Starting phenix.real_space_refine on Sat Feb 7 16:12:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3y_36867/02_2026/8k3y_36867.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3y_36867/02_2026/8k3y_36867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3y_36867/02_2026/8k3y_36867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3y_36867/02_2026/8k3y_36867.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3y_36867/02_2026/8k3y_36867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3y_36867/02_2026/8k3y_36867.cif" } resolution = 4.42 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 120 5.16 5 C 21815 2.51 5 N 6081 2.21 5 O 6565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34589 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 4136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 4136 Classifications: {'peptide': 531} Link IDs: {'PTRANS': 32, 'TRANS': 498} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.07, per 1000 atoms: 0.26 Number of scatterers: 34589 At special positions: 0 Unit cell: (169.76, 196.285, 171.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 8 15.00 O 6565 8.00 N 6081 7.00 C 21815 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: 3.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8154 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 41 sheets defined 47.6% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 30 through 39 removed outlier: 3.684A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 3.707A pdb=" N VAL A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 157 through 169 removed outlier: 3.721A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 Processing helix chain 'A' and resid 184 through 234 removed outlier: 3.743A pdb=" N ARG A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.807A pdb=" N GLU A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 Processing helix chain 'A' and resid 280 through 295 removed outlier: 3.632A pdb=" N THR A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.064A pdb=" N GLU A 317 " --> pdb=" O GLN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.700A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.640A pdb=" N ILE A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 447 through 451 Processing helix chain 'A' and resid 461 through 465 removed outlier: 4.196A pdb=" N LYS A 464 " --> pdb=" O ASP A 461 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 465 " --> pdb=" O LEU A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 461 through 465' Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.604A pdb=" N LEU A 482 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 removed outlier: 3.808A pdb=" N ARG A 503 " --> pdb=" O GLN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.751A pdb=" N ALA A 646 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 693 removed outlier: 4.175A pdb=" N THR A 685 " --> pdb=" O ILE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 removed outlier: 3.697A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 738 No H-bonds generated for 'chain 'A' and resid 736 through 738' Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 761 through 766 removed outlier: 3.774A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 766' Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.561A pdb=" N VAL B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 137 removed outlier: 3.877A pdb=" N VAL B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 136 " --> pdb=" O PHE B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 152 removed outlier: 3.979A pdb=" N GLN B 148 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B 149 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU B 150 " --> pdb=" O TYR B 147 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 152 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.828A pdb=" N ASP B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.918A pdb=" N LYS B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 241 removed outlier: 3.855A pdb=" N LYS B 207 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 225 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 233 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 removed outlier: 3.953A pdb=" N GLU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 280 through 293 removed outlier: 4.207A pdb=" N THR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 3.673A pdb=" N LEU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.479A pdb=" N LYS B 323 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 4.491A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 403 through 413 Processing helix chain 'B' and resid 423 through 427 removed outlier: 3.776A pdb=" N LYS B 426 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.353A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 505 through 515 Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 540 through 560 removed outlier: 3.833A pdb=" N GLU B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 Processing helix chain 'B' and resid 584 through 588 Processing helix chain 'B' and resid 630 through 647 Processing helix chain 'B' and resid 679 through 693 removed outlier: 3.594A pdb=" N MET B 683 " --> pdb=" O ALA B 679 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 688 " --> pdb=" O ALA B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 728 Processing helix chain 'B' and resid 738 through 744 removed outlier: 4.839A pdb=" N ALA B 741 " --> pdb=" O ASP B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 770 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.703A pdb=" N ARG C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 139 removed outlier: 3.815A pdb=" N ALA C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 143 removed outlier: 3.755A pdb=" N ARG C 143 " --> pdb=" O LYS C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.773A pdb=" N LEU C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 151 " --> pdb=" O TYR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.903A pdb=" N ILE C 165 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 169 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 Processing helix chain 'C' and resid 184 through 238 removed outlier: 3.511A pdb=" N GLN C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 257 removed outlier: 4.215A pdb=" N GLY C 242 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.565A pdb=" N ASP C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 338 removed outlier: 3.659A pdb=" N ILE