Starting phenix.real_space_refine on Mon Jul 6 15:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypi_34001/07_2026/7ypi_34001.map" } resolution = 3.8 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 128 5.16 5 C 23012 2.51 5 N 6412 2.21 5 O 6918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36476 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "B" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "C" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "D" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "E" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "F" Number of atoms: 6069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 773, 6069 Classifications: {'peptide': 773} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 43, 'TRANS': 727} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.44, per 1000 atoms: 0.20 Number of scatterers: 36476 At special positions: 0 Unit cell: (189.24, 177.62, 186.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 6 15.00 O 6918 8.00 N 6412 7.00 C 23012 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: 2.09 Conformation dependent library (CDL) restraints added in 1.5 seconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 39 sheets defined 46.5% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 removed outlier: 4.312A pdb=" N VAL A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.662A pdb=" N ALA A 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP A 41 " --> pdb=" O MET A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 41' Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.678A pdb=" N LEU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 139 removed outlier: 4.136A pdb=" N HIS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 removed outlier: 3.763A pdb=" N VAL A 152 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 153 " --> pdb=" O GLU A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 149 through 153' Processing helix chain 'A' and resid 157 through 170 removed outlier: 3.952A pdb=" N LEU A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 4.035A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 181 " --> pdb=" O GLN A 177 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 235 removed outlier: 3.639A pdb=" N LEU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.765A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 Processing helix chain 'A' and resid 282 through 295 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.902A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 335 " --> pdb=" O GLU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.666A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 449 removed outlier: 4.006A pdb=" N ASN A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 523 through 534 removed outlier: 3.586A pdb=" N ILE A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 561 Processing helix chain 'A' and resid 573 through 578 Processing helix chain 'A' and resid 630 through 647 Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 717 through 728 removed outlier: 4.444A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 743 Processing helix chain 'A' and resid 747 through 753 removed outlier: 3.614A pdb=" N LEU A 751 " --> pdb=" O PRO A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 769 Processing helix chain 'B' and resid 30 through 39 Processing helix chain 'B' and resid 118 through 137 removed outlier: 3.595A pdb=" N ARG B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 removed outlier: 4.201A pdb=" N SER B 141 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 143 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 4.064A pdb=" N LEU B 161 " --> pdb=" O ASP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 180 Processing helix chain 'B' and resid 184 through 233 removed outlier: 3.668A pdb=" N THR B 219 " --> pdb=" O GLU B 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 280 through 296 Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.583A pdb=" N LEU B 322 " --> pdb=" O HIS B 319 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 323 " --> pdb=" O TYR B 320 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 319 through 323' Processing helix chain 'B' and resid 325 through 339 removed outlier: 4.063A pdb=" N TYR B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 386 through 390 removed outlier: 4.044A pdb=" N GLU B 389 " --> pdb=" O ASP B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 435 through 444 removed outlier: 3.538A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 Processing helix chain 'B' and resid 473 through 477 removed outlier: 3.960A pdb=" N THR B 476 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 477 " --> pdb=" O LEU B 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 473 through 477' Processing helix chain 'B' and resid 478 through 482 Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 4.066A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 630 through 646 removed outlier: 3.646A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 3.654A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 738 No H-bonds generated for 'chain 'B' and resid 736 through 738' Processing helix chain 'B' and resid 739 through 745 Processing helix chain 'B' and resid 761 through 770 removed