Starting phenix.real_space_refine on Tue Aug 26 03:34:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6t_35206/08_2025/8i6t_35206_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6t_35206/08_2025/8i6t_35206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i6t_35206/08_2025/8i6t_35206_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6t_35206/08_2025/8i6t_35206_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6t_35206/08_2025/8i6t_35206.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6t_35206/08_2025/8i6t_35206.map" } resolution = 3.7 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 210 5.16 5 C 20926 2.51 5 N 5658 2.21 5 O 6189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32983 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "E" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "F" Number of atoms: 5463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5463 Classifications: {'peptide': 682} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 657} Chain breaks: 1 Time building chain proxies: 8.35, per 1000 atoms: 0.25 Number of scatterers: 32983 At special positions: 0 Unit cell: (177.62, 176.55, 162.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 210 16.00 O 6189 8.00 N 5658 7.00 C 20926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7708 Finding SS restraints... Secondary structure from input PDB file: 221 helices and 8 sheets defined 61.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.572A pdb=" N ASP A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 111 removed outlier: 3.690A pdb=" N LEU A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 removed outlier: 4.245A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 163 removed outlier: 4.777A pdb=" N MET A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA A 157 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 162 " --> pdb=" O CYS A 158 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.709A pdb=" N PHE A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLN A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.619A pdb=" N HIS A 188 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.641A pdb=" N HIS A 243 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.593A pdb=" N HIS A 251 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 276 Processing helix chain 'A' and resid 277 through 288 removed outlier: 4.306A pdb=" N THR A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 303 removed outlier: 3.982A pdb=" N TYR A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 297 " --> pdb=" O CYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 4.082A pdb=" N LEU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 334 removed outlier: 4.020A pdb=" N HIS A 334 " --> pdb=" O ILE A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 331 through 334' Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.906A pdb=" N GLU A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ASP A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 removed outlier: 3.724A pdb=" N GLY A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.937A pdb=" N VAL A 387 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 389 " --> pdb=" O CYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 419 removed outlier: 3.509A pdb=" N ARG A 417 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 447 removed outlier: 3.512A pdb=" N SER A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.864A pdb=" N VAL A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.722A pdb=" N LEU A 485 " --> pdb=" O ARG A 482 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 486 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 487 " --> pdb=" O TYR A 484 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 482 through 487' Processing helix chain 'A' and resid 508 through 510 No H-bonds generated for 'chain 'A' and resid 508 through 510' Processing helix chain 'A' and resid 511 through 528 removed outlier: 4.433A pdb=" N ALA A 517 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.941A pdb=" N TRP A 536 " --> pdb=" O GLY A 532 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 541 " --> pdb=" O TYR A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 563 removed outlier: 3.779A pdb=" N MET A 555 " --> pdb=" O GLN A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 570 Processing helix chain 'A' and resid 571 through 591 removed outlier: 4.044A pdb=" N LEU A 575 " --> pdb=" O ALA A 571 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 584 " --> pdb=" O VAL A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 removed outlier: 4.049A pdb=" N LEU A 610 " --> pdb=" O LEU A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 618 Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.600A pdb=" N GLU A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 659 removed outlier: 4.020A pdb=" N VAL A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 695 removed outlier: 4.250A pdb=" N LEU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 675 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 679 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N CYS A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG A 689 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 691 " --> pdb=" O LEU A 687 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 721 removed outlier: 4.836A pdb=" N GLN A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 712 " --> pdb=" O GLN A 708 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 714 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 747 removed outlier: 3.858A pdb=" N GLU A 734 " --> pdb=" O ARG A 730 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 740 " --> pdb=" O PHE A 736 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 762 removed outlier: 4.522A pdb=" N SER A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS A 757 " --> pdb=" O THR A 753 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.716A pdb=" N ALA B 90 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 106 through 111 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 147 through 156 removed outlier: 4.099A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.548A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 removed outlier: 3.518A pdb=" N CYS B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 176 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 206 removed outlier: 3.518A pdb=" N LEU B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 235 removed outlier: 4.226A pdb=" N ILE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 235 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.519A pdb=" N HIS B 243 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 290 through 304 removed outlier: 3.848A pdb=" N GLU B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 300 " --> pdb=" O TYR B 296 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 303 " --> pdb=" O GLY B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.683A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.550A pdb=" N PHE B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 384 through 392 removed outlier: 3.791A pdb=" N VAL B 387 " --> pdb=" O ASP B 384 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 390 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE B 391 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU B 392 " --> pdb=" O LYS B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 419 removed outlier: 3.933A pdb=" N THR B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N TYR B 416 " --> pdb=" O MET B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 447 removed outlier: 3.867A pdb=" N VAL B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER B 439 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY B 446 " --> pdb=" O GLN B 442 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 468 removed outlier: 3.675A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.786A pdb=" N SER B 475 " --> pdb=" O TRP B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.636A pdb=" N LEU B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.853A pdb=" N TYR B 488 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 493 Processing helix chain 'B' and resid 508 through 540 removed outlier: 3.924A pdb=" N LEU B 512 " --> pdb=" O ASN B 508 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 522 " --> pdb=" O ASP B 518 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 525 " --> pdb=" O ASN B 521 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B 530 " --> pdb=" O CYS B 526 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP B 536 " --> pdb=" O GLY B 532 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 563 removed outlier: 4.030A pdb=" N LEU B 560 " --> pdb=" O THR B 556 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 584 removed outlier: 3.526A pdb=" N ALA B 578 " --> pdb=" O ARG B 574 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 595 removed outlier: 3.798A pdb=" N ARG B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG B 593 " --> pdb=" O SER B 589 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 594 " --> pdb=" O HIS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 607 removed outlier: 3.738A pdb=" N GLU B 606 " --> pdb=" O ASN B 603 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 607 " --> pdb=" O LEU B 604 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 607' Processing helix chain 'B' and resid 620 through 635 removed outlier: 4.253A pdb=" N ALA B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 631 " --> pdb=" O GLN B 627 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TRP B 632 " --> pdb=" O TRP B 628 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 657 removed outlier: 3.983A pdb=" N ALA B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ILE B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU B 655 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 695 removed outlier: 3.698A pdb=" N LEU B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 675 " --> pdb=" O TRP B 671 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 677 " --> pdb=" O TYR B 673 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 679 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 681 " --> pdb=" O GLU B 677 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 682 " --> pdb=" O GLN B 678 