C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 371 Processing helix chain 'C' and resid 380 through 384 removed outlier: 4.050A pdb=" N GLY C 383 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.685A pdb=" N HIS C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 444 Processing helix chain 'C' and resid 444 through 449 removed outlier: 4.291A pdb=" N ASN C 449 " --> pdb=" O PRO C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 505 through 514 Processing helix chain 'C' and resid 523 through 534 Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.580A pdb=" N GLU C 546 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 551 " --> pdb=" O LEU C 547 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS C 556 " --> pdb=" O ARG C 552 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 578 Processing helix chain 'C' and resid 586 through 590 Processing helix chain 'C' and resid 630 through 647 Processing helix chain 'C' and resid 675 through 680 removed outlier: 4.394A pdb=" N ALA C 679 " --> pdb=" O GLY C 676 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY C 680 " --> pdb=" O PRO C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 692 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.847A pdb=" N LEU C 723 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 741 removed outlier: 4.181A pdb=" N ALA C 741 " --> pdb=" O ASP C 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.731A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 39 removed outlier: 3.622A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 140 Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 157 through 169 removed outlier: 3.531A pdb=" N LEU D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP D 163 " --> pdb=" O ALA D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 185 through 233 Processing helix chain 'D' and resid 239 through 256 removed outlier: 3.501A pdb=" N LEU D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.664A pdb=" N LYS D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 295 removed outlier: 3.613A pdb=" N THR D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TRP D 292 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 325 through 339 removed outlier: 3.777A pdb=" N TYR D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.643A pdb=" N GLY D 365 " --> pdb=" O LYS D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.776A pdb=" N HIS D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.629A pdb=" N MET D 427 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 444 removed outlier: 3.602A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 removed outlier: 3.965A pdb=" N LYS D 464 " --> pdb=" O ASP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.803A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) removed outlier: 3.679A 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 478 through 482 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.582A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 560 Processing helix chain 'D' and resid 630 through 647 Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 727 removed outlier: 4.140A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 Processing helix chain 'D' and resid 747 through 753 removed outlier: 3.544A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY D 753 " --> pdb=" O GLU D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 770 removed outlier: 3.648A pdb=" N GLU D 767 " --> pdb=" O GLY D 763 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR D 768 " --> pdb=" O GLU D 764 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 38 removed outlier: 3.747A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET E 38 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 58 through 60 No H-bonds generated for 'chain 'E' and resid 58 through 60' Processing helix chain 'E' and resid 117 through 138 Processing helix chain 'E' and resid 145 through 152 removed outlier: 3.623A pdb=" N VAL E 152 " --> pdb=" O GLN E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.661A pdb=" N ASP E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR E 164 " --> pdb=" O MET E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.109A pdb=" N GLU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 237 Processing helix chain 'E' and resid 237 through 257 Processing helix chain 'E' and resid 259 through 273 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.696A pdb=" N THR E 294 " --> pdb=" O LEU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 320 removed outlier: 4.357A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N TYR E 320 " --> pdb=" O ASP E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 337 removed outlier: 4.160A pdb=" N ILE E 329 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 386 through 391 removed outlier: 3.741A pdb=" N ILE E 390 " --> pdb=" O ASP E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 412 removed outlier: 3.660A pdb=" N GLN E 411 " --> pdb=" O HIS E 407 " (cutoff:3.500A) removed outlier: 4.037A 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 436 through 444 removed outlier: 3.575A pdb=" N LEU E 440 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU E 441 " --> pdb=" O SER E 437 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 465 removed outlier: 3.529A pdb=" N LYS E 464 " --> pdb=" O ASP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 483 removed outlier: 4.271A pdb=" N ASP E 483 " --> pdb=" O PRO E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 523 through 535 Processing helix chain 'E' and resid 540 through 556 Processing helix chain 'E' and resid 573 through 578 Processing helix chain 'E' and resid 630 through 646 Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 728 removed outlier: 3.709A pdb=" N ALA E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 744 removed outlier: 3.685A pdb=" N GLU E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 752 removed outlier: 3.738A pdb=" N LEU E 751 " --> pdb=" O PRO E 747 " (cutoff:3.500A) Processing helix chain 'E' and resid 761 through 767 removed outlier: 4.214A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.703A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 273 removed outlier: 3.502A pdb=" N THR F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LYS F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 293 removed outlier: 3.718A pdb=" N ASP F 291 " --> pdb=" O ARG F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.513A pdb=" N GLN F 313 " --> pdb=" O ASN F 309 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU F 315 " --> pdb=" O THR F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 Processing helix chain 'F' and resid 360 through 372 removed outlier: 3.850A pdb=" N LEU F 364 " --> pdb=" O GLY F 360 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY F 365 " --> pdb=" O LYS F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 391 Processing helix chain 'F' and resid 403 through 409 Processing helix chain 'F' and resid 435 through 444 removed outlier: 3.728A pdb=" N MET F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 445 through 450 removed outlier: 4.248A pdb=" N ASN F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 483 Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 506 through 515 removed outlier: 3.589A pdb=" N GLN F 510 " --> pdb=" O LEU F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 removed outlier: 3.639A pdb=" N GLU F 533 " --> pdb=" O ARG F 529 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 560 removed outlier: 3.766A pdb=" N ARG F 545 " --> pdb=" O ARG F 541 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU F 546 " --> pdb=" O GLY F 542 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU F 547 " --> pdb=" O LEU F 543 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 560 " --> pdb=" O LYS F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 removed outlier: 3.637A pdb=" N LYS F 634 " --> pdb=" O GLY F 630 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA F 639 " --> pdb=" O GLU F 635 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 652 removed outlier: 3.733A pdb=" N TYR F 651 " --> pdb=" O THR F 648 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY F 652 " --> pdb=" O GLN F 649 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 648 through 652' Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 728 removed outlier: 3.913A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 736 through 746 removed outlier: 3.933A pdb=" N GLU F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 750 through 754 removed outlier: 4.043A pdb=" N GLY F 753 " --> pdb=" O VAL F 750 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 754 " --> pdb=" O LEU F 751 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 750 through 754' Processing helix chain 'F' and resid 761 through 766 removed outlier: 4.142A pdb=" N VAL F 765 " --> pdb=" O ASP F 761 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 766 " --> pdb=" O VAL F 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 761 through 766' Processing helix chain 'F' and resid 767 through 770 removed outlier: 3.885A pdb=" N LEU F 770 " --> pdb=" O GLU F 767 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 767 through 770' Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 removed outlier: 6.354A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE A 45 " --> pdb=" O PRO A 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 5 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 105 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 378 removed outlier: 3.753A pdb=" N ILE A 419 " --> pdb=" O PHE A 466 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 468 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 522 removed outlier: 5.829A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 596 through 597 removed outlier: 3.980A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 600 through 603 Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.700A pdb=" N ILE A 733 " --> pdb=" O GLU A 755 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 757 " --> pdb=" O ILE A 733 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.721A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 23 through 25 removed outlier: 7.793A pdb=" N GLN B 83 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA B 74 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET B 85 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLN B 68 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG B 91 " --> pdb=" O GLY B 66 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY B 66 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 5.831A pdb=" N HIS B 377 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE B 419 " --> pdb=" O ILE B 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AB4, first strand: chain 'B' and resid 596 through 601 removed outlier: 3.666A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 666 " --> pdb=" O GLU B 613 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS B 622 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 665 " --> pdb=" O LYS B 622 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER B 624 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.698A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.700A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN C 83 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA C 74 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N MET C 85 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 72 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG C 89 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN C 68 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG C 91 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY C 66 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN C 93 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR C 64 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N THR C 95 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 11.396A pdb=" N LEU C 62 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP C 65 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA C 48 " --> pdb=" O TRP C 65 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 21 through 25 removed outlier: 3.700A pdb=" N THR C 21 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 23 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 84 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG C 106 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N TYR C 97 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ARG C 104 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB9, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.659A pdb=" N HIS C 377 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU C 420 " --> pdb=" O HIS C 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 520 through 522 removed outlier: 5.981A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 593 through 594 Processing sheet with id=AC3, first strand: chain 'C' and resid 598 through 600 Processing sheet with id=AC4, first