 removed outlier: 3.934A pdb=" N ARG B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 139 removed outlier: 3.875A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN B 138 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 removed outlier: 3.703A pdb=" N GLU B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 184 through 236 removed outlier: 4.000A pdb=" N ARG B 188 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.569A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 391 Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.801A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 removed outlier: 4.161A pdb=" N MET B 427 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.106A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 449 removed outlier: 4.025A pdb=" N ASN B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 515 Processing helix chain 'B' and resid 524 through 534 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 574 through 579 Processing helix chain 'B' and resid 586 through 590 removed outlier: 3.918A pdb=" N GLU B 589 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 646 Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.681A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 745 removed outlier: 3.647A pdb=" N GLU B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 745 " --> pdb=" O ALA B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 4.227A pdb=" N LEU B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.986A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.730A pdb=" N VAL A 86 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 84 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLN A 93 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 105 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 5 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LEU A 43 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE A 45 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 44 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 69 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 375 through 380 removed outlier: 6.360A pdb=" N LYS A 375 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU A 420 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP A 422 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE A 379 " --> pdb=" O ASP A 422 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE A 468 " --> pdb=" O PRO A 417 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ILE A 419 " --> pdb=" O ILE A 468 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 470 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A 421 " --> pdb=" O THR A 470 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL A 354 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 5.586A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 598 Processing sheet with id=AA5, first strand: chain 'A' and resid 615 through 618 Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736 removed outlier: 7.057A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.752A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU C 82 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ARG C 76 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL C 84 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL C 86 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LYS C 72 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C 88 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL C 70 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 90 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N TRP C 65 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ALA C 48 " --> pdb=" O TRP C 65 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU C 5 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C 105 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 104 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.752A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 91 " --> pdb=" O SER C 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 377 through 380 removed outlier: 6.972A pdb=" N HIS C 377 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ASP C 422 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE C 379 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 522 removed outlier: 7.008A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 597 through 600 removed outlier: 3.892A pdb=" N ALA C 597 " --> pdb=" O ILE C 612 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 614 through 616 removed outlier: 6.167A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 732 through 736 removed outlier: 7.173A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 7 removed outlier: 4.147A pdb=" N LEU E 103 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.575A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL E 67 " --> pdb=" O LEU E 46 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.575A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ARG E 91 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE E 110 " --> pdb=" O ARG E 91 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLN E 93 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 378 through 380 removed outlier: 5.773A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 520 through 522 removed outlier: 6.061A pdb=" N GLU E 521 " --> pdb=" O ILE E 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 596 through 597 removed outlier: 3.514A pdb=" N ALA E 597 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 732 through 733 removed outlier: 3.715A pdb=" N ILE E 733 " --> pdb=" O GLU E 755 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.886A pdb=" N ARG D 106 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL D 25 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.886A pdb=" N ARG D 106 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP D 96 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL D 86 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS D 72 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA D 88 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 70 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA D 90 " --> pdb=" O GLN D 68 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 354 removed outlier: 3.746A pdb=" N ILE D 488 " --> pdb=" O VAL D 352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 378 through 380 removed outlier: 3.522A pdb=" N ILE D 379 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP D 422 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 419 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 520 through 522 removed outlier: 6.486A pdb=" N GLU D 521 " --> pdb=" O ILE D 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 596 through 601 