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 685 " --> pdb=" O SER B 681 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 723 removed outlier: 4.002A pdb=" N GLU B 704 " --> pdb=" O THR B 700 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 707 " --> pdb=" O VAL B 703 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLN B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU B 712 " --> pdb=" O GLN B 708 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 722 " --> pdb=" O THR B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 749 removed outlier: 3.670A pdb=" N ARG B 733 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU B 734 " --> pdb=" O ARG B 730 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 740 " --> pdb=" O PHE B 736 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA B 747 " --> pdb=" O PHE B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.099A pdb=" N ASP B 755 " --> pdb=" O PRO B 751 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 758 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 3.519A pdb=" N ILE C 87 " --> pdb=" O MET C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 removed outlier: 3.564A pdb=" N LEU C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 131 removed outlier: 3.796A pdb=" N VAL C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.506A pdb=" N ARG C 151 " --> pdb=" O MET C 147 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N MET C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 171 through 176 Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 202 through 210 removed outlier: 3.524A pdb=" N ASP C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET C 208 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.505A pdb=" N LEU C 250 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 286 removed outlier: 4.386A pdb=" N ALA C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 304 removed outlier: 4.564A pdb=" N TYR C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 297 " --> pdb=" O CYS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 330 removed outlier: 3.610A pdb=" N LEU C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 321 " --> pdb=" O TYR C 317 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 325 " --> pdb=" O TRP C 321 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 334 removed outlier: 3.829A pdb=" N HIS C 334 " --> pdb=" O ILE C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 331 through 334' Processing helix chain 'C' and resid 335 through 350 removed outlier: 4.455A pdb=" N GLU C 340 " --> pdb=" O THR C 336 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 341 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 343 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 348 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 349 " --> pdb=" O TYR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 removed outlier: 3.554A pdb=" N LEU C 375 " --> pdb=" O MET C 371 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 408 through 418 removed outlier: 4.034A pdb=" N MET C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN C 414 " --> pdb=" O THR C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 443 removed outlier: 3.884A pdb=" N GLU C 434 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 435 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 438 " --> pdb=" O GLU C 434 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N SER C 439 " --> pdb=" O VAL C 435 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 460 through 470 removed outlier: 3.820A pdb=" N VAL C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 466 " --> pdb=" O GLY C 462 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP C 469 " --> pdb=" O GLU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 removed outlier: 3.631A pdb=" N SER C 475 " --> pdb=" O TRP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 486 removed outlier: 3.763A pdb=" N LEU C 485 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 538 removed outlier: 4.356A pdb=" N SER C 520 " --> pdb=" O LYS C 516 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TRP C 536 " --> pdb=" O GLY C 532 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR C 537 " --> pdb=" O LEU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 560 removed outlier: 4.313A pdb=" N THR C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 560 " --> pdb=" O THR C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.626A pdb=" N VAL C 580 " --> pdb=" O GLY C 576 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL C 587 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 592 " --> pdb=" O SER C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 599 removed outlier: 4.328A pdb=" N LYS C 598 " --> pdb=" O GLY C 595 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN C 599 " --> pdb=" O GLY C 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 595 through 599' Processing helix chain 'C' and resid 606 through 611 removed outlier: 3.767A pdb=" N VAL C 611 " --> pdb=" O ILE C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 635 removed outlier: 3.741A pdb=" N ALA C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP C 625 " --> pdb=" O LEU C 621 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET C 630 " --> pdb=" O LYS C 626 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA C 631 " --> pdb=" O GLN C 627 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP C 632 " --> pdb=" O TRP C 628 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 658 removed outlier: 3.600A pdb=" N LEU C 649 " --> pdb=" O ASP C 645 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 650 " --> pdb=" O THR C 646 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU C 655 " --> pdb=" O VAL C 651 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE C 656 " --> pdb=" O ARG C 652 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 696 removed outlier: 3.650A pdb=" N SER C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 679 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS C 684 " --> pdb=" O THR C 680 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS C 685 " --> pdb=" O SER C 681 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C 686 " --> pdb=" O SER C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 702 through 711 Processing helix chain 'C' and resid 711 through 723 removed outlier: 3.701A pdb=" N GLN C 715 " --> pdb=" O ASP C 711 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 717 " --> pdb=" O GLU C 713 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 718 " --> pdb=" O MET C 714 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 721 " --> pdb=" O LEU C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 747 removed outlier: 4.225A pdb=" N THR C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 740 " --> pdb=" O PHE C 736 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER C 742 " --> pdb=" O HIS C 738 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 747 " --> pdb=" O PHE C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 762 removed outlier: 3.507A pdb=" N ILE C 762 " --> pdb=" O ILE C 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 92 removed outlier: 4.332A pdb=" N GLY D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 4.332A pdb=" N LEU D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 removed outlier: 3.566A pdb=" N ASP D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE D 130 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.588A pdb=" N ILE D 152 " --> pdb=" O MET D 148 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N MET D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 177 removed outlier: 3.934A pdb=" N GLY D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.821A pdb=" N LEU D 202 " --> pdb=" O PHE D 198 " (cutoff:3.500A) Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 220 through 235 removed outlier: 3.812A pdb=" N ALA D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 235 " --> pdb=" O GLU D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.871A pdb=" N LEU D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS D 251 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 252' Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.639A pdb=" N LYS D 266 " --> pdb=" O LYS D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 288 removed outlier: 3.557A pdb=" N THR D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 300 removed outlier: 3.719A pdb=" N GLU D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU D 297 " --> pdb=" O CYS D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 4.155A pdb=" N PHE D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 330 removed outlier: 3.608A pdb=" N LEU D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 327 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 334 Processing helix chain 'D' and resid 335 through 340 Processing helix chain 'D' and resid 343 through 349 Processing helix chain 'D' and resid 365 through 375 removed outlier: 3.852A pdb=" N THR D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 380 Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.288A pdb=" N VAL D 387 " --> pdb=" O ASP D 384 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 419 removed outlier: 3.601A pdb=" N ASN D 414 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR D 416 " --> pdb=" O MET D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 446 removed outlier: 4.343A pdb=" N GLY D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL D 435 " --> pdb=" O GLY D 431 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 436 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 438 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 removed outlier: 4.009A pdb=" N TYR D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 468 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 486 removed outlier: 3.753A pdb=" N THR D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 540 removed outlier: 3.520A pdb=" N ALA D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA D 517 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 518 " --> pdb=" O ALA D 514 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE D 522 " --> pdb=" O ASP D 518 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 523 " --> pdb=" O PHE D 519 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU D 525 " --> pdb=" O