strand: chain 'C' and resid 613 through 618 removed outlier: 8.390A pdb=" N SER C 624 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 663 " --> pdb=" O SER C 624 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 626 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL C 665 " --> pdb=" O THR C 626 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC6, first strand: chain 'D' and resid 21 through 22 removed outlier: 4.487A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D 86 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N MET D 85 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 72 " --> pdb=" O MET D 85 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 70 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N GLN D 68 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG D 91 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY D 66 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 379 through 380 removed outlier: 3.822A pdb=" N ASP D 422 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N LEU D 351 " --> pdb=" O THR D 469 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC9, first strand: chain 'D' and resid 600 through 602 Processing sheet with id=AD1, first strand: chain 'D' and resid 613 through 618 Processing sheet with id=AD2, first strand: chain 'D' and resid 700 through 701 removed outlier: 7.112A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.002A 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 'E' and resid 20 through 25 removed outlier: 7.666A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 68 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA E 48 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TRP E 65 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 46 " --> pdb=" O TRP E 65 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 67 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE E 44 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AD5, first strand: chain 'E' and resid 352 through 354 removed outlier: 6.717A pdb=" N VAL E 352 " --> pdb=" O ILE E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 375 through 376 removed outlier: 6.257A pdb=" N LYS E 375 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU E 420 " --> pdb=" O LYS E 375 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 520 through 522 Processing sheet with id=AD8, first strand: chain 'E' and resid 601 through 602 Processing sheet with id=AD9, first strand: chain 'E' and resid 613 through 615 removed outlier: 3.778A pdb=" N VAL E 667 " --> pdb=" O THR E 626 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N GLN E 628 " --> pdb=" O VAL E 667 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP E 669 " --> pdb=" O GLN E 628 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 700 through 702 removed outlier: 3.587A pdb=" N VAL E 734 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 733 " --> pdb=" O LYS E 757 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL E 759 " --> pdb=" O ILE E 733 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU E 735 " --> pdb=" O VAL E 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 351 through 352 removed outlier: 7.373A pdb=" N LEU F 351 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N HIS F 377 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP F 422 " --> pdb=" O HIS F 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 601 through 602 Processing sheet with id=AE4, first strand: chain 'F' and resid 613 through 618 removed outlier: 3.924A pdb=" N THR F 626 " --> pdb=" O VAL F 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 732 through 735 removed outlier: 3.576A pdb=" N LYS F 757 " --> pdb=" O ILE F 733 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 735 " --> pdb=" O LYS F 757 " (cutoff:3.500A) 1414 hydrogen bonds defined for protein. 4086 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: 7.41 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 11143 1.34 - 1.46: 6819 1.46 - 1.58: 17000 1.58 - 1.71: 12 1.71 - 1.83: 240 Bond restraints: 35214 Sorted by residual: bond pdb=" N ILE A 350 " pdb=" CA ILE A 350 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.09e-02 8.42e+03 1.16e+01 bond pdb=" N VAL A 614 " pdb=" CA VAL A 614 " ideal model delta sigma weight residual 1.459 1.494 -0.036 1.19e-02 7.06e+03 9.06e+00 bond pdb=" N ILE A 379 " pdb=" CA ILE A 379 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.22e-02 6.72e+03 8.38e+00 bond pdb=" N ARG A 374 " pdb=" CA ARG A 374 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.14e+00 bond pdb=" N VAL E 458 " pdb=" CA VAL E 458 " ideal model delta sigma weight residual 1.465 1.494 -0.029 1.02e-02 9.61e+03 8.11e+00 ... (remaining 35209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 46143 2.80 - 5.60: 1332 5.60 - 8.40: 211 8.40 - 11.20: 44 11.20 - 14.00: 9 Bond angle restraints: 47739 Sorted by residual: angle pdb=" N GLU E 760 " pdb=" CA GLU E 760 " pdb=" C GLU E 760 " ideal model delta sigma weight residual 114.75 105.08 9.67 1.26e+00 6.30e-01 5.89e+01 angle pdb=" N VAL C 296 " pdb=" CA VAL C 296 " pdb=" C VAL C 296 " ideal model delta sigma weight residual 108.95 102.68 6.27 9.80e-01 1.04e+00 4.09e+01 angle pdb=" N LYS C 300 " pdb=" CA LYS C 300 " pdb=" C LYS C 300 " ideal model delta sigma weight residual 110.52 101.84 8.68 1.48e+00 4.57e-01 3.44e+01 angle pdb=" N LEU E 443 " pdb=" CA LEU E 443 " pdb=" C LEU E 443 " ideal model delta sigma weight residual 110.97 117.03 -6.06 1.09e+00 8.42e-01 3.09e+01 angle pdb=" N GLU D 295 " pdb=" CA GLU D 295 " pdb=" C GLU D 295 " ideal model delta sigma weight residual 111.33 104.64 6.69 1.21e+00 6.83e-01 3.06e+01 ... (remaining 47734 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.74: 21289 33.74 - 67.48: 398 67.48 - 101.21: 36 101.21 - 134.95: 3 134.95 - 168.69: 6 Dihedral angle restraints: 21732 sinusoidal: 9063 harmonic: 12669 Sorted by residual: dihedral pdb=" O1B ADP E 801 " pdb=" O3A ADP E 801 " pdb=" PB ADP E 801 " pdb=" PA ADP E 801 " ideal model delta sinusoidal sigma weight residual -60.00 108.69 -168.69 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C2' ADP C 801 " pdb=" C1' ADP C 801 " pdb=" N9 ADP C 801 " pdb=" C4 ADP C 801 " ideal model delta sinusoidal sigma weight residual 91.55 -76.03 167.58 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" N9 ADP B 801 " pdb=" C4 ADP B 801 " ideal model delta sinusoidal sigma weight residual 91.55 -68.70 160.25 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 21729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 