removed outlier: 4.301A pdb=" N ALA D 597 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 705 through 706 removed outlier: 3.682A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 732 through 736 removed outlier: 6.843A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.642A pdb=" N LEU F 5 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 105 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 104 " --> pdb=" O ILE F 98 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG F 106 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP F 96 " --> pdb=" O ARG F 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.939A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU F 82 " --> pdb=" O ARG F 76 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ARG F 76 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 84 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA F 74 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL F 86 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS F 72 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TRP F 65 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA F 48 " --> pdb=" O TRP F 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 375 through 380 removed outlier: 7.623A pdb=" N ILE F 468 " --> pdb=" O PRO F 417 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 520 through 522 Processing sheet with id=AD7, first strand: chain 'F' and resid 596 through 601 removed outlier: 3.960A pdb=" N ALA F 615 " --> pdb=" O HIS F 664 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N HIS F 664 " --> pdb=" O ALA F 615 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL F 617 " --> pdb=" O ASP F 662 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 662 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL F 665 " --> pdb=" O SER F 624 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 700 through 702 removed outlier: 6.863A pdb=" N ALA F 701 " --> pdb=" O VAL F 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.740A pdb=" N VAL B 47 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA B 48 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP B 65 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET B 85 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 25 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 7 through 10 removed outlier: 3.740A pdb=" N VAL B 47 " --> pdb=" O ILE B 8 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA B 48 " --> pdb=" O TRP B 65 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TRP B 65 " --> pdb=" O ALA B 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY B 66 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA B 92 " --> pdb=" O GLY B 66 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 379 through 380 removed outlier: 6.952A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR B 470 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU B 421 " --> pdb=" O THR B 470 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N LEU B 353 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 352 " --> pdb=" O ILE B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 599 through 600 Processing sheet with id=AE4, first strand: chain 'B' and resid 613 through 616 removed outlier: 3.541A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 615 " --> pdb=" O HIS B 664 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 705 through 706 removed outlier: 3.855A pdb=" N GLU B 705 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 732 through 735 removed outlier: 6.427A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 1496 hydrogen bonds defined for protein. 4365 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: 6.79 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11078 1.33 - 1.45: 6155 1.45 - 1.58: 19618 1.58 - 1.70: 1 1.70 - 1.82: 252 Bond restraints: 37104 Sorted by residual: bond pdb=" C ALA A 671 " pdb=" N THR A 672 " ideal model delta sigma weight residual 1.330 1.214 0.116 1.37e-02 5.33e+03 7.20e+01 bond pdb=" C ARG A 479 " pdb=" N PRO A 480 " ideal model delta sigma weight residual 1.337 1.390 -0.053 1.11e-02 8.12e+03 2.28e+01 bond pdb=" C VAL B 712 " pdb=" N MET B 713 " ideal model delta sigma weight residual 1.333 1.218 0.114 2.74e-02 1.33e+03 1.74e+01 bond pdb=" C ASP C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 1.334 1.408 -0.074 2.34e-02 1.83e+03 1.01e+01 bond pdb=" C GLN E 504 " pdb=" N TYR E 505 " ideal model delta sigma weight residual 1.333 1.291 0.042 1.34e-02 5.57e+03 9.89e+00 ... (remaining 37099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.23: 49526 4.23 - 8.47: 684 8.47 - 12.70: 62 12.70 - 16.93: 7 16.93 - 21.17: 1 Bond angle restraints: 50280 Sorted by residual: angle pdb=" N HIS B 319 " pdb=" CA HIS B 319 " pdb=" C HIS B 319 " ideal model delta sigma weight residual 112.72 99.60 13.12 1.28e+00 6.10e-01 1.05e+02 angle pdb=" C ALA A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta sigma weight residual 120.60 134.43 -13.83 1.53e+00 4.27e-01 8.17e+01 angle pdb=" C HIS A 319 " pdb=" N TYR A 320 " pdb=" CA TYR A 320 " ideal model delta sigma weight residual 121.31 133.46 -12.15 1.49e+00 4.50e-01 6.65e+01 angle pdb=" C ASP A 457 " pdb=" N VAL A 458 " pdb=" CA VAL A 458 " ideal model delta sigma weight residual 123.33 117.38 5.95 8.70e-01 1.32e+00 4.68e+01 angle pdb=" N ALA B 679 " pdb=" CA ALA B 679 " pdb=" C ALA B 679 " ideal model delta sigma weight residual 111.71 103.42 8.29 1.34e+00 5.57e-01 3.83e+01 ... (remaining 50275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 21460 16.57 - 33.14: 1203 33.14 - 49.71: 204 49.71 - 66.29: 11 66.29 - 82.86: 48 Dihedral angle restraints: 22926 sinusoidal: 9540 harmonic: 13386 Sorted by residual: dihedral pdb=" CA ASP F 51 " pdb=" C ASP F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta harmonic sigma weight residual -180.00 -105.92 -74.08 0 5.00e+00 4.00e-02 2.19e+02 dihedral pdb=" CA ASP D 51 " pdb=" C ASP D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta harmonic sigma weight residual -180.00 -108.96 -71.04 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA ASP E 51 " pdb=" C ASP E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta harmonic sigma weight residual -180.00 -113.58 -66.42 0 5.00e+00 4.00e-02 1.76e+02 ... (remaining 22923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 5103 0.104 - 0.208: 588 0.208 - 0.312: 30 0.312 - 0.416: 2 0.416 - 0.521: 1 Chirality restraints: 5724 Sorted by residual: chirality pdb=" CB ILE D 574 " pdb=" CA ILE D 574 " pdb=" CG1 ILE D 574 " pdb=" CG2 ILE D 574 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CG LEU C 290 " pdb=" CB LEU C 290 " pdb=" CD1 LEU C 290 " pdb=" CD2 LEU C 290 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.47e+00 chirality pdb=" CG