ASN D 521 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS D 526 " --> pdb=" O PHE D 522 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG D 527 " --> pdb=" O GLN D 523 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 565 removed outlier: 3.736A pdb=" N THR D 553 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 554 " --> pdb=" O PRO D 550 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 589 removed outlier: 3.663A pdb=" N ALA D 578 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 580 " --> pdb=" O GLY D 576 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP D 585 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER D 589 " --> pdb=" O ASP D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 595 removed outlier: 3.672A pdb=" N ILE D 594 " --> pdb=" O HIS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 600 Processing helix chain 'D' and resid 603 through 611 removed outlier: 3.536A pdb=" N LEU D 607 " --> pdb=" O LEU D 604 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 608 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL D 611 " --> pdb=" O ILE D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 633 removed outlier: 3.887A pdb=" N MET D 630 " --> pdb=" O LYS D 626 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 631 " --> pdb=" O GLN D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 652 removed outlier: 3.682A pdb=" N VAL D 651 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 696 removed outlier: 3.787A pdb=" N GLN D 675 " --> pdb=" O TRP D 671 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 679 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS D 685 " --> pdb=" O SER D 681 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS D 686 " --> pdb=" O SER D 682 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER D 688 " --> pdb=" O CYS D 684 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG D 689 " --> pdb=" O CYS D 685 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 693 " --> pdb=" O ARG D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 722 Processing helix chain 'D' and resid 730 through 747 removed outlier: 4.007A pdb=" N GLU D 734 " --> pdb=" O ARG D 730 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THR D 735 " --> pdb=" O LEU D 731 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER D 742 " --> pdb=" O HIS D 738 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR D 745 " --> pdb=" O LYS D 741 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA D 747 " --> pdb=" O PHE D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.574A pdb=" N SER D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.796A pdb=" N ALA E 90 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 124 through 131 Processing helix chain 'E' and resid 149 through 164 removed outlier: 3.566A pdb=" N MET E 153 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU E 156 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 157 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL E 159 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 162 " --> pdb=" O CYS E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 181 removed outlier: 3.568A pdb=" N PHE E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU E 181 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 210 removed outlier: 3.662A pdb=" N ASP E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 235 removed outlier: 3.528A pdb=" N LYS E 224 " --> pdb=" O GLU E 220 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 231 " --> pdb=" O TYR E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.591A pdb=" N MET E 245 " --> pdb=" O VAL E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 264 removed outlier: 3.662A pdb=" N LYS E 263 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 288 removed outlier: 4.025A pdb=" N THR E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN E 286 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN E 287 " --> pdb=" O THR E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 303 removed outlier: 3.549A pdb=" N TYR E 296 " --> pdb=" O LYS E 292 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL E 301 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 303 " --> pdb=" O GLY E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 330 removed outlier: 3.879A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 320 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 323 " --> pdb=" O ARG E 319 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASP E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 325 " --> pdb=" O TRP E 321 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 326 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 334 No H-bonds generated for 'chain 'E' and resid 332 through 334' Processing helix chain 'E' and resid 335 through 348 removed outlier: 3.849A pdb=" N ASP E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TYR E 345 " --> pdb=" O ASP E 341 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE E 346 " --> pdb=" O CYS E 342 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 375 removed outlier: 3.618A pdb=" N MET E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.885A pdb=" N LEU E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS E 390 " --> pdb=" O VAL E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 417 removed outlier: 4.004A pdb=" N MET E 412 " --> pdb=" O SER E 408 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 414 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 445 removed outlier: 3.655A pdb=" N SER E 439 " --> pdb=" O VAL E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 468 removed outlier: 4.306A pdb=" N VAL E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET E 468 " --> pdb=" O VAL E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 488 removed outlier: 3.920A pdb=" N LEU E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 485 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP E 486 " --> pdb=" O ARG E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 541 removed outlier: 3.923A pdb=" N ALA E 514 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 515 " --> pdb=" O TYR E 511 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS E 516 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA E 517 " --> pdb=" O LYS E 513 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER E 520 " --> pdb=" O LYS E 516 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU E 525 " --> pdb=" O ASN E 521 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 529 " --> pdb=" O GLU E 525 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU E 530 " --> pdb=" O CYS E 526 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 531 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY E 532 " --> pdb=" O VAL E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 546 removed outlier: 4.114A pdb=" N PHE E 545 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 549 through 563 removed outlier: 3.832A pdb=" N THR E 553 " --> pdb=" O ASP E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 593 removed outlier: 4.540A pdb=" N ARG E 579 " --> pdb=" O LEU E 575 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL E 587 " --> pdb=" O LEU E 583 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG E 592 " --> pdb=" O SER E 588 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG E 593 " --> pdb=" O SER E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 603 through 611 removed outlier: 4.061A pdb=" N GLU E 606 " --> pdb=" O ASN E 603 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E 607 " --> pdb=" O LEU E 604 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ILE E 608 " --> pdb=" O GLU E 605 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 610 " --> pdb=" O LEU E 607 " (cutoff:3.500A) Processing helix chain 'E' and resid 620 through 629 Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 642 through 658 removed outlier: 3.800A pdb=" N ALA E 647 " --> pdb=" O GLU E 643 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU E 649 " --> pdb=" O ASP E 645 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 650 " --> pdb=" O THR E 646 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 652 " --> pdb=" O ILE E 648 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 654 " --> pdb=" O LEU E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 666 through 685 removed outlier: 4.107A pdb=" N LEU E 670 " --> pdb=" O GLN E 666 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP E 671 " --> pdb=" O ARG E 667 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN E 675 " --> pdb=" O TRP E 671 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR E 680 " --> pdb=" O LEU E 676 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS E 684 " --> pdb=" O THR E 680 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS E 685 " --> pdb=" O SER E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 686 through 696 Processing helix chain 'E' and resid 699 through 706 removed outlier: 3.555A pdb=" N GLU E 704 " --> pdb=" O THR E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 723 removed outlier: 3.578A pdb=" N VAL E 710 " --> pdb=" O ILE E 706 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP E 711 " --> pdb=" O ASP E 707 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU E 712 " --> pdb=" O GLN E 708 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 719 " --> pdb=" O GLN E 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 720 " --> pdb=" O GLU E 716 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN E 723 " --> pdb=" O ARG E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 746 removed outlier: 3.762A pdb=" N LEU E 737 " --> pdb=" O ARG E 733 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 739 " --> pdb=" O THR E 735 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL E 740 " --> pdb=" O PHE E 736 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR E 745 " --> pdb=" O LYS E 741 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 746 " --> pdb=" O SER E 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 92 removed outlier: 3.913A pdb=" N GLY F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 87 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA F 90 " --> pdb=" O GLY F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 126 through 131 Processing helix chain 'F' and resid 150 through 