5088 0.120 - 0.240: 321 0.240 - 0.360: 23 0.360 - 0.480: 1 0.480 - 0.599: 2 Chirality restraints: 5435 Sorted by residual: chirality pdb=" CB ILE E 253 " pdb=" CA ILE E 253 " pdb=" CG1 ILE E 253 " pdb=" CG2 ILE E 253 " both_signs ideal model delta sigma weight residual False 2.64 2.05 0.60 2.00e-01 2.50e+01 8.98e+00 chirality pdb=" CB ILE E 379 " pdb=" CA ILE E 379 " pdb=" CG1 ILE E 379 " pdb=" CG2 ILE E 379 " both_signs ideal model delta sigma weight residual False 2.64 2.07 0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" CB ILE D 612 " pdb=" CA ILE D 612 " pdb=" CG1 ILE D 612 " pdb=" CG2 ILE D 612 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 ... (remaining 5432 not shown) Planarity restraints: 6200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 563 " -0.029 2.00e-02 2.50e+03 2.90e-02 2.10e+01 pdb=" CG TRP C 563 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 563 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP C 563 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 563 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 563 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 563 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 563 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP C 563 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 773 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO D 774 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO D 774 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO D 774 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 768 " -0.016 2.00e-02 2.50e+03 3.43e-02 1.17e+01 pdb=" C TYR A 768 " 0.059 2.00e-02 2.50e+03 pdb=" O TYR A 768 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU A 769 " -0.020 2.00e-02 2.50e+03 ... (remaining 6197 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6078 2.77 - 3.30: 35919 3.30 - 3.83: 66592 3.83 - 4.37: 78275 4.37 - 4.90: 121421 Nonbonded interactions: 308285 Sorted by model distance: nonbonded pdb=" O LEU E 290 " pdb=" OG1 THR E 294 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP F 422 " pdb=" OG1 THR F 470 " model vdw 2.243 3.040 nonbonded pdb=" O LEU C 351 " pdb=" OG1 THR C 469 " model vdw 2.248 3.040 nonbonded pdb=" O GLN E 510 " pdb=" OG SER E 514 " model vdw 2.249 3.040 nonbonded pdb=" O THR B 682 " pdb=" OG1 THR B 685 " model vdw 2.258 3.040 ... (remaining 308280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 774) selection = (chain 'C' and resid 2 through 774) selection = (chain 'D' and resid 2 through 774) selection = (chain 'E' and resid 2 through 774) } 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: 2.570 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: 0.470 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 34.170 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.090 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 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 : 0.006 0.070 35214 Z= 0.304 Angle : 1.148 14.001 47739 Z= 0.619 Chirality : 0.065 0.599 5435 Planarity : 0.008 0.113 6200 Dihedral : 14.644 168.690 13578 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.89 % Favored : 93.09 % Rotamer: Outliers : 0.05 % Allowed : 1.08 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.11), residues: 4384 helix: -1.94 (0.10), residues: 1823 sheet: -2.11 (0.25), residues: 397 loop : -2.09 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 694 TYR 0.057 0.003 TYR C 455 PHE 0.045 0.003 PHE B 466 TRP 0.074 0.003 TRP C 563 HIS 0.012 0.002 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00613 (35214) covalent geometry : angle 1.14849 (47739) hydrogen bonds : bond 0.17767 ( 1408) hydrogen bonds : angle 8.29611 ( 4086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.323 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: A 258 MET cc_start: 0.3737 (ptp) cc_final: 0.2944 (pmm) REVERT: B 38 MET cc_start: 0.2954 (mtt) cc_final: 0.2566 (mtt) REVERT: B 424 ILE cc_start: 0.9165 (mp) cc_final: 0.8587 (mp) REVERT: C 132 PHE cc_start: 0.8555 (m-80) cc_final: 0.8230 (m-80) REVERT: D 260 GLU cc_start: 0.9715 (mm-30) cc_final: 0.9505 (mm-30) REVERT: D 702 MET cc_start: 0.6009 (ptm) cc_final: 0.5436 (tmm) REVERT: E 258 MET cc_start: 0.7687 (mmp) cc_final: 0.6843 (mmp) REVERT: E 427 MET cc_start: 0.7201 (mmt) cc_final: 0.6619 (mmt) REVERT: E 698 MET cc_start: 0.8063 (mmp) cc_final: 0.7668 (mmp) REVERT: F 427 MET cc_start: 0.4534 (tpt) cc_final: 0.4064 (tpt) REVERT: F 439 MET cc_start: 0.7979 (mpp) cc_final: 0.7676 (mpp) REVERT: F 633 MET cc_start: 0.9164 (mmp) cc_final: 0.8723 (mmm) REVERT: F 693 ARG cc_start: 0.8647 (mmp-170) cc_final: 0.8390 (mmm160) outliers start: 2 outliers final: 0 residues processed: 185 average time/residue: 0.2132 time to fit residues: 66.6573 Evaluate side-chains 155 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 20.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 229 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN B 659 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 666 HIS D 373 ASN E 277 GLN ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 647 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.100631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.055250 restraints weight = 444845.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.055526 restraints weight = 370531.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.055797 restraints weight = 345633.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.055483 restraints weight = 326505.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.055381 restraints weight = 321126.182| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35214 Z= 0.177 Angle : 0.716 10.588 47739 Z= 0.365 Chirality : 0.044 0.195 5435 Planarity : 0.006 0.083 6200 Dihedral : 9.235 172.144 4874 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 22.