outlier: 4.134A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 39 Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.607A pdb=" N ASP C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 62 " --> pdb=" O PRO C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 62' Processing helix chain 'C' and resid 117 through 138 removed outlier: 3.731A pdb=" N VAL C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.563A pdb=" N GLN C 148 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.584A pdb=" N LEU C 161 " --> pdb=" O ASP C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 182 removed outlier: 3.747A pdb=" N LYS C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 234 removed outlier: 3.593A pdb=" N ARG C 188 " --> pdb=" O ASP C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.000A pdb=" N ALA C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 259 through 273 removed outlier: 3.556A pdb=" N ASP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 296 Processing helix chain 'C' and resid 308 through 318 Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.561A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 372 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 435 through 442 Processing helix chain 'C' and resid 447 through 451 removed outlier: 3.620A pdb=" N PHE C 451 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.893A pdb=" N ASP C 483 " --> pdb=" O PRO C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 506 Processing helix chain 'C' and resid 506 through 515 Processing helix chain 'C' and resid 523 through 533 Processing helix chain 'C' and resid 541 through 560 removed outlier: 3.685A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.583A pdb=" N THR C 576 " --> pdb=" O SER C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 647 Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 removed outlier: 3.784A pdb=" N LYS C 721 " --> pdb=" O GLY C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 740 No H-bonds generated for 'chain 'C' and resid 738 through 740' Processing helix chain 'C' and resid 741 through 745 removed outlier: 3.576A pdb=" N GLU C 744 " --> pdb=" O ALA C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.777A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 38 removed outlier: 4.086A pdb=" N ARG D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.582A pdb=" N VAL D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 184 through 233 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 245 through 255 Processing helix chain 'D' and resid 259 through 272 Processing helix chain 'D' and resid 281 through 296 removed outlier: 4.105A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 318 removed outlier: 4.042A pdb=" N ASP D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 386 through 391 Processing helix chain 'D' and resid 403 through 412 removed outlier: 3.564A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 439 removed outlier: 3.604A pdb=" N ALA D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 494 through 506 removed outlier: 3.942A pdb=" N GLN D 504 " --> pdb=" O ALA D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 514 Processing helix chain 'D' and resid 524 through 535 removed outlier: 3.615A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.744A pdb=" N GLU D 544 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 545 " --> pdb=" O ARG D 541 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 546 " --> pdb=" O GLY D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.780A pdb=" N THR D 576 " --> pdb=" O ASP D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 590 removed outlier: 4.081A pdb=" N GLU D 589 " --> pdb=" O ASP D 586 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 590 " --> pdb=" O LYS D 587 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 586 through 590' Processing helix chain 'D' and resid 630 through 645 removed outlier: 3.522A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 647 No H-bonds generated for 'chain 'D' and resid 646 through 647' Processing helix chain 'D' and resid 648 through 652 removed outlier: 3.638A pdb=" N GLY D 652 " --> pdb=" O GLN D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 693 Processing helix chain 'D' and resid 717 through 728 removed outlier: 3.850A pdb=" N LYS D 721 " --> pdb=" O GLY D 717 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA D 728 " --> pdb=" O ALA D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 745 Processing helix chain 'D' and resid 747 through 752 removed outlier: 4.356A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 767 removed outlier: 3.560A pdb=" N VAL D 765 " --> pdb=" O ASP D 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 38 removed outlier: 4.251A pdb=" N ARG E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 139 removed outlier: 3.957A pdb=" N VAL E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 143 Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.655A pdb=" N LEU E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 150 " --> pdb=" O TYR E 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 146 through 150' Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.568A pdb=" N LEU E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 181 Processing helix chain 'E' and