163 removed outlier: 3.589A pdb=" N THR F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU F 156 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA F 157 " --> pdb=" O MET F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.555A pdb=" N CYS F 172 " --> pdb=" O HIS F 168 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET F 183 " --> pdb=" O ILE F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 209 removed outlier: 3.565A pdb=" N ASP F 207 " --> pdb=" O PRO F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 225 Processing helix chain 'F' and resid 226 through 230 Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 240 through 245 removed outlier: 3.917A pdb=" N MET F 245 " --> pdb=" O VAL F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 removed outlier: 4.127A pdb=" N LEU F 250 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS F 251 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER F 252 " --> pdb=" O LEU F 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 252' Processing helix chain 'F' and resid 260 through 265 removed outlier: 3.872A pdb=" N LEU F 265 " --> pdb=" O TRP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 268 No H-bonds generated for 'chain 'F' and resid 266 through 268' Processing helix chain 'F' and resid 281 through 286 removed outlier: 3.715A pdb=" N PHE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 281 through 286' Processing helix chain 'F' and resid 290 through 304 removed outlier: 3.768A pdb=" N PHE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 330 removed outlier: 3.831A pdb=" N VAL F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 326 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 334 removed outlier: 3.925A pdb=" N HIS F 334 " --> pdb=" O ILE F 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 331 through 334' Processing helix chain 'F' and resid 335 through 349 removed outlier: 3.746A pdb=" N GLU F 340 " --> pdb=" O THR F 336 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASP F 344 " --> pdb=" O GLU F 340 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TYR F 345 " --> pdb=" O ASP F 341 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE F 346 " --> pdb=" O CYS F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 377 removed outlier: 3.516A pdb=" N THR F 369 " --> pdb=" O ASP F 365 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET F 371 " --> pdb=" O ASP F 367 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F 375 " --> pdb=" O MET F 371 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 376 " --> pdb=" O GLY F 372 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG F 377 " --> pdb=" O PHE F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 390 removed outlier: 3.807A pdb=" N LEU F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS F 389 " --> pdb=" O CYS F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 419 removed outlier: 4.147A pdb=" N MET F 412 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR F 416 " --> pdb=" O MET F 412 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG F 417 " --> pdb=" O TYR F 413 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER F 419 " --> pdb=" O THR F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 443 removed outlier: 3.797A pdb=" N VAL F 435 " --> pdb=" O GLY F 431 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N CYS F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 438 " --> pdb=" O GLU F 434 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER F 439 " --> pdb=" O VAL F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 468 removed outlier: 3.760A pdb=" N VAL F 464 " --> pdb=" O ILE F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 475 Processing helix chain 'F' and resid 477 through 485 removed outlier: 4.026A pdb=" N THR F 481 " --> pdb=" O PRO F 477 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LEU F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 529 removed outlier: 3.775A pdb=" N LYS F 513 " --> pdb=" O ASP F 509 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG F 527 " --> pdb=" O GLN F 523 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 529 " --> pdb=" O GLU F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 540 removed outlier: 4.143A pdb=" N LEU F 533 " --> pdb=" O GLU F 529 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU F 538 " --> pdb=" O ARG F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 562 removed outlier: 3.535A pdb=" N PHE F 559 " --> pdb=" O MET F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 567 through 569 No H-bonds generated for 'chain 'F' and resid 567 through 569' Processing helix chain 'F' and resid 570 through 595 removed outlier: 4.004A pdb=" N ARG F 574 " --> pdb=" O ARG F 570 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 579 " --> pdb=" O LEU F 575 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL F 580 " --> pdb=" O GLY F 576 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP F 585 " --> pdb=" O ALA F 581 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 586 " --> pdb=" O LEU F 582 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL F 587 " --> pdb=" O LEU F 583 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 588 " --> pdb=" O ALA F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 596 through 600 removed outlier: 4.082A pdb=" N ASN F 599 " --> pdb=" O GLY F 596 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER F 600 " --> pdb=" O PRO F 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 596 through 600' Processing helix chain 'F' and resid 606 through 610 removed outlier: 3.864A pdb=" N SER F 609 " --> pdb=" O GLU F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 618 removed outlier: 3.884A pdb=" N TYR F 617 " --> pdb=" O ASP F 614 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER F 618 " --> pdb=" O ASP F 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 614 through 618' Processing helix chain 'F' and resid 619 through 636 removed outlier: 3.795A pdb=" N ALA F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 631 " --> pdb=" O GLN F 627 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TRP F 632 " --> pdb=" O TRP F 628 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 656 removed outlier: 4.022A pdb=" N THR F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 686 removed outlier: 4.185A pdb=" N LEU F 670 " --> pdb=" O GLN F 666 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU F 672 " --> pdb=" O PRO F 668 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN F 675 " --> pdb=" O TRP F 671 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR F 680 " --> pdb=" O LEU F 676 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER F 681 " --> pdb=" O GLU F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 692 removed outlier: 4.233A pdb=" N VAL F 691 " --> pdb=" O LEU F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 722 removed outlier: 3.681A pdb=" N VAL F 703 " --> pdb=" O SER F 699 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN F 709 " --> pdb=" O GLU F 705 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU F 713 " --> pdb=" O GLN F 709 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET F 714 " --> pdb=" O VAL F 710 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN F 715 " --> pdb=" O ASP F 711 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 722 " --> pdb=" O THR F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 733 through 746 removed outlier: 3.854A pdb=" N LEU F 737 " --> pdb=" O ARG F 733 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 741 " --> pdb=" O LEU F 737 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 742 " --> pdb=" O HIS F 738 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL F 746 " --> pdb=" O SER F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 749 No H-bonds generated for 'chain 'F' and resid 747 through 749' Processing helix chain 'F' and resid 750 through 760 removed outlier: 3.721A pdb=" N ILE F 754 " --> pdb=" O SER F 750 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP F 755 " --> pdb=" O PRO F 751 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER F 756 " --> pdb=" O GLU F 752 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP F 759 " --> pdb=" O ASP F 755 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 455 through 456 removed outlier: 3.598A pdb=" N VAL A 494 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 455 through 456 removed outlier: 3.626A pdb=" N ILE B 456 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 494 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AA4, first strand: chain 'D' and resid 495 through 496 removed outlier: 4.191A pdb=" N HIS D 501 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 392 through 393 Processing sheet with id=AA6, first strand: chain 'E' and resid 455 through 456 removed outlier: 3.606A pdb=" N VAL E 494 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 392 through 393 Processing sheet with id=AA8, first strand: chain 'F' and resid 495 through 496 1139 hydrogen bonds defined for protein. 