LEU E 351 " pdb=" CB LEU E 351 " pdb=" CD1 LEU E 351 " pdb=" CD2 LEU E 351 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 5721 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 51 " 0.058 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO E 52 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO E 52 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO E 52 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 51 " 0.058 5.00e-02 4.00e+02 8.96e-02 1.28e+01 pdb=" N PRO F 52 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO F 52 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO F 52 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 668 " -0.017 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C PRO F 668 " 0.061 2.00e-02 2.50e+03 pdb=" O PRO F 668 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 669 " -0.020 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 1403 2.68 - 3.24: 34795 3.24 - 3.79: 60839 3.79 - 4.35: 77441 4.35 - 4.90: 122419 Nonbonded interactions: 296897 Sorted by model distance: nonbonded pdb=" O PRO E 297 " pdb=" OH TYR E 460 " model vdw 2.131 3.040 nonbonded pdb=" OG1 THR C 535 " pdb=" OE1 GLU C 546 " model vdw 2.186 3.040 nonbonded pdb=" O GLU D 260 " pdb=" OG1 THR D 264 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR F 672 " pdb=" O LYS F 674 " model vdw 2.213 3.040 nonbonded pdb=" O PRO B 297 " pdb=" OH TYR B 460 " model vdw 2.239 3.040 ... (remaining 296892 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.640 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 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 : 0.010 0.116 37104 Z= 0.458 Angle : 1.337 21.167 50280 Z= 0.758 Chirality : 0.065 0.521 5724 Planarity : 0.009 0.090 6552 Dihedral : 11.311 82.858 14310 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.86 % Favored : 90.94 % Rotamer: Outliers : 0.59 % Allowed : 3.65 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 5.30 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.13 (0.10), residues: 4626 helix: -2.56 (0.09), residues: 1915 sheet: -2.34 (0.21), residues: 492 loop : -2.98 (0.11), residues: 2219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG E 567 TYR 0.050 0.004 TYR C 651 PHE 0.033 0.004 PHE A 557 TRP 0.057 0.006 TRP B 563 HIS 0.021 0.005 HIS D 726 Details of bonding type rmsd covalent geometry : bond 0.00969 (37104) covalent geometry : angle 1.33664 (50280) hydrogen bonds : bond 0.17483 ( 1480) hydrogen bonds : angle 7.74403 ( 4365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 492 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.5686 (mmt) cc_final: 0.5271 (mpp) REVERT: A 446 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9099 (mp0) REVERT: A 633 MET cc_start: 0.8772 (mmm) cc_final: 0.8435 (mtm) REVERT: A 657 PHE cc_start: 0.6603 (p90) cc_final: 0.6300 (p90) REVERT: A 683 MET cc_start: 0.9115 (mtt) cc_final: 0.8794 (mtt) REVERT: C 437 SER cc_start: 0.8720 (m) cc_final: 0.8489 (p) REVERT: C 509 LYS cc_start: 0.8721 (mttm) cc_final: 0.8462 (mptt) REVERT: C 545 ARG cc_start: 0.8770 (mtm180) cc_final: 0.8291 (mmp80) REVERT: C 663 LEU cc_start: 0.8871 (mt) cc_final: 0.8623 (mp) REVERT: C 698 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6150 (pp-130) REVERT: E 430 ASP cc_start: 0.6698 (m-30) cc_final: 0.6273 (p0) REVERT: E 545 ARG cc_start: 0.7592 (mtm180) cc_final: 0.6499 (mmt180) REVERT: E 632 VAL cc_start: 0.8710 (m) cc_final: 0.7794 (m) REVERT: E 633 MET cc_start: 0.8457 (mmt) cc_final: 0.8114 (mmt) REVERT: D 38 MET cc_start: 0.1800 (mmt) cc_final: 0.0958 (mtt) REVERT: D 220 ASN cc_start: 0.7154 (m110) cc_final: 0.6852 (m-40) REVERT: D 230 MET cc_start: 0.7077 (ttp) cc_final: 0.6758 (ttp) REVERT: D 536 ARG cc_start: 0.7254 (mmt180) cc_final: 0.6757 (mmt180) REVERT: D 590 THR cc_start: 0.7761 (m) cc_final: 0.7200 (m) REVERT: D 702 MET cc_start: 0.8821 (pmt) cc_final: 0.8378 (pmm) REVERT: F 97 TYR cc_start: 0.7436 (p90) cc_final: 0.7117 (p90) REVERT: F 138 ASN cc_start: 0.7333 (m110) cc_final: 0.7129 (m110) REVERT: F 328 ARG cc_start: 0.8972 (mpt90) cc_final: 0.8513 (mmm-85) REVERT: F 368 ILE cc_start: 0.8800 (mt) cc_final: 0.8538 (mt) REVERT: F 505 TYR cc_start: 0.7654 (m-80) cc_final: 0.7332 (m-10) REVERT: F 625 LEU cc_start: 0.8628 (pt) cc_final: 0.8132 (mp) REVERT: F 633 MET cc_start: 0.9178 (mmt) cc_final: 0.8855 (mtt) REVERT: F 642 THR cc_start: 0.8776 (m) cc_final: 0.8566 (m) REVERT: F 702 MET cc_start: 0.7051 (ptp) cc_final: 0.6521 (pmm) REVERT: B 520 ILE cc_start: 0.7335 (mt) cc_final: 0.7117 (mm) outliers start: 23 outliers final: 7 residues processed: 511 average time/residue: 0.2347 time to fit residues: 185.5921 Evaluate side-chains 319 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 311 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 40.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 40.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 278 GLN A 310 HIS ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN A 649 GLN A 739 ASN C 73 GLN C 83 GLN C 234 GLN C 664 HIS E 310 HIS E 346 ASN ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 HIS E 666 HIS E 727 GLN E 739 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN D 377 HIS D 447 GLN D 472 ASN D 504 GLN F 18 HIS F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 739 ASN B 138 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN B 377 HIS B 393 HIS B 510 GLN ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.131859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.090789 restraints weight = 133159.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.089435 restraints weight = 128621.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.088912 restraints weight = 120083.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088708 restraints weight = 112523.