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.08 % Allowed : 5.10 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.12), residues: 4384 helix: -1.07 (0.11), residues: 1883 sheet: -1.90 (0.25), residues: 408 loop : -1.88 (0.13), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG A 545 TYR 0.027 0.002 TYR C 455 PHE 0.032 0.002 PHE A 467 TRP 0.025 0.002 TRP C 563 HIS 0.009 0.001 HIS D 664 Details of bonding type rmsd covalent geometry : bond 0.00352 (35214) covalent geometry : angle 0.71596 (47739) hydrogen bonds : bond 0.05074 ( 1408) hydrogen bonds : angle 6.34238 ( 4086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 1.387 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: A 702 MET cc_start: 0.1207 (tpp) cc_final: 0.0989 (mmm) REVERT: B 424 ILE cc_start: 0.9384 (mp) cc_final: 0.9144 (mp) REVERT: D 260 GLU cc_start: 0.9775 (mm-30) cc_final: 0.9554 (tp30) REVERT: F 647 HIS cc_start: 0.7865 (t70) cc_final: 0.7548 (t70) REVERT: F 683 MET cc_start: 0.9539 (mpp) cc_final: 0.8941 (ptt) outliers start: 3 outliers final: 0 residues processed: 179 average time/residue: 0.1984 time to fit residues: 60.3725 Evaluate side-chains 152 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 170 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 398 optimal weight: 0.9990 chunk 324 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 327 optimal weight: 50.0000 chunk 65 optimal weight: 50.0000 chunk 411 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN B 313 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.099359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.071077 restraints weight = 449819.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.067925 restraints weight = 417465.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.068781 restraints weight = 313719.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.068371 restraints weight = 242714.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.068381 restraints weight = 223998.572| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 35214 Z= 0.204 Angle : 0.735 13.546 47739 Z= 0.371 Chirality : 0.045 0.315 5435 Planarity : 0.006 0.085 6200 Dihedral : 9.069 176.741 4874 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 28.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.08 % Allowed : 5.18 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.12), residues: 4384 helix: -0.68 (0.11), residues: 1882 sheet: -2.10 (0.24), residues: 429 loop : -1.81 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 582 TYR 0.023 0.002 TYR C 455 PHE 0.036 0.002 PHE A 467 TRP 0.023 0.002 TRP C 563 HIS 0.010 0.002 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00410 (35214) covalent geometry : angle 0.73533 (47739) hydrogen bonds : bond 0.04861 ( 1408) hydrogen bonds : angle 6.12005 ( 4086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 1.277 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: C 401 MET cc_start: 0.8539 (mmp) cc_final: 0.8310 (tpp) REVERT: E 258 MET cc_start: 0.9098 (mmp) cc_final: 0.8826 (mmp) REVERT: F 647 HIS cc_start: 0.8503 (t70) cc_final: 0.8198 (t70) REVERT: F 683 MET cc_start: 0.9621 (mpp) cc_final: 0.9287 (ptt) outliers start: 3 outliers final: 2 residues processed: 179 average time/residue: 0.2030 time to fit residues: 61.3476 Evaluate side-chains 152 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 110 optimal weight: 1.9990 chunk 405 optimal weight: 7.9990 chunk 157 optimal weight: 50.0000 chunk 199 optimal weight: 6.9990 chunk 404 optimal weight: 40.0000 chunk 415 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 191 optimal weight: 0.8980 chunk 290 optimal weight: 30.0000 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 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 313 GLN ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** C 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** 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 = 0.4215 r_free = 0.4215 target = 0.099685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.064081 restraints weight = 449701.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.061973 restraints weight = 422953.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.063287 restraints weight = 296815.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.061281 restraints weight = 263950.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.061136 restraints weight = 236892.434| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35214 Z= 0.183 Angle : 0.706 11.739 47739 Z= 0.354 Chirality : 0.045 0.202 5435 Planarity : 0.005 0.067 6200 Dihedral : 8.948 178.462 4874 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 27.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.12), residues: 4384 helix: -0.50 (0.12), residues: 1886 sheet: -2.00 (0.24), residues: 429 loop : -1.78 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 479 TYR 0.031 0.002 TYR C 455 PHE 0.033 0.002 PHE A 467 TRP 0.021 0.002 TRP C 563 HIS 0.009 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00375 (35214) covalent geometry : angle 0.70592 (47739) hydrogen bonds : bond 0.04545 ( 1408) hydrogen bonds : angle 5.96662 ( 4086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.338 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: B 485 MET cc_start: 0.6409 (pmm) cc_final: 0.6177 (pmm) REVERT: E 258 MET cc_start: 0.9158 (mmp) cc_final: 0.8919 (mmp) REVERT: F 647 HIS cc_start: 0.7730 (t70) cc_final: 0.7358 (t70) REVERT: F 683 MET cc_start: 0.9594 (mpp) cc_final: 0.8981 (ptt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1902 time to fit residues: 57.9870 Evaluate side-chains 156 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 325 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 357 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 423 optimal weight: 9.9990 chunk 93 optimal weight: 50.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN C 593 GLN C 666 HIS ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS ** D 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.098744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.061412 restraints weight = 452266.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.058278 restraints weight = 472651.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.057667 restraints weight = 380108.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.057551 restraints weight = 342874.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.057006 restraints weight = 313161.412| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 35214 Z= 0.211 Angle : 0.744 11.896 47739 Z= 0.373 Chirality : 0.046 0.326 5435 Planarity : 0.006 0.072 6200 Dihedral : 8.964 179.847 4874 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 30.