3243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10765 1.34 - 1.46: 7678 1.46 - 1.58: 14962 1.58 - 1.70: 1 1.70 - 1.82: 312 Bond restraints: 33718 Sorted by residual: bond pdb=" C ILE D 460 " pdb=" N PRO D 461 " ideal model delta sigma weight residual 1.335 1.382 -0.047 9.40e-03 1.13e+04 2.50e+01 bond pdb=" C ARG D 667 " pdb=" N PRO D 668 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.19e-02 7.06e+03 1.64e+01 bond pdb=" C ARG A 667 " pdb=" N PRO A 668 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" C PHE A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.334 1.360 -0.026 8.40e-03 1.42e+04 9.71e+00 bond pdb=" CA MET B 412 " pdb=" C MET B 412 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.80e-02 3.09e+03 6.91e+00 ... (remaining 33713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 44371 2.49 - 4.98: 1085 4.98 - 7.47: 134 7.47 - 9.96: 31 9.96 - 12.45: 7 Bond angle restraints: 45628 Sorted by residual: angle pdb=" N VAL B 323 " pdb=" CA VAL B 323 " pdb=" C VAL B 323 " ideal model delta sigma weight residual 113.71 106.50 7.21 9.50e-01 1.11e+00 5.77e+01 angle pdb=" N ILE A 706 " pdb=" CA ILE A 706 " pdb=" C ILE A 706 " ideal model delta sigma weight residual 113.47 106.97 6.50 1.01e+00 9.80e-01 4.15e+01 angle pdb=" CA PHE D 178 " pdb=" C PHE D 178 " pdb=" N ILE D 179 " ideal model delta sigma weight residual 118.06 111.26 6.80 1.26e+00 6.30e-01 2.92e+01 angle pdb=" C GLU A 716 " pdb=" N LEU A 717 " pdb=" CA LEU A 717 " ideal model delta sigma weight residual 120.38 127.54 -7.16 1.37e+00 5.33e-01 2.73e+01 angle pdb=" C LYS B 393 " pdb=" N ASP B 394 " pdb=" CA ASP B 394 " ideal model delta sigma weight residual 121.54 130.55 -9.01 1.91e+00 2.74e-01 2.23e+01 ... (remaining 45623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 17607 17.99 - 35.98: 2086 35.98 - 53.96: 370 53.96 - 71.95: 88 71.95 - 89.94: 40 Dihedral angle restraints: 20191 sinusoidal: 8236 harmonic: 11955 Sorted by residual: dihedral pdb=" CA MET B 183 " pdb=" C MET B 183 " pdb=" N TRP B 184 " pdb=" CA TRP B 184 " ideal model delta harmonic sigma weight residual 180.00 153.43 26.57 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU B 212 " pdb=" C LEU B 212 " pdb=" N ASP B 213 " pdb=" CA ASP B 213 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER C 638 " pdb=" C SER C 638 " pdb=" N GLN C 639 " pdb=" CA GLN C 639 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 20188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4613 0.096 - 0.192: 336 0.192 - 0.288: 18 0.288 - 0.384: 1 0.384 - 0.480: 1 Chirality restraints: 4969 Sorted by residual: chirality pdb=" CB ILE C 642 " pdb=" CA ILE C 642 " pdb=" CG1 ILE C 642 " pdb=" CG2 ILE C 642 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.76e+00 chirality pdb=" CG LEU F 320 " pdb=" CB LEU F 320 " pdb=" CD1 LEU F 320 " pdb=" CD2 LEU F 320 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA THR C 410 " pdb=" N THR C 410 " pdb=" C THR C 410 " pdb=" CB THR C 410 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 4966 not shown) Planarity restraints: 5870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 135 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.26e+00 pdb=" N PRO C 136 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 136 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 136 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 611 " -0.046 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO E 612 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 612 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 612 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 460 " -0.046 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO B 461 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 461 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 461 " -0.039 5.00e-02 4.00e+02 ... (remaining 5867 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6965 2.77 - 3.30: 30930 3.30 - 3.83: 54232 3.83 - 4.37: 64031 4.37 - 4.90: 102175 Nonbonded interactions: 258333 Sorted by model distance: nonbonded pdb=" O ALA E 209 " pdb=" OH TYR E 218 " model vdw 2.235 3.040 nonbonded pdb=" O ILE B 642 " pdb=" OG1 THR B 646 " model vdw 2.243 3.040 nonbonded pdb=" O THR B 89 " pdb=" OG SER B 93 " model vdw 2.246 3.040 nonbonded pdb=" O GLU E 606 " pdb=" OG SER E 609 " model vdw 2.256 3.040 nonbonded pdb=" O PHE C 274 " pdb=" OG SER C 280 " model vdw 2.258 3.040 ... (remaining 258328 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' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'B' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'C' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'D' and (resid 80 through 544 or resid 551 through 767)) selection = (chain 'E' and (resid 80 through 544 or resid 551 through 767)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 30.700 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.005 0.080 33718 Z= 0.249 Angle : 0.984 12.446 45628 Z= 0.566 Chirality : 0.053 0.480 4969 Planarity : 0.007 0.072 5870 Dihedral : 16.224 89.942 12483 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.59 % Allowed : 12.19 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -5.42 (0.09), residues: 4108 helix: -4.23 (0.06), residues: 2166 sheet: None (None), residues: 0 loop : -2.71 (0.11), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 174 TYR 0.029 0.003 TYR D 227 PHE 0.023 0.003 PHE F 397 TRP 0.021 0.003 TRP A 261 HIS 0.009 0.002 HIS D 738 Details of bonding type rmsd covalent geometry : bond 0.00502 (33718) covalent geometry : angle 0.98450 (45628) hydrogen bonds : bond 0.31806 ( 1139) hydrogen bonds : angle 10.37221 ( 3243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 288 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.6430 (m) cc_final: 0.6184 (p) REVERT: A 148 MET cc_start: 0.7520 (ttp) cc_final: 0.7285 (ptm) REVERT: A 245 MET cc_start: 0.5601 (ptm) cc_final: 0.5191 (pmm) REVERT: A 412 MET cc_start: 0.7847 (mmt) cc_final: 0.7623 (mmm) REVERT: B 98 GLU cc_start: 0.6563 (mp0) cc_final: 0.6309 (mp0) REVERT: B 148 MET cc_start: 0.5994 (tpp) cc_final: 0.5708 (tmm) REVERT: B 183 MET cc_start: 0.7152 (mtm) cc_final: 0.6812 (mmm) REVERT: B 303 LYS cc_start: 0.7422 (ptpt) cc_final: 0.7121 (tttt) REVERT: B 304 PHE cc_start: 0.6853 (m-80) cc_final: 0.6636 (m-80) REVERT: B 488 TYR cc_start: 0.6312 (t80) cc_final: 0.5962 (t80) REVERT: C 303 LYS cc_start: 0.6816 (tmtt) cc_final: 0.6556 (tttp) REVERT: C 412 MET cc_start: 0.8529 (mmt) cc_final: 0.7903 (mmt) REVERT: C 473 LYS cc_start: 0.8289 (mtmm) cc_final: 0.8007 (tmmt) REVERT: C 677 GLU cc_start: 0.7489 (tt0) cc_final: 0.7117 (mt-10) REVERT: D 194 MET cc_start: 0.6456 (tpt) cc_final: 0.5706 (mmm) REVERT: D 232 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7533 (mtt90) REVERT: D 338 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7058 (mt-10) REVERT: E 83 MET cc_start: 0.6480 (ptp) cc_final: 0.6160 (ptm) REVERT: E 148 MET cc_start: 0.5300 (tpt) cc_final: 0.4842 (tpp) REVERT: E 153 MET cc_start: 0.7792 (tpp) cc_final: 0.7467 (tpp) REVERT: E 208 MET cc_start: 0.5582 (ppp) cc_final: 0.5257 (mmp) REVERT: E 456 ILE cc_start: 0.6311 (OUTLIER) cc_final: 0.6068 (mt) REVERT: F 153 MET cc_start: 0.8232 (tpt) cc_final: 0.7950 (tmm) REVERT: F 614 ASP cc_start: 0.5261 (OUTLIER) cc_final: 0.4967 (p0) REVERT: F 714 MET cc_start: 0.8079 (tpp) cc_final: 0.7613 (tpp) outliers start: 21 outliers final: 7 residues processed: 309 average time/residue: 0.2087 time to fit residues: 101.3094 Evaluate side-chains 182 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 614 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 ASN A 590 HIS ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 405 ASN B 414 ASN B 694 GLN B 709 GLN C 168 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 HIS C 401 HIS C 442 GLN C 448 ASN C 661 HIS C 666 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 420 GLN D 487 GLN D 501 HIS E 251 HIS E 334 HIS E 357 HIS ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 666 GLN E 715 GLN F 122 GLN F 180 GLN F 334 HIS ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN F 694 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.033950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.025629 restraints weight = 374363.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.026492 restraints weight = 203869.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.027097 restraints weight = 135392.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.027524 restraints weight = 100526.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.027823 restraints weight = 80579.112| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33718 Z= 0.171 Angle : 0.686 8.500 45628 Z= 0.365 Chirality : 0.044 0.189 4969 Planarity : 0.006 0.066 5870 Dihedral : 6.351 48.715 4532 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.82 % Allowed : 16.13 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -4.11 (0.11), residues: 4108 helix: -2.90 (0.08), residues: 2266 sheet: None (None), residues: 0 loop : -2.35 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 622 TYR 0.032 0.002 TYR D 227 PHE 0.026 0.002 PHE E 440 TRP 0.019 0.002 TRP D 628 HIS 0.006 0.001 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00360 (33718) covalent geometry : angle 0.68554 (45628) hydrogen bonds : bond 0.05555 ( 1139) hydrogen bonds : angle 6.07569 ( 3243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 190 time to evaluate : 1.346 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 245 MET cc_start: 0.5536 (ptm) cc_final: 0.5155 (pmm) REVERT: A 371 MET cc_start: 0.7292 (ttp) cc_final: 0.7033 (ptm) REVERT: B 655 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7675 (tt0) REVERT: C 303 LYS cc_start: 0.6966 (tmtt) cc_final: 0.6746 (tttp) REVERT: C 412 MET cc_start: 0.8358 (mmt) cc_final: 0.8080 (mmt) REVERT: C 473 LYS cc_start: 0.8094 (mtmm) cc_final: 0.7599 (tmmt) REVERT: C 537 TYR cc_start: 0.8501 (t80) cc_final: 0.8188 (t80) REVERT: C 542 LEU cc_start: 0.8621 (tp) cc_final: 0.8237 (pt) REVERT: C 583 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8418 (mm) REVERT: D 94 ILE cc_start: 0.6301 (mm) cc_final: 0.5780 (mp) REVERT: D 232 ARG cc_start: 0.8041 (mtm180) cc_final: 0.7827 (mtt90) REVERT: D 412 MET cc_start: 0.7717 (tpp) cc_final: 0.7387 (tpp) REVERT: D 522 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.5882 (p90) REVERT: E 83 MET cc_start: 0.6454 (ptp) cc_final: 0.6128 (ptp) REVERT: E 148 MET cc_start: 0.4900 (tpt) cc_final: 0.4307 (tpp) REVERT: E 153 MET cc_start: 0.8162 (tpp) cc_final: 0.7779 (tpp) REVERT: E 208 MET cc_start: 0.5655 (ppp) cc_final: 0.5379 (mmp) REVERT: F 332 SER cc_start: 0.6559 (OUTLIER) cc_final: 0.6314 (m) REVERT: F 714 MET cc_start: 0.8280 (tpp) cc_final: 0.8000 (tpp) outliers start: 65 outliers final: 32 residues processed: 249 average time/residue: 0.1921 time to fit residues: 80.3566 Evaluate side-chains 196 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 122 GLN Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 332 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 115 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 206 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 302 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 211 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 723 GLN D 180 GLN ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN E 182 ASN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.033879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.025646 restraints weight = 375960.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.026477 restraints weight = 209825.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.027055 restraints weight = 141132.