resid 186 through 223 Processing helix chain 'E' and resid 224 through 234 Processing helix chain 'E' and resid 239 through 256 removed outlier: 3.505A pdb=" N SER E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 273 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 308 through 319 removed outlier: 3.953A pdb=" N ASP E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 337 removed outlier: 3.796A pdb=" N LEU E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL E 335 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG E 336 " --> pdb=" O TYR E 332 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 372 Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 434 through 444 removed outlier: 4.261A pdb=" N ALA E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 465 removed outlier: 3.566A pdb=" N LYS E 464 " --> pdb=" O ASP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 482 Processing helix chain 'E' and resid 494 through 505 Processing helix chain 'E' and resid 505 through 514 Processing helix chain 'E' and resid 523 through 535 removed outlier: 4.053A pdb=" N THR E 535 " --> pdb=" O ILE E 531 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 573 through 579 Processing helix chain 'E' and resid 630 through 646 removed outlier: 4.132A pdb=" N LYS E 634 " --> pdb=" O GLY E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 652 removed outlier: 3.972A pdb=" N GLY E 652 " --> pdb=" O GLN E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 693 Processing helix chain 'E' and resid 717 through 729 removed outlier: 3.957A pdb=" N LYS E 721 " --> pdb=" O GLY E 717 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 740 No H-bonds generated for 'chain 'E' and resid 738 through 740' Processing helix chain 'E' and resid 761 through 767 removed outlier: 4.200A pdb=" N VAL E 765 " --> pdb=" O ASP E 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 38 removed outlier: 3.559A pdb=" N ALA F 33 " --> pdb=" O LYS F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 139 removed outlier: 3.609A pdb=" N VAL F 121 " --> pdb=" O ASP F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 151 Processing helix chain 'F' and resid 157 through 169 removed outlier: 3.910A pdb=" N LEU F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 182 removed outlier: 3.978A pdb=" N LYS F 176 " --> pdb=" O THR F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 238 removed outlier: 3.695A pdb=" N LYS F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN F 220 " --> pdb=" O GLN F 216 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU F 236 " --> pdb=" O ALA F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 256 removed outlier: 4.337A pdb=" N GLU F 254 " --> pdb=" O ARG F 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 272 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 308 through 316 Processing helix chain 'F' and resid 324 through 338 removed outlier: 3.975A pdb=" N ARG F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 372 removed outlier: 3.677A pdb=" N GLY F 365 " --> pdb=" O LYS F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 412 Processing helix chain 'F' and resid 435 through 443 Processing helix chain 'F' and resid 478 through 483 removed outlier: 3.697A pdb=" N ASP F 483 " --> pdb=" O ARG F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 505 Processing helix chain 'F' and resid 505 through 515 Processing helix chain 'F' and resid 523 through 534 Processing helix chain 'F' and resid 540 through 560 Processing helix chain 'F' and resid 573 through 579 removed outlier: 3.716A pdb=" N LEU F 578 " --> pdb=" O ILE F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 647 removed outlier: 4.207A pdb=" N LYS F 634 " --> pdb=" O GLY F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 651 removed outlier: 3.729A pdb=" N TYR F 651 " --> pdb=" O THR F 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 648 through 651' Processing helix chain 'F' and resid 679 through 693 Processing helix chain 'F' and resid 717 through 728 removed outlier: 3.967A pdb=" N LYS F 721 " --> pdb=" O GLY F 717 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 740 No H-bonds generated for 'chain 'F' and resid 738 through 740' Processing helix chain 'F' and resid 741 through 746 removed outlier: 3.632A pdb=" N GLU F 745 " --> pdb=" O ALA F 741 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 752 removed outlier: 4.016A pdb=" N LEU F 751 " --> pdb=" O PRO F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 761 through 766 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 3.622A pdb=" N VAL A 47 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 10 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 46 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 67 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA A 48 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N TRP A 65 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 90 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 70 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA A 88 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS A 72 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N VAL A 86 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ALA A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL A 84 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 378 removed outlier: 6.048A pdb=" N HIS A 377 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU A 353 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE A 488 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A 354 " --> pdb=" O ILE A 488 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.105A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 603 removed outlier: 3.702A pdb=" N ALA A 601 " --> pdb=" O THR A 608 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 613 " --> pdb=" O HIS A 666 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A 666 " --> pdb=" O GLU A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.290A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 705 through 706 removed outlier: 3.670A pdb=" N GLU A 705 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.509A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 22 removed outlier: 3.509A pdb=" N THR B 21 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 45 " --> pdb=" O PRO B 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 105 " --> pdb=" O LEU B 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.551A pdb=" N ILE B 379 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 488 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 599 through 600 Processing sheet with id=AB2, first strand: chain 'B' and resid 613 through 618 removed outlier: 3.565A pdb=" N GLU B 613 " --> pdb=" O HIS B 666 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS B 664 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AB4, first strand: chain 'C' and resid 20 through 25 removed outlier: 4.129A pdb=" N VAL C 86 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 82 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR C 81 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG C 76 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN C 83 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA C 74 " --> pdb=" O GLN C 83 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N MET C 85 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 72 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 87 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN C 68 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG C 91 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY C 66 " --> pdb=" O ARG C 91 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE C 45 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE C 8 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL C 47 " --> pdb=" O ILE C 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 378 through 380 removed outlier: 4.404A pdb=" N ILE C 379 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASP C 422 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 419 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N THR C 470 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU C 421 " --> pdb=" O THR C 470 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 520 through 522 removed outlier: 6.129A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 593 through 594 removed outlier: 3.550A pdb=" N GLN C 593 " --> pdb=" O ALA C 696 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.793A pdb=" N THR C 608 " --> pdb=" O ALA C 601 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 603 " --> pdb=" O GLY C 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 613 through 615 removed outlier: 3.533A pdb=" N GLU C 613 " --> pdb=" O HIS C 666 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS C 666 " --> pdb=" O GLU C 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 700 through 702 removed outlier: 6.789A pdb=" N ILE C 733 " --> pdb=" O LYS C 757 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 759 " --> pdb=" O ILE C 733 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU C 735 " --> pdb=" O VAL C 759 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.878A pdb=" N ARG D 104 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 98 " --> pdb=" O ARG D 104 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.567A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 21 through 25 removed outlier: 3.567A pdb=" N THR D 21 " --> pdb=" O VAL D 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 376 through 377 removed outlier: 3.924A pdb=" N LEU D 420 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 419 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR D 470 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU D 421 " --> pdb=" O THR D 470 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU D 351 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL D 352 " --> pdb=" O ILE D 488 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 520 through 522 Processing sheet with id=AC7, first strand: chain 'D' and resid 623 through 625 removed outlier: 3.541A pdb=" N ASP D 662 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 617 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 613 " --> pdb=" O HIS D 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 705 through 707 removed outlier: 4.445A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 732 through 736 removed outlier: 5.963A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 21 through 23 removed outlier: 4.055A