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.088675 restraints weight = 113055.016| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 37104 Z= 0.194 Angle : 0.770 14.926 50280 Z= 0.398 Chirality : 0.046 0.244 5724 Planarity : 0.007 0.077 6552 Dihedral : 7.100 62.353 5106 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.87 % Favored : 93.06 % Rotamer: Outliers : 0.15 % Allowed : 3.29 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 3.03 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.11), residues: 4626 helix: -1.11 (0.11), residues: 1969 sheet: -2.11 (0.22), residues: 483 loop : -2.71 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 212 TYR 0.024 0.002 TYR A 577 PHE 0.020 0.002 PHE B 657 TRP 0.028 0.003 TRP D 563 HIS 0.012 0.002 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00417 (37104) covalent geometry : angle 0.77013 (50280) hydrogen bonds : bond 0.04837 ( 1480) hydrogen bonds : angle 5.79165 ( 4365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 384 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 ILE cc_start: 0.8287 (mp) cc_final: 0.7952 (mp) REVERT: A 409 MET cc_start: 0.9340 (tpt) cc_final: 0.9063 (tpt) REVERT: A 633 MET cc_start: 0.8790 (mmm) cc_final: 0.8261 (mtm) REVERT: A 657 PHE cc_start: 0.6949 (p90) cc_final: 0.6701 (p90) REVERT: C 258 MET cc_start: 0.0691 (mmt) cc_final: 0.0284 (mmt) REVERT: C 485 MET cc_start: 0.8010 (mpp) cc_final: 0.7475 (pmm) REVERT: C 545 ARG cc_start: 0.8808 (mtm180) cc_final: 0.8394 (mmp80) REVERT: C 663 LEU cc_start: 0.8987 (mt) cc_final: 0.8652 (mp) REVERT: E 337 GLN cc_start: 0.6716 (mm-40) cc_final: 0.6506 (mm-40) REVERT: E 430 ASP cc_start: 0.6624 (m-30) cc_final: 0.6172 (m-30) REVERT: E 633 MET cc_start: 0.8627 (mmt) cc_final: 0.8236 (mmt) REVERT: E 635 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: D 38 MET cc_start: 0.2854 (mmt) cc_final: 0.2165 (mtt) REVERT: D 139 HIS cc_start: 0.5638 (m90) cc_final: 0.3818 (m90) REVERT: D 203 PHE cc_start: 0.7211 (t80) cc_final: 0.6907 (m-80) REVERT: D 258 MET cc_start: 0.2994 (mtt) cc_final: 0.2167 (mtt) REVERT: F 328 ARG cc_start: 0.8974 (mpt90) cc_final: 0.8620 (mmm160) REVERT: F 549 LYS cc_start: 0.8075 (tmtt) cc_final: 0.7787 (tmtt) REVERT: F 625 LEU cc_start: 0.8619 (pt) cc_final: 0.8101 (mp) REVERT: F 633 MET cc_start: 0.9135 (mmt) cc_final: 0.8803 (mtt) REVERT: F 702 MET cc_start: 0.6892 (ptp) cc_final: 0.6158 (pmm) REVERT: B 377 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7228 (t-90) REVERT: B 421 LEU cc_start: 0.9595 (mt) cc_final: 0.9387 (mt) REVERT: B 427 MET cc_start: 0.7231 (ptp) cc_final: 0.6788 (ptp) REVERT: B 632 VAL cc_start: 0.8613 (m) cc_final: 0.7913 (m) outliers start: 6 outliers final: 1 residues processed: 389 average time/residue: 0.2182 time to fit residues: 133.1856 Evaluate side-chains 289 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 286 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 461 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 chunk 409 optimal weight: 30.0000 chunk 451 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 overall best weight: 7.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 GLN E 407 HIS E 649 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 377 HIS ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN F 454 HIS ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 HIS ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 234 GLN B 407 HIS ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.129706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.083888 restraints weight = 142911.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.083473 restraints weight = 128456.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.083362 restraints weight = 119647.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.083194 restraints weight = 108018.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.083183 restraints weight = 108492.321| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.163 37104 Z= 0.239 Angle : 0.793 16.195 50280 Z= 0.406 Chirality : 0.047 0.231 5724 Planarity : 0.006 0.079 6552 Dihedral : 6.841 60.438 5106 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.84 % Favored : 91.07 % Rotamer: Outliers : 0.13 % Allowed : 4.39 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.64 (0.11), residues: 4626 helix: -0.71 (0.11), residues: 1985 sheet: -2.34 (0.21), residues: 491 loop : -2.63 (0.12), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 336 TYR 0.035 0.002 TYR B 493 PHE 0.023 0.002 PHE B 657 TRP 0.050 0.003 TRP B 563 HIS 0.010 0.002 HIS D 647 Details of bonding type rmsd covalent geometry : bond 0.00511 (37104) covalent geometry : angle 0.79343 (50280) hydrogen bonds : bond 0.04772 ( 1480) hydrogen bonds : angle 5.59383 ( 4365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 339 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.9391 (tpt) cc_final: 0.9014 (tpt) REVERT: A 496 MET cc_start: 0.8817 (mpp) cc_final: 0.8559 (mpp) REVERT: A 516 MET cc_start: 0.4053 (ttt) cc_final: 0.3178 (ttt) REVERT: A 633 MET cc_start: 0.8829 (mmm) cc_final: 0.8411 (mtm) REVERT: A 657 PHE cc_start: 0.6987 (p90) cc_final: 0.6730 (p90) REVERT: C 160 MET cc_start: -0.1049 (mpp) cc_final: -0.1957 (ppp) REVERT: C 246 LEU cc_start: 0.4619 (mp) cc_final: 0.4291 (tp) REVERT: C 258 MET cc_start: 0.1117 (mmt) cc_final: 0.0483 (mmt) REVERT: C 545 ARG cc_start: 0.8749 (mtm180) cc_final: 0.8464 (mmp80) REVERT: C 663 LEU cc_start: 0.8976 (mt) cc_final: 0.8675 (mp) REVERT: E 85 MET cc_start: 0.2583 (mmp) cc_final: 0.2126 (ttt) REVERT: E 409 MET cc_start: 0.7982 (tpt) cc_final: 0.7592 (tpt) REVERT: E 493 TYR cc_start: 0.6101 (OUTLIER) cc_final: 0.5429 (m-10) REVERT: E 633 MET cc_start: 0.8484 (mmt) cc_final: 0.8026 (mmt) REVERT: D 38 MET cc_start: 0.3001 (mmt) cc_final: 0.2383 (mtt) REVERT: D 139 HIS cc_start: 0.5595 (m90) cc_final: 0.5086 (m90) REVERT: D 258 MET cc_start: 0.3329 (mtt) cc_final: 0.2775 (mtt) REVERT: D 276 MET cc_start: 0.6298 (ttm) cc_final: 0.5979 (ttt) REVERT: D 602 TRP cc_start: 0.6017 (t-100) cc_final: 0.5234 (t-100) REVERT: D 675 ASP cc_start: 0.8759 (m-30) cc_final: 0.7909 (p0) REVERT: F 427 MET cc_start: 0.5239 (tpp) cc_final: 0.4145 (mmm) REVERT: F 625 LEU cc_start: 0.8599 (pt) cc_final: 0.8211 (mp) REVERT: F 631 GLU cc_start: 0.9303 (pm20) cc_final: 0.9102 (pm20) REVERT: F 702 MET cc_start: 0.6846 (ptp) cc_final: 0.5834 (pmm) REVERT: B 422 ASP cc_start: 0.8740 (m-30) cc_final: 0.8309 (m-30) outliers start: 5 outliers final: 1 residues processed: 343 average time/residue: 0.2068 time to fit residues: 113.8116 Evaluate side-chains 273 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 234 optimal weight: 20.0000 chunk 354 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 50.0000 chunk 336 optimal weight: 40.0000 chunk 409 optimal weight: 9.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 649 GLN E 407 HIS E 593 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.130419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.084269 restraints weight = 141016.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.083736 restraints weight = 131721.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.083166 restraints weight = 129347.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.083224 restraints weight = 114056.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.083072 restraints weight = 110345.357| |-----------------------------------------------------------------------------| r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 37104 Z= 0.223 Angle : 0.760 14.064 50280 Z= 0.387 Chirality : 0.047 0.229 5724 Planarity : 0.006 0.078 6552 Dihedral : 6.633 57.625 5106 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 20.