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027464 restraints weight = 105881.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.027744 restraints weight = 85408.171| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33718 Z= 0.157 Angle : 0.647 8.053 45628 Z= 0.340 Chirality : 0.043 0.183 4969 Planarity : 0.005 0.058 5870 Dihedral : 5.947 45.470 4522 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 2.82 % Allowed : 17.94 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -3.47 (0.11), residues: 4108 helix: -2.31 (0.09), residues: 2293 sheet: None (None), residues: 0 loop : -2.15 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 622 TYR 0.030 0.002 TYR D 227 PHE 0.020 0.002 PHE E 440 TRP 0.016 0.002 TRP D 628 HIS 0.005 0.001 HIS D 738 Details of bonding type rmsd covalent geometry : bond 0.00335 (33718) covalent geometry : angle 0.64692 (45628) hydrogen bonds : bond 0.04891 ( 1139) hydrogen bonds : angle 5.64018 ( 3243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 178 time to evaluate : 1.498 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: A 245 MET cc_start: 0.5548 (ptm) cc_final: 0.5139 (pmm) REVERT: A 716 GLU cc_start: 0.7425 (tp30) cc_final: 0.7030 (pm20) REVERT: B 655 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7595 (tt0) REVERT: C 148 MET cc_start: 0.6964 (mtm) cc_final: 0.6689 (ttt) REVERT: C 367 ASP cc_start: 0.6994 (m-30) cc_final: 0.6751 (m-30) REVERT: C 473 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7659 (tmmt) REVERT: C 542 LEU cc_start: 0.8557 (tp) cc_final: 0.8267 (pt) REVERT: D 94 ILE cc_start: 0.6307 (mm) cc_final: 0.5717 (mp) REVERT: D 232 ARG cc_start: 0.8071 (mtm180) cc_final: 0.7847 (mtt90) REVERT: D 412 MET cc_start: 0.7834 (tpp) cc_final: 0.7475 (tpp) REVERT: D 522 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.5929 (p90) REVERT: E 83 MET cc_start: 0.6477 (ptp) cc_final: 0.6093 (ptp) REVERT: E 148 MET cc_start: 0.4982 (tpt) cc_final: 0.4348 (tpp) REVERT: E 153 MET cc_start: 0.8249 (tpp) cc_final: 0.7861 (tpp) REVERT: E 208 MET cc_start: 0.5670 (ppp) cc_final: 0.5359 (mmp) REVERT: E 375 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6946 (mp) REVERT: F 153 MET cc_start: 0.8291 (tmm) cc_final: 0.7724 (ppp) outliers start: 101 outliers final: 63 residues processed: 275 average time/residue: 0.1916 time to fit residues: 90.0917 Evaluate side-chains 222 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 157 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 456 ILE Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 676 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 91 optimal weight: 40.0000 chunk 146 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 404 optimal weight: 8.9990 chunk 366 optimal weight: 0.9980 chunk 113 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 374 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** D 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 GLN E 521 ASN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.033775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.025568 restraints weight = 374954.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.026388 restraints weight = 209700.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.026965 restraints weight = 141218.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.027371 restraints weight = 105990.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.027644 restraints weight = 85526.051| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33718 Z= 0.162 Angle : 0.655 8.502 45628 Z= 0.341 Chirality : 0.044 0.190 4969 Planarity : 0.005 0.060 5870 Dihedral : 5.869 45.274 4520 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 3.61 % Allowed : 19.20 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -3.18 (0.12), residues: 4108 helix: -2.05 (0.10), residues: 2298 sheet: None (None), residues: 0 loop : -2.05 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 579 TYR 0.032 0.002 TYR D 227 PHE 0.022 0.002 PHE A 304 TRP 0.016 0.002 TRP D 321 HIS 0.005 0.001 HIS D 738 Details of bonding type rmsd covalent geometry : bond 0.00346 (33718) covalent geometry : angle 0.65459 (45628) hydrogen bonds : bond 0.04618 ( 1139) hydrogen bonds : angle 5.51328 ( 3243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 165 time to evaluate : 1.149 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 245 MET cc_start: 0.5644 (ptm) cc_final: 0.5189 (pmm) REVERT: B 655 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7628 (tt0) REVERT: C 148 MET cc_start: 0.6885 (mtm) cc_final: 0.6552 (ttm) REVERT: C 465 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: C 473 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7621 (tmmt) REVERT: C 542 LEU cc_start: 0.8481 (tp) cc_final: 0.8210 (pt) REVERT: C 583 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8490 (mm) REVERT: D 94 ILE cc_start: 0.6256 (mm) cc_final: 0.6053 (mm) REVERT: D 412 MET cc_start: 0.7848 (tpp) cc_final: 0.7490 (tpp) REVERT: E 83 MET cc_start: 0.6313 (ptp) cc_final: 0.5932 (ptp) REVERT: E 148 MET cc_start: 0.5041 (tpt) cc_final: 0.4520 (tpt) REVERT: E 153 MET cc_start: 0.8254 (tpp) cc_final: 0.7861 (tpp) REVERT: E 208 MET cc_start: 0.5725 (ppp) cc_final: 0.5384 (mmp) REVERT: F 332 SER cc_start: 0.6467 (OUTLIER) cc_final: 0.6248 (m) REVERT: F 656 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6851 (mt) outliers start: 129 outliers final: 100 residues processed: 287 average time/residue: 0.1649 time to fit residues: 82.1247 Evaluate side-chains 258 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 154 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 714 MET Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 712 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 555 MET Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 173 GLU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 221 optimal weight: 0.0980 chunk 338 optimal weight: 0.8980 chunk 381 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 250 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 362 optimal weight: 0.5980 chunk 126 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 348 optimal weight: 8.9990 overall best weight: 3.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN D 243 HIS D 305 ASN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.033766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.025554 restraints weight = 371331.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.026370 restraints weight = 208957.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.026946 restraints weight = 141341.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.027349 restraints weight = 106215.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.027635 restraints weight = 86170.381| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33718 Z= 0.134 Angle : 0.610 9.061 45628 Z= 0.316 Chirality : 0.043 0.169 4969 Planarity : 0.005 0.058 5870 Dihedral : 5.573 45.042 4520 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.63 % Allowed : 20.26 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.87 (0.12), residues: 4108 helix: -1.79 (0.10), residues: 2298 sheet: None (None), residues: 0 loop : -1.92 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 432 TYR 0.028 0.002 TYR D 227 PHE 0.021 0.001 PHE A 304 TRP 0.015 0.001 TRP D 321 HIS 0.004 0.001 HIS D 738 Details of bonding type rmsd covalent geometry : bond 0.00290 (33718) covalent geometry : angle 0.60971 (45628) hydrogen bonds : bond 0.04187 ( 1139) hydrogen bonds : angle 5.24863 ( 3243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 169 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.5656 (ptm) cc_final: 0.5202 (pmm) REVERT: A 716 GLU cc_start: 0.7418 (tp30) cc_final: 0.6994 (pm20) REVERT: A 722 LEU cc_start: 0.7593 (tp) cc_final: 0.7213 (tt) REVERT: B 655 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7734 (tt0) REVERT: C 148 MET cc_start: 0.6895 (mtm) cc_final: 0.6589 (ttt) REVERT: C 465 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: C 473 LYS cc_start: 0.8173 (mtmm) cc_final: 0.7629 (tmmt) REVERT: C 542 LEU cc_start: 0.8435 (tp) cc_final: 0.8206 (pt) REVERT: C 583 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8496 (mm) REVERT: D 105 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7232 (t0) REVERT: D 414 ASN cc_start: 0.8465 (m-40) cc_final: 0.8108 (p0) REVERT: E 83 MET cc_start: 0.6070 (ptp) cc_final: 0.5645 (ptp) REVERT: E 148 MET cc_start: 0.5327 (tpt) cc_final: 0.4826 (tpt) REVERT: E 153 MET cc_start: 0.8199 (tpp) cc_final: 0.7783 (tpp) REVERT: E 208 MET cc_start: 0.5678 (ppp) cc_final: 0.5373 (mmp) REVERT: E 233 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6291 (mptt) REVERT: E 672 GLU cc_start: 0.8719 (tt0) cc_final: 0.8487 (mp0) REVERT: E 714 MET cc_start: 0.7999 (ptp) cc_final: 0.7632 (ptm) REVERT: F 208 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.5003 (mmt) REVERT: F 332 SER cc_start: 0.6453 (OUTLIER) cc_final: 0.6219 (m) outliers start: 130 outliers final: 94 residues processed: 289 average time/residue: 0.1581 time to fit residues: 79.2767 Evaluate side-chains 256 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 156 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 486 ASP Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 766 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 582 LEU Chi-restraints excluded: chain E residue 594 ILE Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 691 VAL Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 208 MET Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 494 VAL Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 396 optimal weight: 10.0000 chunk 383 optimal weight: 0.1980 chunk 291 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 319 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 180 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.033763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.025414 restraints weight = 360279.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.026249 restraints weight = 201889.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.026834 restraints weight = 136537.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.027252 restraints weight = 102338.