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.12), residues: 4384 helix: -0.45 (0.12), residues: 1892 sheet: -2.06 (0.25), residues: 418 loop : -1.80 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 370 TYR 0.030 0.002 TYR C 455 PHE 0.039 0.002 PHE A 467 TRP 0.022 0.002 TRP A 431 HIS 0.010 0.002 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00428 (35214) covalent geometry : angle 0.74361 (47739) hydrogen bonds : bond 0.04647 ( 1408) hydrogen bonds : angle 5.95917 ( 4086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.345 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: B 485 MET cc_start: 0.6200 (pmm) cc_final: 0.5993 (pmm) REVERT: D 698 MET cc_start: 0.8115 (mmm) cc_final: 0.7807 (mmm) REVERT: F 647 HIS cc_start: 0.7721 (t70) cc_final: 0.7351 (t70) REVERT: F 683 MET cc_start: 0.9599 (mpp) cc_final: 0.9024 (ptt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1912 time to fit residues: 56.3724 Evaluate side-chains 152 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 273 optimal weight: 7.9990 chunk 83 optimal weight: 20.0000 chunk 174 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 395 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 39 optimal weight: 0.0970 chunk 375 optimal weight: 9.9990 chunk 422 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 647 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.100125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.059170 restraints weight = 445983.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.058211 restraints weight = 380229.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.056469 restraints weight = 298327.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.056320 restraints weight = 261938.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.056321 restraints weight = 235679.270| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35214 Z= 0.157 Angle : 0.696 11.077 47739 Z= 0.345 Chirality : 0.045 0.216 5435 Planarity : 0.005 0.061 6200 Dihedral : 8.788 177.499 4874 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 26.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.12), residues: 4384 helix: -0.28 (0.12), residues: 1889 sheet: -1.97 (0.25), residues: 413 loop : -1.75 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 378 TYR 0.031 0.002 TYR C 455 PHE 0.030 0.002 PHE A 467 TRP 0.059 0.002 TRP E 292 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00332 (35214) covalent geometry : angle 0.69554 (47739) hydrogen bonds : bond 0.04208 ( 1408) hydrogen bonds : angle 5.77721 ( 4086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.976 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: C 132 PHE cc_start: 0.7239 (m-80) cc_final: 0.6997 (m-80) REVERT: D 260 GLU cc_start: 0.9771 (mm-30) cc_final: 0.9565 (tp30) REVERT: D 401 MET cc_start: 0.9740 (tpt) cc_final: 0.9351 (pmm) REVERT: D 698 MET cc_start: 0.8054 (mmm) cc_final: 0.7781 (mmm) REVERT: F 328 ARG cc_start: 0.6854 (mmp-170) cc_final: 0.6306 (tpt170) REVERT: F 647 HIS cc_start: 0.7778 (t70) cc_final: 0.7394 (t-90) REVERT: F 683 MET cc_start: 0.9590 (mpp) cc_final: 0.8986 (ptt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2009 time to fit residues: 60.7407 Evaluate side-chains 152 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 399 optimal weight: 1.9990 chunk 309 optimal weight: 50.0000 chunk 140 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 391 optimal weight: 8.9990 chunk 318 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 68 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 221 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 ASN ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.100385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.059037 restraints weight = 445022.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.055961 restraints weight = 413444.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.055912 restraints weight = 373013.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.055734 restraints weight = 352450.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.055808 restraints weight = 343541.309| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35214 Z= 0.152 Angle : 0.694 10.940 47739 Z= 0.342 Chirality : 0.045 0.212 5435 Planarity : 0.005 0.060 6200 Dihedral : 8.631 174.678 4874 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.12), residues: 4384 helix: -0.16 (0.12), residues: 1887 sheet: -1.94 (0.25), residues: 420 loop : -1.72 (0.14), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 479 TYR 0.028 0.002 TYR C 455 PHE 0.030 0.002 PHE A 467 TRP 0.037 0.002 TRP E 292 HIS 0.007 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00324 (35214) covalent geometry : angle 0.69431 (47739) hydrogen bonds : bond 0.04061 ( 1408) hydrogen bonds : angle 5.66150 ( 4086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.463 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: D 401 MET cc_start: 0.9750 (tpt) cc_final: 0.9421 (pmm) REVERT: E 38 MET cc_start: 0.7307 (pmm) cc_final: 0.7028 (mpp) REVERT: F 328 ARG cc_start: 0.7525 (mmp-170) cc_final: 0.6941 (tpt170) REVERT: F 647 HIS cc_start: 0.7780 (t70) cc_final: 0.7425 (t-90) REVERT: F 683 MET cc_start: 0.9579 (mpp) cc_final: 0.8984 (ptt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2186 time to fit residues: 65.2508 Evaluate side-chains 154 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 232 optimal weight: 40.0000 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 88 optimal weight: 0.0770 chunk 430 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 2.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** 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 = 0.4244 r_free = 0.4244 target = 0.100753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.056223 restraints weight = 443879.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.056386 restraints weight = 335209.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.056386 restraints weight = 296808.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.056386 restraints weight = 296808.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.056386 restraints weight = 296808.715| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 35214 Z= 0.144 Angle : 0.693 10.792 47739 Z= 0.339 Chirality : 0.045 0.353 5435 Planarity : 0.005 0.116 6200 Dihedral : 8.543 173.034 4874 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.12), residues: 4384 helix: -0.12 (0.12), residues: 1893 sheet: -1.93 (0.24), residues: 430 loop : -1.72 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 374 TYR 0.024 0.001 TYR C 455 PHE 0.029 0.002 PHE A 467 TRP 0.068 0.002 TRP E 298 HIS 0.006 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00311 (35214) covalent geometry : angle 0.69264 (47739) hydrogen bonds : bond 0.03918 ( 1408) hydrogen bonds : angle 5.57876 ( 4086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.371 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: B 485 MET cc_start: 0.6135 (pmm) cc_final: 0.5924 (pmm) REVERT: C 132 PHE cc_start: 0.6904 (m-80) cc_final: 0.6632 (m-80) REVERT: D 401 MET cc_start: 0.9748 (tpt) cc_final: 0.9431 (pmm) REVERT: E 38 MET cc_start: 0.7424 (pmm) cc_final: 0.7111 (mpp) REVERT: F 647 HIS cc_start: 0.7827 (t70) cc_final: 0.7466 (t-90) REVERT: F 683 MET cc_start: 0.9573 (mpp) cc_final: 0.8971 (ptt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2075 time to fit residues: 62.2557 Evaluate side-chains 154 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 333 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 348 optimal weight: 8.9990 chunk 11 optimal weight: 50.0000 chunk 271 optimal weight: 3.9990 chunk 401 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 258 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN D 310 HIS ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.099176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.054828 restraints weight = 448616.