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 0.03 % Allowed : 3.36 % Favored : 96.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.12), residues: 4626 helix: -0.41 (0.11), residues: 1983 sheet: -2.31 (0.21), residues: 503 loop : -2.57 (0.12), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 484 TYR 0.032 0.002 TYR B 493 PHE 0.023 0.002 PHE B 657 TRP 0.044 0.002 TRP B 602 HIS 0.010 0.002 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00481 (37104) covalent geometry : angle 0.75969 (50280) hydrogen bonds : bond 0.04488 ( 1480) hydrogen bonds : angle 5.41427 ( 4365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6395 (tpt) cc_final: 0.6071 (tpt) REVERT: A 406 ILE cc_start: 0.8079 (mp) cc_final: 0.7868 (mp) REVERT: A 409 MET cc_start: 0.9356 (tpt) cc_final: 0.8978 (tpt) REVERT: A 496 MET cc_start: 0.8811 (mpp) cc_final: 0.8486 (mpp) REVERT: A 516 MET cc_start: 0.4154 (ttt) cc_final: 0.3617 (ttt) REVERT: A 633 MET cc_start: 0.8865 (mmm) cc_final: 0.8652 (mpp) REVERT: A 657 PHE cc_start: 0.6995 (p90) cc_final: 0.6470 (p90) REVERT: C 160 MET cc_start: -0.1169 (mpp) cc_final: -0.2035 (ppp) REVERT: C 258 MET cc_start: 0.1288 (mmt) cc_final: 0.0571 (mmt) REVERT: C 545 ARG cc_start: 0.8780 (mtm180) cc_final: 0.8478 (mmp80) REVERT: C 633 MET cc_start: 0.8533 (mpp) cc_final: 0.8271 (mmt) REVERT: C 663 LEU cc_start: 0.8960 (mt) cc_final: 0.8697 (mp) REVERT: E 75 MET cc_start: 0.3649 (pmm) cc_final: 0.3033 (pmm) REVERT: E 85 MET cc_start: 0.2140 (mmp) cc_final: 0.1776 (ttt) REVERT: E 237 LEU cc_start: 0.6197 (pt) cc_final: 0.5889 (pt) REVERT: E 427 MET cc_start: 0.8583 (tmm) cc_final: 0.8372 (tmm) REVERT: E 633 MET cc_start: 0.8529 (mmt) cc_final: 0.8025 (mmt) REVERT: E 683 MET cc_start: 0.8795 (mtt) cc_final: 0.8099 (mtt) REVERT: D 38 MET cc_start: 0.3019 (mmt) cc_final: 0.2272 (mtt) REVERT: D 276 MET cc_start: 0.6569 (ttm) cc_final: 0.6329 (ttm) REVERT: D 602 TRP cc_start: 0.6165 (t-100) cc_final: 0.5379 (t-100) REVERT: D 675 ASP cc_start: 0.8704 (m-30) cc_final: 0.7902 (p0) REVERT: F 427 MET cc_start: 0.5342 (tpp) cc_final: 0.4987 (tpt) REVERT: F 475 GLN cc_start: 0.8609 (mt0) cc_final: 0.8265 (mp10) REVERT: F 625 LEU cc_start: 0.8590 (pt) cc_final: 0.8214 (mp) REVERT: F 702 MET cc_start: 0.6702 (ptp) cc_final: 0.5685 (pmm) REVERT: B 331 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7814 (mt-10) REVERT: B 602 TRP cc_start: 0.5364 (p-90) cc_final: 0.4738 (p-90) outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.2078 time to fit residues: 113.6806 Evaluate side-chains 263 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 250 optimal weight: 50.0000 chunk 154 optimal weight: 50.0000 chunk 279 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 161 optimal weight: 0.6980 chunk 75 optimal weight: 0.0030 chunk 232 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 356 optimal weight: 4.9990 chunk 255 optimal weight: 30.0000 chunk 405 optimal weight: 20.0000 overall best weight: 3.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 277 GLN D 472 ASN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 638 GLN ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.142239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.104973 restraints weight = 248436.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.105319 restraints weight = 177063.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.105377 restraints weight = 134338.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.104995 restraints weight = 126892.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.105036 restraints weight = 122710.864| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 37104 Z= 0.144 Angle : 0.660 11.982 50280 Z= 0.337 Chirality : 0.044 0.220 5724 Planarity : 0.006 0.077 6552 Dihedral : 6.213 55.632 5106 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.12), residues: 4626 helix: 0.02 (0.11), residues: 1997 sheet: -2.00 (0.22), residues: 494 loop : -2.48 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 432 TYR 0.032 0.002 TYR B 768 PHE 0.013 0.001 PHE A 45 TRP 0.051 0.002 TRP D 563 HIS 0.007 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00312 (37104) covalent geometry : angle 0.66042 (50280) hydrogen bonds : bond 0.03907 ( 1480) hydrogen bonds : angle 5.02668 ( 4365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6353 (tpt) cc_final: 0.6004 (tpt) REVERT: A 496 MET cc_start: 0.8844 (mpp) cc_final: 0.8520 (mpp) REVERT: A 516 MET cc_start: 0.4399 (ttt) cc_final: 0.4026 (ttt) REVERT: A 633 MET cc_start: 0.8924 (mmm) cc_final: 0.8541 (mtm) REVERT: A 683 MET cc_start: 0.8973 (mtt) cc_final: 0.8735 (mtt) REVERT: A 748 LYS cc_start: 0.6780 (mmtt) cc_final: 0.6012 (mmpt) REVERT: C 160 MET cc_start: -0.1975 (mpp) cc_final: -0.2777 (ppp) REVERT: C 258 MET cc_start: 0.1806 (mmt) cc_final: 0.1184 (mmt) REVERT: C 545 ARG cc_start: 0.8765 (mtm180) cc_final: 0.8407 (mmp80) REVERT: C 663 LEU cc_start: 0.8919 (mt) cc_final: 0.8714 (mp) REVERT: E 75 MET cc_start: 0.4021 (pmm) cc_final: 0.3566 (pmm) REVERT: E 85 MET cc_start: 0.2317 (mmp) cc_final: 0.2037 (ttt) REVERT: E 409 MET cc_start: 0.7734 (tpt) cc_final: 0.6914 (tpt) REVERT: E 427 MET cc_start: 0.8749 (tmm) cc_final: 0.8313 (tmm) REVERT: E 545 ARG cc_start: 0.7698 (ttp-110) cc_final: 0.7006 (mmt180) REVERT: E 633 MET cc_start: 0.8332 (mmt) cc_final: 0.7796 (mmt) REVERT: E 683 MET cc_start: 0.8772 (mtt) cc_final: 0.7725 (mtt) REVERT: D 38 MET cc_start: 0.5608 (mmt) cc_final: 0.5236 (mtt) REVERT: D 483 ASP cc_start: 0.7270 (p0) cc_final: 0.7009 (p0) REVERT: D 485 MET cc_start: 0.6787 (mmm) cc_final: 0.6523 (mmm) REVERT: D 602 TRP cc_start: 0.5987 (t-100) cc_final: 0.5257 (t-100) REVERT: D 633 MET cc_start: 0.8276 (mtm) cc_final: 0.7993 (mtt) REVERT: D 675 ASP cc_start: 0.8637 (m-30) cc_final: 0.7861 (p0) REVERT: F 309 ASN cc_start: 0.9093 (m-40) cc_final: 0.8885 (m110) REVERT: F 485 MET cc_start: 0.6571 (mmp) cc_final: 0.6162 (tpp) REVERT: F 625 LEU cc_start: 0.8624 (pt) cc_final: 0.8096 (mp) REVERT: F 702 MET cc_start: 0.6338 (ptp) cc_final: 0.5655 (pmm) REVERT: B 331 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7800 (mt-10) REVERT: B 332 TYR cc_start: 0.6813 (t80) cc_final: 0.6447 (t80) REVERT: B 378 ARG cc_start: 0.8289 (mtp180) cc_final: 0.8075 (mtp180) REVERT: B 632 VAL cc_start: 0.8290 (m) cc_final: 0.8076 (m) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.2519 time to fit residues: 140.8356 Evaluate side-chains 274 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 10 optimal weight: 50.0000 chunk 388 optimal weight: 50.0000 chunk 171 optimal weight: 8.9990 chunk 332 optimal weight: 10.0000 chunk 459 optimal weight: 8.9990 chunk 268 optimal weight: 0.0010 chunk 445 optimal weight: 1.9990 chunk 375 optimal weight: 8.9990 chunk 250 optimal weight: 50.0000 chunk 283 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 659 ASN ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 337 GLN D 138 ASN D 472 ASN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.131863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.088592 restraints weight = 138970.