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.027552 restraints weight = 82616.629| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33718 Z= 0.106 Angle : 0.558 11.364 45628 Z= 0.287 Chirality : 0.042 0.208 4969 Planarity : 0.004 0.056 5870 Dihedral : 5.120 44.062 4520 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.13 % Allowed : 21.21 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.52 (0.12), residues: 4108 helix: -1.49 (0.10), residues: 2333 sheet: None (None), residues: 0 loop : -1.79 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.027 0.001 TYR D 227 PHE 0.015 0.001 PHE A 304 TRP 0.013 0.001 TRP D 628 HIS 0.004 0.001 HIS E 757 Details of bonding type rmsd covalent geometry : bond 0.00227 (33718) covalent geometry : angle 0.55811 (45628) hydrogen bonds : bond 0.03669 ( 1139) hydrogen bonds : angle 4.86274 ( 3243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 178 time to evaluate : 1.349 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: A 245 MET cc_start: 0.5650 (ptm) cc_final: 0.5226 (pmm) REVERT: A 722 LEU cc_start: 0.7522 (tp) cc_final: 0.7147 (tt) REVERT: B 645 ASP cc_start: 0.7733 (p0) cc_final: 0.7245 (p0) REVERT: B 655 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7666 (tt0) REVERT: C 148 MET cc_start: 0.6794 (mtm) cc_final: 0.6501 (ttt) REVERT: C 465 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: C 473 LYS cc_start: 0.8108 (mtmm) cc_final: 0.7501 (tmmt) REVERT: D 94 ILE cc_start: 0.6455 (mm) cc_final: 0.5773 (mp) REVERT: D 96 GLU cc_start: 0.8048 (mp0) cc_final: 0.7815 (tt0) REVERT: D 105 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7276 (t0) REVERT: D 371 MET cc_start: 0.7381 (tpp) cc_final: 0.6933 (tpp) REVERT: D 414 ASN cc_start: 0.8375 (m-40) cc_final: 0.7924 (p0) REVERT: D 522 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6083 (p90) REVERT: E 83 MET cc_start: 0.6022 (ptp) cc_final: 0.5615 (ptp) REVERT: E 148 MET cc_start: 0.5308 (tpt) cc_final: 0.4817 (tpt) REVERT: E 153 MET cc_start: 0.8174 (tpp) cc_final: 0.7758 (tpp) REVERT: E 208 MET cc_start: 0.5739 (ppp) cc_final: 0.5428 (mmp) REVERT: E 233 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6323 (mptt) REVERT: E 714 MET cc_start: 0.7908 (ptp) cc_final: 0.7593 (ptm) REVERT: F 208 MET cc_start: 0.5678 (ptm) cc_final: 0.5193 (mmt) REVERT: F 332 SER cc_start: 0.6338 (OUTLIER) cc_final: 0.6110 (m) REVERT: F 412 MET cc_start: 0.7606 (mmt) cc_final: 0.6323 (ptm) outliers start: 112 outliers final: 78 residues processed: 285 average time/residue: 0.1816 time to fit residues: 88.3860 Evaluate side-chains 240 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 157 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 494 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 718 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 216 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 54 optimal weight: 0.4980 chunk 303 optimal weight: 0.4980 chunk 114 optimal weight: 20.0000 chunk 162 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 403 optimal weight: 0.9980 chunk 395 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 GLN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.033853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.025473 restraints weight = 360113.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.026312 restraints weight = 201494.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.026895 restraints weight = 135995.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.027315 restraints weight = 102265.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.027618 restraints weight = 82381.140| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33718 Z= 0.097 Angle : 0.548 9.897 45628 Z= 0.278 Chirality : 0.041 0.199 4969 Planarity : 0.004 0.055 5870 Dihedral : 4.842 43.334 4520 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.10 % Allowed : 21.80 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.21 (0.13), residues: 4108 helix: -1.24 (0.10), residues: 2332 sheet: None (None), residues: 0 loop : -1.65 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.025 0.001 TYR D 227 PHE 0.017 0.001 PHE A 304 TRP 0.013 0.001 TRP D 628 HIS 0.004 0.001 HIS E 757 Details of bonding type rmsd covalent geometry : bond 0.00210 (33718) covalent geometry : angle 0.54823 (45628) hydrogen bonds : bond 0.03386 ( 1139) hydrogen bonds : angle 4.62390 ( 3243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 167 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.5775 (ptm) cc_final: 0.5352 (pmm) REVERT: A 503 MET cc_start: 0.5310 (mpp) cc_final: 0.5013 (mpp) REVERT: A 716 GLU cc_start: 0.7096 (tp30) cc_final: 0.6688 (pm20) REVERT: A 722 LEU cc_start: 0.7509 (tp) cc_final: 0.7120 (tt) REVERT: B 645 ASP cc_start: 0.7497 (p0) cc_final: 0.6930 (p0) REVERT: B 655 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7669 (tt0) REVERT: C 148 MET cc_start: 0.6938 (mtm) cc_final: 0.6634 (ttt) REVERT: C 183 MET cc_start: 0.7381 (mmm) cc_final: 0.7062 (mmm) REVERT: C 465 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: C 473 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7553 (tmmt) REVERT: C 643 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8100 (tt0) REVERT: C 666 GLN cc_start: 0.7253 (mp10) cc_final: 0.6664 (mt0) REVERT: D 96 GLU cc_start: 0.8152 (mp0) cc_final: 0.7929 (tt0) REVERT: D 105 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7407 (t0) REVERT: D 371 MET cc_start: 0.7459 (tpp) cc_final: 0.6968 (tpp) REVERT: D 414 ASN cc_start: 0.8398 (m-40) cc_final: 0.7943 (p0) REVERT: D 522 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.5941 (p90) REVERT: E 83 MET cc_start: 0.6177 (ptp) cc_final: 0.5755 (ptp) REVERT: E 126 THR cc_start: 0.5038 (OUTLIER) cc_final: 0.4799 (t) REVERT: E 148 MET cc_start: 0.5247 (tpt) cc_final: 0.4720 (tpt) REVERT: E 153 MET cc_start: 0.8176 (tpp) cc_final: 0.7772 (tpp) REVERT: E 208 MET cc_start: 0.5798 (ppp) cc_final: 0.5382 (mmp) REVERT: E 233 LYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6315 (mmtt) REVERT: E 319 ARG cc_start: 0.6400 (mtt90) cc_final: 0.6129 (mtm-85) REVERT: E 672 GLU cc_start: 0.8642 (tt0) cc_final: 0.8427 (mp0) REVERT: E 704 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8110 (tm-30) REVERT: E 714 MET cc_start: 0.7914 (ptp) cc_final: 0.7653 (ptm) REVERT: F 153 MET cc_start: 0.8197 (tmm) cc_final: 0.7837 (ppp) REVERT: F 208 MET cc_start: 0.5670 (ptm) cc_final: 0.5212 (mmt) REVERT: F 332 SER cc_start: 0.6336 (OUTLIER) cc_final: 0.6098 (m) REVERT: F 412 MET cc_start: 0.7531 (mmt) cc_final: 0.6228 (ptm) outliers start: 111 outliers final: 78 residues processed: 273 average time/residue: 0.1618 time to fit residues: 77.4307 Evaluate side-chains 242 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 157 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 494 VAL Chi-restraints excluded: chain F residue 538 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 72 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 382 optimal weight: 8.9990 chunk 389 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 chunk 346 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 GLN ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.033696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.025532 restraints weight = 377971.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.026355 restraints weight = 215152.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.026914 restraints weight = 145621.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.027305 restraints weight = 109534.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.027581 restraints weight = 88818.131| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 33718 Z= 0.189 Angle : 0.698 9.601 45628 Z= 0.357 Chirality : 0.045 0.204 4969 Planarity : 0.006 0.060 5870 Dihedral : 5.606 45.457 4520 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.63 % Allowed : 21.69 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.53 (0.12), residues: 4108 helix: -1.53 (0.10), residues: 2293 sheet: None (None), residues: 0 loop : -1.74 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 502 TYR 0.039 0.002 TYR E 558 PHE 0.018 0.002 PHE A 613 TRP 0.019 0.002 TRP D 321 HIS 0.007 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00409 (33718) covalent geometry : angle 0.69793 (45628) hydrogen bonds : bond 0.04383 ( 1139) hydrogen bonds : angle 5.29479 ( 3243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 159 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.5697 (ptm) cc_final: 0.5236 (pmm) REVERT: A 318 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8002 (pt0) REVERT: B 645 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7367 (p0) REVERT: B 655 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7715 (tt0) REVERT: C 148 MET cc_start: 0.6869 (mtm) cc_final: 0.6511 (ttt) REVERT: C 465 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: C 473 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7868 (pttp) REVERT: D 94 ILE cc_start: 0.6248 (mm) cc_final: 0.5685 (mp) REVERT: D 105 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7269 (t0) REVERT: D 249 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7376 (mm) REVERT: D 414 ASN cc_start: 0.8452 (m-40) cc_final: 0.7956 (p0) REVERT: E 83 MET cc_start: 0.6212 (ptp) cc_final: 0.5763 (ptp) REVERT: E 126 THR cc_start: 0.5110 (OUTLIER) cc_final: 0.4892 (t) REVERT: E 148 MET cc_start: 0.5351 (tpt) cc_final: 0.4953 (tpt) REVERT: E 153 MET cc_start: 0.8173 (tpp) cc_final: 0.7752 (tpp) REVERT: E 208 MET cc_start: 0.5559 (ppp) cc_final: 0.5223 (mmp) REVERT: E 704 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8039 (tm-30) REVERT: E 714 MET cc_start: 0.7994 (ptp) cc_final: 0.7676 (ptm) REVERT: F 153 MET cc_start: 0.8172 (tmm) cc_final: 0.7818 (ppp) REVERT: F 332 SER cc_start: 0.6720 (OUTLIER) cc_final: 0.6491 (m) REVERT: F 672 GLU cc_start: 0.8563 (tt0) cc_final: 0.8338 (pp20) outliers start: 130 outliers final: 108 residues processed: 282 average time/residue: 0.1607 time to fit residues: 78.9006 Evaluate side-chains 267 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 152 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain E residue 767 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 494 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 245 optimal weight: 30.0000 chunk 39 optimal weight: 0.6980 chunk 285 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 297 optimal weight: 10.0000 chunk 210 optimal weight: 40.0000 chunk 386 optimal weight: 20.0000 chunk 372 optimal weight: 4.9990 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 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.033810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.025593 restraints weight = 374686.