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.055272 restraints weight = 363418.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.054393 restraints weight = 331663.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.054254 restraints weight = 334539.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.054254 restraints weight = 322661.365| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 35214 Z= 0.201 Angle : 0.749 11.197 47739 Z= 0.370 Chirality : 0.046 0.286 5435 Planarity : 0.005 0.094 6200 Dihedral : 8.610 171.918 4874 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 30.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4384 helix: -0.17 (0.12), residues: 1892 sheet: -2.04 (0.24), residues: 439 loop : -1.76 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 479 TYR 0.026 0.002 TYR C 455 PHE 0.029 0.002 PHE A 467 TRP 0.049 0.003 TRP E 298 HIS 0.009 0.002 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00416 (35214) covalent geometry : angle 0.74900 (47739) hydrogen bonds : bond 0.04255 ( 1408) hydrogen bonds : angle 5.68806 ( 4086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 1.175 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: C 132 PHE cc_start: 0.6967 (m-80) cc_final: 0.6725 (m-80) REVERT: E 38 MET cc_start: 0.7510 (pmm) cc_final: 0.7296 (mpp) REVERT: E 683 MET cc_start: 0.9265 (ptp) cc_final: 0.9034 (ptp) REVERT: F 647 HIS cc_start: 0.7810 (t70) cc_final: 0.7437 (t-90) REVERT: F 683 MET cc_start: 0.9562 (mpp) cc_final: 0.8920 (ptt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1987 time to fit residues: 57.4459 Evaluate side-chains 150 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 64 optimal weight: 30.0000 chunk 212 optimal weight: 0.8980 chunk 385 optimal weight: 50.0000 chunk 295 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 282 optimal weight: 0.0670 chunk 381 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 94 optimal weight: 40.0000 chunk 303 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 overall best weight: 4.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** 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 = 0.4213 r_free = 0.4213 target = 0.099705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.053377 restraints weight = 448019.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052432 restraints weight = 350198.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052322 restraints weight = 304899.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.052377 restraints weight = 302259.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.052377 restraints weight = 300806.022| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 35214 Z= 0.173 Angle : 0.721 11.244 47739 Z= 0.355 Chirality : 0.046 0.403 5435 Planarity : 0.005 0.087 6200 Dihedral : 8.559 172.045 4874 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 28.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.13), residues: 4384 helix: -0.15 (0.12), residues: 1894 sheet: -2.00 (0.24), residues: 449 loop : -1.73 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 378 TYR 0.029 0.002 TYR C 455 PHE 0.029 0.002 PHE A 467 TRP 0.045 0.002 TRP E 298 HIS 0.008 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00366 (35214) covalent geometry : angle 0.72138 (47739) hydrogen bonds : bond 0.04096 ( 1408) hydrogen bonds : angle 5.63522 ( 4086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8768 Ramachandran restraints generated. 4384 Oldfield, 0 Emsley, 4384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.179 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: E 38 MET cc_start: 0.7527 (pmm) cc_final: 0.7306 (mpp) REVERT: E 427 MET cc_start: 0.8872 (mmt) cc_final: 0.8658 (mmt) REVERT: F 647 HIS cc_start: 0.7900 (t70) cc_final: 0.7563 (t-90) REVERT: F 683 MET cc_start: 0.9594 (mpp) cc_final: 0.9174 (ptt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2016 time to fit residues: 59.3074 Evaluate side-chains 158 residues out of total 3687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 57 optimal weight: 6.9990 chunk 247 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 231 optimal weight: 50.0000 chunk 279 optimal weight: 0.9990 chunk 315 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 263 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 311 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 504 GLN ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.100250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.052818 restraints weight = 442822.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.051929 restraints weight = 373437.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.051958 restraints weight = 359220.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.051958 restraints weight = 360388.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.051958 restraints weight = 360388.876| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35214 Z= 0.152 Angle : 0.702 10.934 47739 Z= 0.344 Chirality : 0.046 0.342 5435 Planarity : 0.005 0.086 6200 Dihedral : 8.468 171.015 4874 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.13), residues: 4384 helix: -0.06 (0.12), residues: 1885 sheet: -1.95 (0.24), residues: 451 loop : -1.71 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 395 TYR 0.029 0.002 TYR C 455 PHE 0.028 0.002 PHE A 467 TRP 0.038 0.002 TRP E 298 HIS 0.007 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00327 (35214) covalent geometry : angle 0.70227 (47739) hydrogen bonds : bond 0.03928 ( 1408) hydrogen bonds : angle 5.55178 ( 4086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20478.60 seconds wall clock time: 347 minutes 50.74 seconds (20870.74 seconds total)