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.084367 restraints weight = 136080.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.083794 restraints weight = 127299.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.083856 restraints weight = 113892.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.083858 restraints weight = 111165.169| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 37104 Z= 0.185 Angle : 0.710 12.579 50280 Z= 0.360 Chirality : 0.045 0.215 5724 Planarity : 0.006 0.134 6552 Dihedral : 6.177 54.295 5106 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.50 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.65 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.12), residues: 4626 helix: 0.09 (0.11), residues: 1996 sheet: -1.99 (0.22), residues: 501 loop : -2.42 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 484 TYR 0.024 0.002 TYR B 493 PHE 0.038 0.002 PHE B 203 TRP 0.046 0.002 TRP B 602 HIS 0.007 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00400 (37104) covalent geometry : angle 0.71007 (50280) hydrogen bonds : bond 0.04054 ( 1480) hydrogen bonds : angle 5.09675 ( 4365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6360 (tpt) cc_final: 0.5992 (tpt) REVERT: A 370 ARG cc_start: 0.8202 (mtm180) cc_final: 0.7268 (ttt-90) REVERT: A 496 MET cc_start: 0.8797 (mpp) cc_final: 0.8559 (mpp) REVERT: A 516 MET cc_start: 0.4211 (ttt) cc_final: 0.3768 (ttt) REVERT: C 160 MET cc_start: -0.2042 (mpp) cc_final: -0.2842 (ppp) REVERT: C 258 MET cc_start: 0.0380 (mmt) cc_final: -0.0248 (mmt) REVERT: C 545 ARG cc_start: 0.8845 (mtm180) cc_final: 0.8477 (mmp80) REVERT: C 633 MET cc_start: 0.8782 (mpp) cc_final: 0.8521 (mmt) REVERT: C 663 LEU cc_start: 0.9189 (mt) cc_final: 0.8963 (mp) REVERT: E 75 MET cc_start: 0.3433 (pmm) cc_final: 0.2691 (pmm) REVERT: E 85 MET cc_start: 0.1921 (mmp) cc_final: 0.1421 (ttt) REVERT: E 230 MET cc_start: 0.7618 (ppp) cc_final: 0.7398 (ppp) REVERT: E 276 MET cc_start: 0.6009 (ttp) cc_final: 0.5679 (ttm) REVERT: E 331 GLU cc_start: 0.8464 (pm20) cc_final: 0.8097 (pm20) REVERT: E 409 MET cc_start: 0.7653 (tpt) cc_final: 0.6786 (tpt) REVERT: E 633 MET cc_start: 0.8506 (mmt) cc_final: 0.7934 (mmt) REVERT: E 698 MET cc_start: 0.6255 (mtm) cc_final: 0.6044 (mtp) REVERT: D 38 MET cc_start: 0.2623 (mmt) cc_final: 0.1830 (mtt) REVERT: D 258 MET cc_start: 0.2751 (mtt) cc_final: 0.1927 (mtt) REVERT: D 602 TRP cc_start: 0.6090 (t-100) cc_final: 0.5202 (t-100) REVERT: D 675 ASP cc_start: 0.8780 (m-30) cc_final: 0.8060 (p0) REVERT: F 97 TYR cc_start: 0.7678 (p90) cc_final: 0.7425 (p90) REVERT: F 309 ASN cc_start: 0.8910 (m-40) cc_final: 0.8626 (m110) REVERT: F 625 LEU cc_start: 0.8545 (pt) cc_final: 0.8048 (mp) REVERT: F 664 HIS cc_start: 0.8372 (p90) cc_final: 0.7874 (p-80) REVERT: F 702 MET cc_start: 0.6979 (ptp) cc_final: 0.5895 (pmm) REVERT: B 331 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 378 ARG cc_start: 0.8307 (mtp180) cc_final: 0.8086 (mtp180) REVERT: B 385 ARG cc_start: 0.9257 (mtm180) cc_final: 0.9045 (mtm110) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.2527 time to fit residues: 132.9476 Evaluate side-chains 260 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 62 optimal weight: 20.0000 chunk 440 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 446 optimal weight: 3.9990 chunk 19 optimal weight: 50.0000 chunk 171 optimal weight: 7.9990 chunk 154 optimal weight: 50.0000 chunk 349 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 138 ASN A 177 GLN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN E 407 HIS D 472 ASN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 638 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.138960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.101781 restraints weight = 252300.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.102155 restraints weight = 184181.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.101227 restraints weight = 141797.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.101604 restraints weight = 128427.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.099222 restraints weight = 118661.588| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 37104 Z= 0.262 Angle : 0.835 14.833 50280 Z= 0.423 Chirality : 0.049 0.207 5724 Planarity : 0.007 0.086 6552 Dihedral : 6.557 55.589 5106 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.29 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.12), residues: 4626 helix: -0.22 (0.11), residues: 1991 sheet: -2.23 (0.23), residues: 475 loop : -2.47 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 432 TYR 0.036 0.002 TYR B 493 PHE 0.031 0.002 PHE B 203 TRP 0.038 0.003 TRP D 563 HIS 0.012 0.002 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00568 (37104) covalent geometry : angle 0.83470 (50280) hydrogen bonds : bond 0.04626 ( 1480) hydrogen bonds : angle 5.46070 ( 4365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7856 (tpt) cc_final: 0.7147 (tpt) REVERT: A 427 MET cc_start: 0.7573 (mmp) cc_final: 0.7143 (mmp) REVERT: A 496 MET cc_start: 0.8855 (mpp) cc_final: 0.8522 (mpp) REVERT: A 516 MET cc_start: 0.4636 (ttt) cc_final: 0.4295 (ttt) REVERT: C 258 MET cc_start: 0.1509 (mmt) cc_final: 0.0690 (mmt) REVERT: C 545 ARG cc_start: 0.8796 (mtm180) cc_final: 0.8467 (mmp80) REVERT: C 663 LEU cc_start: 0.9110 (mt) cc_final: 0.8864 (mp) REVERT: E 75 MET cc_start: 0.4083 (pmm) cc_final: 0.3564 (pmm) REVERT: E 85 MET cc_start: 0.2232 (mmp) cc_final: 0.1952 (ttt) REVERT: E 217 MET cc_start: 0.7085 (tpt) cc_final: 0.6852 (mmt) REVERT: E 230 MET cc_start: 0.7574 (ppp) cc_final: 0.7215 (ppp) REVERT: E 258 MET cc_start: 0.5778 (mtt) cc_final: 0.5293 (mtt) REVERT: E 276 MET cc_start: 0.5542 (ttp) cc_final: 0.4515 (ttm) REVERT: E 409 MET cc_start: 0.7817 (tpt) cc_final: 0.7067 (tpt) REVERT: E 633 MET cc_start: 0.8435 (mmt) cc_final: 0.7929 (mmt) REVERT: E 635 GLU cc_start: 0.8273 (pm20) cc_final: 0.7873 (pm20) REVERT: E 683 MET cc_start: 0.8913 (mtt) cc_final: 0.7434 (mtt) REVERT: D 38 MET cc_start: 0.5913 (mmt) cc_final: 0.5546 (mtt) REVERT: D 483 ASP cc_start: 0.7533 (p0) cc_final: 0.7166 (p0) REVERT: D 675 ASP cc_start: 0.8675 (m-30) cc_final: 0.8007 (p0) REVERT: D 713 MET cc_start: 0.8933 (mmm) cc_final: 0.8615 (mmm) REVERT: F 309 ASN cc_start: 0.8995 (m-40) cc_final: 0.8753 (m-40) REVERT: F 427 MET cc_start: 0.5970 (tpt) cc_final: 0.5662 (tpt) REVERT: F 475 GLN cc_start: 0.8639 (mt0) cc_final: 0.8231 (mp10) REVERT: F 485 MET cc_start: 0.6892 (mmp) cc_final: 0.6140 (tpp) REVERT: F 664 HIS cc_start: 0.8201 (p90) cc_final: 0.7874 (p90) REVERT: F 698 MET cc_start: 0.8088 (mtt) cc_final: 0.7658 (mmm) REVERT: F 702 MET cc_start: 0.6564 (ptp) cc_final: 0.5920 (pmm) REVERT: B 331 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7869 (mt-10) REVERT: B 385 ARG cc_start: 0.8460 (mtm180) cc_final: 0.8101 (mtm110) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2470 time to fit residues: 121.9364 Evaluate side-chains 251 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 155 optimal weight: 8.9990 chunk 38 optimal weight: 0.1980 chunk 67 optimal weight: 6.9990 chunk 345 optimal weight: 6.9990 chunk 395 optimal weight: 10.0000 chunk 12 optimal weight: 50.0000 chunk 278 optimal weight: 0.0170 chunk 311 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 overall best weight: 4.4424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN D 666 HIS F 313 GLN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.132046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.086171 restraints weight = 138222.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.085612 restraints weight = 135117.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.085116 restraints weight = 124029.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.084997 restraints weight = 120185.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085129 restraints weight = 112868.741| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 37104 Z= 0.167 Angle : 0.707 14.715 50280 Z= 0.358 Chirality : 0.045 0.203 5724 Planarity : 0.006 0.074 6552 Dihedral : 6.224 53.591 5106 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.12), residues: 4626 helix: 0.08 (0.11), residues: 2000 sheet: -1.95 (0.24), residues: 463 loop : -2.35 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 484 TYR 0.023 0.002 TYR A 460 PHE 0.024 0.002 PHE B 203 TRP 0.053 0.002 TRP B 563 HIS 0.009 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00367 (37104) covalent geometry : angle 0.70747 (50280) hydrogen bonds : bond 0.03952 ( 1480) hydrogen bonds : angle 5.11986 ( 4365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.5710 (tpt) cc_final: 0.5487 (tpt) REVERT: A 496 MET cc_start: 0.8811 (mpp) cc_final: 0.8508 (mpp) REVERT: A 516 MET cc_start: 0.4226 (ttt) cc_final: 0.3915 (ttt) REVERT: C 160 MET cc_start: -0.1802 (mpp) cc_final: -0.2513 (ppp) REVERT: C 258 MET cc_start: 0.0787 (mmt) cc_final: 0.0003 (mmt) REVERT: C 439 MET cc_start: 0.9318 (mmp) cc_final: 0.9114 (mmp) REVERT: C 485 MET cc_start: 0.8149 (mpp) cc_final: 0.7768 (mpp) REVERT: C 545 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8403 (mmp80) REVERT: C 633 MET cc_start: 0.8638 (mpp) cc_final: 0.8341 (mmt) REVERT: C 663 LEU cc_start: 0.8931 (mt) cc_final: 0.8720 (mp) REVERT: E 75 MET cc_start: 0.3858 (pmm) cc_final: 0.3142 (pmm) REVERT: E 85 MET cc_start: 0.1990 (mmp) cc_final: 0.1560 (ttt) REVERT: E 230 MET cc_start: 0.7462 (ppp) cc_final: 0.7120 (ppp) REVERT: E 258 MET cc_start: 0.5728 (mtt) cc_final: 0.5208 (mtt) REVERT: E 276 MET cc_start: 0.5067 (ttp) cc_final: 0.4784 (ttm) REVERT: E 409 MET cc_start: 0.7746 (tpt) cc_final: 0.7006 (tpt) REVERT: E 633 MET cc_start: 0.8508 (mmt) cc_final: 0.7933 (mmt) REVERT: E 635 GLU cc_start: 0.8249 (pm20) cc_final: 0.7871 (pm20) REVERT: E 683 MET cc_start: 0.8850 (mtt) cc_final: 0.7922 (mtt) REVERT: D 38 MET cc_start: 0.3511 (mmt) cc_final: 0.2729 (mtt) REVERT: D 258 MET cc_start: 0.3276 (mtt) cc_final: 0.2519 (mtt) REVERT: D 483 ASP cc_start: 0.7507 (p0) cc_final: 0.7172 (p0) REVERT: D 675 ASP cc_start: 0.8609 (m-30) cc_final: 0.8117 (p0) REVERT: F 309 ASN cc_start: 0.8912 (m-40) cc_final: 0.8610 (m110) REVERT: F 427 MET cc_start: 0.5607 (tpt) cc_final: 0.5215 (tpt) REVERT: F 698 MET cc_start: 0.8111 (mtt) cc_final: 0.7596 (mmt) REVERT: F 702 MET cc_start: 0.6737 (ptp) cc_final: 0.5932 (pmm) REVERT: B 331 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7752 (mt-10) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.2453 time to fit residues: 126.7068 Evaluate side-chains 260 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 253 optimal weight: 10.0000 chunk 386 optimal weight: 50.0000 chunk 418 optimal weight: 8.9990 chunk 381 optimal weight: 9.9990 chunk 146 optimal weight: 0.0020 chunk 391 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 403 optimal weight: 50.0000 chunk 369 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN E 407 HIS E 449 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN F 73 GLN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.140222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.103604 restraints weight = 250068.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.100190 restraints weight = 180500.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.100011 restraints weight = 144447.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.099537 restraints weight = 114078.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.099248 restraints weight = 107169.346| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 37104 Z= 0.197 Angle : 0.745 15.504 50280 Z= 0.376 Chirality : 0.046 0.193 5724 Planarity : 0.006 0.074 6552 Dihedral : 6.214 52.988 5106 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.62 % Favored : 90.36 % Rotamer: Outliers : 0.03 % Allowed : 0.59 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.12), residues: 4626 helix: 0.05 (0.11), residues: 1992 sheet: -1.97 (0.23), residues: 494 loop : -2.34 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 385 TYR 0.025 0.002 TYR B 332 PHE 0.023 0.002 PHE B 203 TRP 0.032 0.002 TRP D 563 HIS 0.008 0.002 HIS B 666 Details of bonding type rmsd covalent geometry : bond 0.00429 (37104) covalent geometry : angle 0.74450 (50280) hydrogen bonds : bond 0.04098 ( 1480) hydrogen bonds : angle 5.18223 ( 4365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 302 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.7751 (tpt) cc_final: 0.7265 (tpt) REVERT: A 427 MET cc_start: 0.7159 (mmp) cc_final: 0.6585 (mmp) REVERT: A 496 MET cc_start: 0.8735 (mpp) cc_final: 0.8531 (mpp) REVERT: A 516 MET cc_start: 0.4485 (ttt) cc_final: 0.4174 (ttt) REVERT: A 683 MET cc_start: 0.7851 (ptp) cc_final: 0.7470 (tmm) REVERT: C 160 MET cc_start: -0.1795 (mpp) cc_final: -0.2477 (ppp) REVERT: C 258 MET cc_start: 0.0148 (mmt) cc_final: -0.0594 (mmt) REVERT: C 545 ARG cc_start: 0.8726 (mtm180) cc_final: 0.8450 (mmp80) REVERT: C 663 LEU cc_start: 0.8919 (mt) cc_final: 0.8702 (mp) REVERT: E 75 MET cc_start: 0.4095 (pmm) cc_final: 0.3668 (pmm) REVERT: E 85 MET cc_start: 0.2207 (mmp) cc_final: 0.1859 (ttt) REVERT: E 258 MET cc_start: 0.4359 (mtt) cc_final: 0.3846 (mtt) REVERT: E 409 MET cc_start: 0.7589 (tpt) cc_final: 0.6829 (tpt) REVERT: E 633 MET cc_start: 