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.026427 restraints weight = 208724.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.027000 restraints weight = 140438.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.027406 restraints weight = 105290.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.027696 restraints weight = 85036.881| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33718 Z= 0.144 Angle : 0.635 10.487 45628 Z= 0.324 Chirality : 0.043 0.183 4969 Planarity : 0.005 0.059 5870 Dihedral : 5.438 44.959 4520 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.49 % Allowed : 21.91 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.48 (0.12), residues: 4108 helix: -1.46 (0.10), residues: 2309 sheet: None (None), residues: 0 loop : -1.75 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 502 TYR 0.037 0.002 TYR E 558 PHE 0.015 0.002 PHE A 304 TRP 0.016 0.001 TRP B 454 HIS 0.005 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00314 (33718) covalent geometry : angle 0.63524 (45628) hydrogen bonds : bond 0.04001 ( 1139) hydrogen bonds : angle 5.11441 ( 3243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 159 time to evaluate : 1.118 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: A 245 MET cc_start: 0.5703 (ptm) cc_final: 0.5262 (pmm) REVERT: A 318 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7956 (pt0) REVERT: A 503 MET cc_start: 0.5296 (mpp) cc_final: 0.5046 (mpp) REVERT: A 722 LEU cc_start: 0.7563 (tp) cc_final: 0.7145 (tt) REVERT: B 560 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7820 (tp) REVERT: B 645 ASP cc_start: 0.7742 (p0) cc_final: 0.7216 (p0) REVERT: B 655 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7737 (tt0) REVERT: B 752 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7942 (mp0) REVERT: C 148 MET cc_start: 0.6967 (mtm) cc_final: 0.6638 (ttt) REVERT: C 465 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: C 473 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7809 (pttp) REVERT: D 94 ILE cc_start: 0.6437 (mm) cc_final: 0.5898 (mp) REVERT: D 105 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7413 (t0) REVERT: D 371 MET cc_start: 0.7463 (tpp) cc_final: 0.7022 (tpp) REVERT: D 414 ASN cc_start: 0.8359 (m-40) cc_final: 0.7872 (p0) REVERT: E 83 MET cc_start: 0.6137 (ptp) cc_final: 0.5696 (ptp) REVERT: E 126 THR cc_start: 0.5101 (OUTLIER) cc_final: 0.4881 (t) REVERT: E 148 MET cc_start: 0.5443 (tpt) cc_final: 0.5078 (tpt) REVERT: E 153 MET cc_start: 0.8167 (tpp) cc_final: 0.7733 (tpp) REVERT: E 208 MET cc_start: 0.5573 (ppp) cc_final: 0.5250 (mmp) REVERT: E 233 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6377 (mmtt) REVERT: E 704 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: E 714 MET cc_start: 0.7952 (ptp) cc_final: 0.7637 (ptm) REVERT: F 153 MET cc_start: 0.8148 (tmm) cc_final: 0.7790 (ppp) REVERT: F 208 MET cc_start: 0.5958 (ppp) cc_final: 0.5522 (mmp) REVERT: F 332 SER cc_start: 0.6465 (OUTLIER) cc_final: 0.6246 (m) REVERT: F 412 MET cc_start: 0.7683 (mmt) cc_final: 0.6339 (ptm) REVERT: F 672 GLU cc_start: 0.8547 (tt0) cc_final: 0.8330 (pp20) outliers start: 125 outliers final: 107 residues processed: 279 average time/residue: 0.1625 time to fit residues: 79.1274 Evaluate side-chains 268 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 154 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain E residue 767 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 494 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 171 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 354 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 ASN F 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.033738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.025528 restraints weight = 368513.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.026344 restraints weight = 210991.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.026910 restraints weight = 143738.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.027307 restraints weight = 108493.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.027598 restraints weight = 87822.452| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33718 Z= 0.155 Angle : 0.658 10.808 45628 Z= 0.335 Chirality : 0.044 0.181 4969 Planarity : 0.005 0.059 5870 Dihedral : 5.549 45.518 4520 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.55 % Allowed : 22.00 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.54 (0.12), residues: 4108 helix: -1.49 (0.10), residues: 2307 sheet: None (None), residues: 0 loop : -1.81 (0.14), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 733 TYR 0.033 0.002 TYR E 558 PHE 0.015 0.002 PHE A 304 TRP 0.019 0.002 TRP B 632 HIS 0.006 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00338 (33718) covalent geometry : angle 0.65812 (45628) hydrogen bonds : bond 0.04139 ( 1139) hydrogen bonds : angle 5.20770 ( 3243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8216 Ramachandran restraints generated. 4108 Oldfield, 0 Emsley, 4108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 152 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8000 (pt0) REVERT: A 503 MET cc_start: 0.5166 (mpp) cc_final: 0.4788 (mpp) REVERT: A 722 LEU cc_start: 0.7581 (tp) cc_final: 0.7163 (tt) REVERT: B 560 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7802 (tp) REVERT: B 645 ASP cc_start: 0.7751 (p0) cc_final: 0.7225 (p0) REVERT: B 655 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7697 (tt0) REVERT: B 752 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7962 (mp0) REVERT: C 148 MET cc_start: 0.6889 (mtm) cc_final: 0.6573 (ttt) REVERT: C 465 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: D 94 ILE cc_start: 0.6427 (mm) cc_final: 0.5860 (mp) REVERT: D 105 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7452 (t0) REVERT: D 414 ASN cc_start: 0.8359 (m-40) cc_final: 0.7886 (p0) REVERT: E 83 MET cc_start: 0.6010 (ptp) cc_final: 0.5580 (ptp) REVERT: E 126 THR cc_start: 0.5121 (OUTLIER) cc_final: 0.4897 (t) REVERT: E 148 MET cc_start: 0.5409 (tpt) cc_final: 0.5091 (tpt) REVERT: E 153 MET cc_start: 0.8195 (tpp) cc_final: 0.7761 (tpp) REVERT: E 208 MET cc_start: 0.5716 (ppp) cc_final: 0.5383 (mmp) REVERT: E 233 LYS cc_start: 0.6648 (OUTLIER) cc_final: 0.6380 (mmtt) REVERT: E 704 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: E 714 MET cc_start: 0.7961 (ptp) cc_final: 0.7630 (ptm) REVERT: F 153 MET cc_start: 0.8105 (tmm) cc_final: 0.7733 (ppp) REVERT: F 208 MET cc_start: 0.6036 (ppp) cc_final: 0.5647 (mmt) REVERT: F 332 SER cc_start: 0.6410 (OUTLIER) cc_final: 0.6190 (m) REVERT: F 412 MET cc_start: 0.7736 (mmt) cc_final: 0.6353 (ptm) outliers start: 127 outliers final: 112 residues processed: 273 average time/residue: 0.1522 time to fit residues: 75.0140 Evaluate side-chains 267 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 148 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 522 PHE Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 310 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 337 SER Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 590 HIS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 208 MET Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 410 THR Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain D residue 464 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 486 ASP Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 522 PHE Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain D residue 691 VAL Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 706 ILE Chi-restraints excluded: chain D residue 739 VAL Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain D residue 754 ILE Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 257 VAL Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 358 THR Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 633 THR Chi-restraints excluded: chain E residue 642 ILE Chi-restraints excluded: chain E residue 649 LEU Chi-restraints excluded: chain E residue 704 GLU Chi-restraints excluded: chain E residue 735 THR Chi-restraints excluded: chain E residue 767 ILE Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 324 ASP Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 386 CYS Chi-restraints excluded: chain F residue 409 VAL Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 494 VAL Chi-restraints excluded: chain F residue 538 LEU Chi-restraints excluded: chain F residue 676 LEU Chi-restraints excluded: chain F residue 718 THR Chi-restraints excluded: chain F residue 728 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 312 optimal weight: 9.9990 chunk 269 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.2980 chunk 171 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 395 optimal weight: 7.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.033908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.025647 restraints weight = 375192.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.026488 restraints weight = 208777.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.027065 restraints weight = 140113.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.027471 restraints weight = 105043.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.027763 restraints weight = 84558.878| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33718 Z= 0.135 Angle : 0.628 10.941 45628 Z= 0.318 Chirality : 0.043 0.177 4969 Planarity : 0.005 0.057 5870 Dihedral : 5.395 45.141 4520 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.44 % Allowed : 22.19 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.03 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -2.45 (0.13), residues: 4108 helix: -1.41 (0.10), residues: 2326 sheet: None (None), residues: 0 loop : -1.78 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 622 TYR 0.033 0.002 TYR E 558 PHE 0.015 0.001 PHE C 591 TRP 0.017 0.001 TRP B 454 HIS 0.005 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00297 (33718) covalent geometry : angle 0.62784 (45628) hydrogen bonds : bond 0.03927 ( 1139) hydrogen bonds : angle 5.05834 ( 3243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4972.33 seconds wall clock time: 87 minutes 6.99 seconds (5226.99 seconds total)