0.8322 (mmt) cc_final: 0.7779 (mmt) REVERT: E 683 MET cc_start: 0.8906 (mtt) cc_final: 0.7858 (mtt) REVERT: D 38 MET cc_start: 0.5716 (mmt) cc_final: 0.5371 (mtt) REVERT: D 217 MET cc_start: 0.7864 (ppp) cc_final: 0.7463 (mtt) REVERT: D 258 MET cc_start: 0.3598 (mtt) cc_final: 0.3008 (mtt) REVERT: D 675 ASP cc_start: 0.8516 (m-30) cc_final: 0.8049 (p0) REVERT: F 309 ASN cc_start: 0.8912 (m-40) cc_final: 0.8667 (m-40) REVERT: F 427 MET cc_start: 0.5592 (tpt) cc_final: 0.5145 (tpt) REVERT: F 475 GLN cc_start: 0.8509 (mt0) cc_final: 0.8096 (mp10) REVERT: F 698 MET cc_start: 0.8138 (mtt) cc_final: 0.7619 (mmt) REVERT: F 702 MET cc_start: 0.6862 (ptp) cc_final: 0.5944 (pmm) REVERT: B 331 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7713 (mt-10) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.2371 time to fit residues: 117.4784 Evaluate side-chains 251 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 267 optimal weight: 5.9990 chunk 115 optimal weight: 0.0070 chunk 178 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 153 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 404 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.132250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.088364 restraints weight = 138571.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.085439 restraints weight = 148392.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.084891 restraints weight = 133809.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.084710 restraints weight = 120301.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.084710 restraints weight = 114830.902| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 37104 Z= 0.164 Angle : 0.707 15.102 50280 Z= 0.356 Chirality : 0.045 0.202 5724 Planarity : 0.006 0.070 6552 Dihedral : 6.077 52.064 5106 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.75 % Favored : 91.22 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.12), residues: 4626 helix: 0.20 (0.12), residues: 1991 sheet: -1.85 (0.23), residues: 502 loop : -2.25 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 370 TYR 0.020 0.002 TYR E 332 PHE 0.020 0.001 PHE B 203 TRP 0.031 0.002 TRP D 563 HIS 0.007 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00361 (37104) covalent geometry : angle 0.70690 (50280) hydrogen bonds : bond 0.03886 ( 1480) hydrogen bonds : angle 5.06462 ( 4365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6357 (tpt) cc_final: 0.5947 (tpt) REVERT: A 496 MET cc_start: 0.8745 (mpp) cc_final: 0.8490 (mpp) REVERT: A 516 MET cc_start: 0.4190 (ttt) cc_final: 0.3909 (ttt) REVERT: A 683 MET cc_start: 0.8304 (ptp) cc_final: 0.7737 (tmm) REVERT: C 160 MET cc_start: -0.1716 (mpp) cc_final: -0.2422 (ppp) REVERT: C 258 MET cc_start: -0.0050 (mmt) cc_final: -0.0766 (mmt) REVERT: C 308 ILE cc_start: 0.8181 (tt) cc_final: 0.7799 (mm) REVERT: C 485 MET cc_start: 0.7713 (mpp) cc_final: 0.7346 (mpp) REVERT: C 545 ARG cc_start: 0.8824 (mtm180) cc_final: 0.8444 (mmp80) REVERT: C 633 MET cc_start: 0.8764 (mpp) cc_final: 0.8520 (mmt) REVERT: C 663 LEU cc_start: 0.9078 (mt) cc_final: 0.8837 (mp) REVERT: E 75 MET cc_start: 0.3608 (pmm) cc_final: 0.2813 (pmm) REVERT: E 85 MET cc_start: 0.1915 (mmp) cc_final: 0.1387 (ttt) REVERT: E 237 LEU cc_start: 0.7801 (pt) cc_final: 0.6780 (pt) REVERT: E 258 MET cc_start: 0.4647 (mtt) cc_final: 0.4090 (mtt) REVERT: E 276 MET cc_start: 0.4579 (mtt) cc_final: 0.4077 (tpp) REVERT: E 409 MET cc_start: 0.7554 (tpt) cc_final: 0.6925 (tpt) REVERT: E 633 MET cc_start: 0.8501 (mmt) cc_final: 0.7928 (mmt) REVERT: E 634 LYS cc_start: 0.8545 (mtmm) cc_final: 0.8343 (mttt) REVERT: E 635 GLU cc_start: 0.8203 (pm20) cc_final: 0.7840 (pm20) REVERT: E 683 MET cc_start: 0.8874 (mtt) cc_final: 0.7966 (mtt) REVERT: D 38 MET cc_start: 0.2856 (mmt) cc_final: 0.2076 (mtt) REVERT: D 217 MET cc_start: 0.7770 (ppp) cc_final: 0.7357 (mtt) REVERT: D 226 LEU cc_start: 0.9043 (tp) cc_final: 0.8488 (tp) REVERT: D 258 MET cc_start: 0.2862 (mtt) cc_final: 0.2015 (mtt) REVERT: D 480 PRO cc_start: 0.8427 (Cg_exo) cc_final: 0.8226 (Cg_endo) REVERT: D 675 ASP cc_start: 0.8681 (m-30) cc_final: 0.8162 (p0) REVERT: F 97 TYR cc_start: 0.7606 (p90) cc_final: 0.7378 (p90) REVERT: F 309 ASN cc_start: 0.8910 (m-40) cc_final: 0.8603 (m110) REVERT: F 475 GLN cc_start: 0.8549 (mt0) cc_final: 0.8171 (mp10) REVERT: F 698 MET cc_start: 0.8071 (mtt) cc_final: 0.7551 (mmt) REVERT: F 702 MET cc_start: 0.6806 (ptp) cc_final: 0.6042 (pmm) REVERT: B 331 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7690 (mt-10) REVERT: B 385 ARG cc_start: 0.9253 (mtm110) cc_final: 0.9022 (mtm110) REVERT: B 422 ASP cc_start: 0.8693 (m-30) cc_final: 0.7914 (m-30) REVERT: B 431 TRP cc_start: 0.7306 (p-90) cc_final: 0.7073 (p-90) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.2125 time to fit residues: 107.6293 Evaluate side-chains 263 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 116 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 354 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 389 optimal weight: 30.0000 chunk 38 optimal weight: 0.7980 chunk 253 optimal weight: 4.9990 chunk 320 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 357 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 HIS ** A 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 GLN E 739 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN F 449 ASN ** F 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.134785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.088023 restraints weight = 134852.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088030 restraints weight = 121931.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.087851 restraints weight = 108881.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.087840 restraints weight = 105657.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.087829 restraints weight = 104547.774| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37104 Z= 0.130 Angle : 0.660 14.868 50280 Z= 0.331 Chirality : 0.044 0.185 5724 Planarity : 0.005 0.069 6552 Dihedral : 5.783 50.611 5106 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.19 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.12), residues: 4626 helix: 0.44 (0.12), residues: 1997 sheet: -1.60 (0.23), residues: 509 loop : -2.18 (0.13), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 370 TYR 0.018 0.002 TYR F 289 PHE 0.018 0.001 PHE B 203 TRP 0.035 0.002 TRP B 602 HIS 0.008 0.001 HIS A 407 Details of bonding type rmsd covalent geometry : bond 0.00288 (37104) covalent geometry : angle 0.66046 (50280) hydrogen bonds : bond 0.03563 ( 1480) hydrogen bonds : angle 4.80079 ( 4365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11035.30 seconds wall clock time: 189 minutes 24.13 seconds (11364.13 seconds total)