pdb=" N THR E 21 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL E 86 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 84 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL E 86 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS E 72 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ALA E 88 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 70 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA E 90 " --> pdb=" O GLN E 68 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 376 through 380 removed outlier: 3.534A pdb=" N HIS E 377 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 420 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE E 419 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR E 470 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU E 421 " --> pdb=" O THR E 470 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU E 353 " --> pdb=" O ALA E 471 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 520 through 522 removed outlier: 3.628A pdb=" N ILE E 569 " --> pdb=" O GLU E 521 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 613 through 618 removed outlier: 3.783A pdb=" N VAL E 617 " --> pdb=" O ASP E 662 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 665 " --> pdb=" O SER E 624 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 700 through 702 removed outlier: 4.075A pdb=" N VAL E 734 " --> pdb=" O ALA E 701 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU E 735 " --> pdb=" O LYS E 757 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 21 through 23 removed outlier: 3.956A pdb=" N THR F 21 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL F 86 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL F 84 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA F 74 " --> pdb=" O VAL F 84 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL F 86 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS F 72 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ALA F 88 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL F 70 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA F 90 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP F 65 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA F 48 " --> pdb=" O TRP F 65 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 376 through 380 removed outlier: 3.650A pdb=" N ASP F 422 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE F 419 " --> pdb=" O ILE F 468 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR F 470 " --> pdb=" O ILE F 419 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU F 421 " --> pdb=" O THR F 470 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU F 353 " --> pdb=" O ALA F 471 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE F 488 " --> pdb=" O VAL F 352 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL F 354 " --> pdb=" O ILE F 488 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 520 through 522 Processing sheet with id=AD9, first strand: chain 'F' and resid 598 through 600 Processing sheet with id=AE1, first strand: chain 'F' and resid 613 through 615 removed outlier: 3.811A pdb=" N HIS F 664 " --> pdb=" O ALA F 615 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 665 " --> pdb=" O SER F 624 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 705 through 706 removed outlier: 4.157A pdb=" N GLU F 705 " --> pdb=" O MET F 713 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 732 through 736 removed outlier: 3.565A pdb=" N LYS F 757 " --> pdb=" O ILE F 733 " (cutoff:3.500A) 1515 hydrogen bonds defined for protein. 4395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.67 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 12503 1.36 - 1.51: 9595 1.51 - 1.65: 14776 1.65 - 1.80: 183 1.80 - 1.95: 71 Bond restraints: 37128 Sorted by residual: bond pdb=" C ASP D 51 " pdb=" N PRO D 52 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.19e-02 7.06e+03 2.48e+01 bond pdb=" C ILE A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.20e-02 6.94e+03 1.30e+01 bond pdb=" C ASP C 51 " pdb=" N PRO C 52 " ideal model delta sigma weight residual 1.332 1.379 -0.047 1.33e-02 5.65e+03 1.26e+01 bond pdb=" CA MET B 516 " pdb=" CB MET B 516 " ideal model delta sigma weight residual 1.528 1.573 -0.045 1.47e-02 4.63e+03 9.44e+00 bond pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.24e-02 6.50e+03 8.95e+00 ... (remaining 37123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 49681 4.41 - 8.83: 572 8.83 - 13.24: 64 13.24 - 17.66: 5 17.66 - 22.07: 2 Bond angle restraints: 50324 Sorted by residual: angle pdb=" CB MET A 439 " pdb=" CG MET A 439 " pdb=" SD MET A 439 " ideal model delta sigma weight residual 112.70 134.77 -22.07 3.00e+00 1.11e-01 5.41e+01 angle pdb=" N THR B 576 " pdb=" CA THR B 576 " pdb=" C THR B 576 " ideal model delta sigma weight residual 114.62 107.02 7.60 1.14e+00 7.69e-01 4.45e+01 angle pdb=" CA GLU D 204 " pdb=" CB GLU D 204 " pdb=" CG GLU D 204 " ideal model delta sigma weight residual 114.10 127.11 -13.01 2.00e+00 2.50e-01 4.23e+01 angle pdb=" N GLN A 229 " pdb=" CA GLN A 229 " pdb=" CB GLN A 229 " ideal model delta sigma weight residual 110.16 119.49 -9.33 1.48e+00 4.57e-01 3.97e+01 angle pdb=" CA ARG F 227 " pdb=" CB ARG F 227 " pdb=" CG ARG F 227 " ideal model delta sigma weight residual 114.10 126.51 -12.41 2.00e+00 2.50e-01 3.85e+01 ... (remaining 50319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.17: 21989 25.17 - 50.34: 858 50.34 - 75.50: 67 75.50 - 100.67: 16 100.67 - 125.84: 2 Dihedral angle restraints: 22932 sinusoidal: 9552 harmonic: 13380 Sorted by residual: dihedral pdb=" CA ALA D 601 " pdb=" C ALA D 601 " pdb=" N TRP D 602 " pdb=" CA TRP D 602 " ideal model delta harmonic sigma weight residual 180.00 150.16 29.84 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA ASP E 386 " pdb=" C ASP E 386 " pdb=" N GLU E 387 " pdb=" CA GLU E 387 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA VAL D 706 " pdb=" C VAL D 706 " pdb=" N SER D 707 " pdb=" CA SER D 707 " ideal model delta harmonic sigma weight residual 180.00 150.36 29.64 0 5.00e+00 4.00e-02 3.51e+01 ... (remaining 22929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4920 0.096 - 0.192: 735 0.192 - 0.288: 61 0.288 - 0.383: 15 0.383 - 0.479: 5 Chirality restraints: 5736 Sorted by residual: chirality pdb=" CG LEU E 249 " pdb=" CB LEU E 249 " pdb=" CD1 LEU E 249 " pdb=" CD2 LEU E 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB ILE F 415 " pdb=" CA ILE F 415 " pdb=" CG1 ILE F 415 " pdb=" CG2 ILE F 415 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.88e+00 ... (remaining 5733 not shown) Planarity restraints: 6548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 534 " 0.045 2.00e-02 2.50e+03 2.99e-02 1.79e+01 pdb=" CG TYR C 534 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR C 534 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 534 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 534 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 534 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 534 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 534 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 203 " 0.034 2.00e-02 2.50e+03 2.82e-02 1.39e+01 pdb=" CG PHE F 203 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE F 203 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE F 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 203 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE F 203 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 203 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 602 " -0.026 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP B 602 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP B 602 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 602 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 602 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 602 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 602 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 602 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 602 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 602 " -0.009 2.00e-02 2.50e+03 ... (remaining 6545 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 86 2.37 - 3.00: 17830 3.00 - 3.63: 60009 3.63 - 4.27: 88533 4.27 - 4.90: 139299 Nonbonded interactions: 305757 Sorted by model distance: nonbonded pdb=" O TYR B 320 " pdb=" OH TYR B 493 " model vdw 1.737 3.040 nonbonded pdb=" CD2 TYR B 320 " pdb=" CE2 TYR B 493 " model vdw 2.012 3.640 nonbonded pdb=" OG1 THR E 626 " pdb=" O VAL E 665 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.239 3.040 nonbonded pdb=" O LEU A 290 " pdb=" OG1 THR A 294 " model vdw 2.248 3.040 ... (remaining 305752 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: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 774) selection = (chain 'B' and resid 2 through 774) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 31.500 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 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 : 0.007 0.098 37128 Z= 0.362 Angle : 1.260 22.072 50324 Z= 0.691 Chirality : 0.068 0.479 5736 Planarity : 0.008 0.074 6548 Dihedral : 13.264 125.839 14316 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 0.13 % Allowed : 0.95 % Favored : 98.92 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.11), residues: 4626 helix: -1.84 (0.10), residues: 1977 sheet: -2.15 (0.22), residues: 470 loop : -1.89 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG D 227 TYR 0.070 0.004 TYR C 534 PHE 0.065 0.004 PHE F 203 TRP 0.062 0.004 TRP B 602 HIS 0.020 0.003 HIS C 407 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.36 (37128) covalent geometry : angle 1.25952 / 0.69 (50324) hydrogen bonds : bond 0.15784 / 10.62 ( 1505) hydrogen bonds : angle 7.76416 / 5.52 ( 4395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 296 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.0127 (mtm) cc_final: -0.0293 (mmt) REVERT: A 258 MET cc_start: 0.6309 (mpp) cc_final: 0.5839 (mpp) REVERT: A 306 LEU cc_start: 0.7068 (mt) cc_final: 0.6623 (mt) REVERT: A 650 ASP cc_start: 0.8136 (m-30) cc_final: 0.7870 (t70) REVERT: A 698 MET cc_start: 0.4316 (tpt) cc_final: 0.3292 (mmm) REVERT: B 38 MET cc_start: 0.3624 (mpp) cc_final: 0.2983 (mpp) REVERT: B 160 MET cc_start: 0.8380 (tmm) cc_final: 0.7291 (ppp) REVERT: B 276 MET cc_start: 0.6760 (tpt) cc_final: 0.6464 (tpt) REVERT: B 319 HIS cc_start: 0.7660 (m-70) cc_final: 0.7454 (m-70) REVERT: B 409 MET cc_start: 0.4274 (ppp) cc_final: 0.4010 (ppp) REVERT: B 432 ARG cc_start: 0.6059 (mtm180) cc_final: 0.5465 (tpt-90) REVERT: B 439 MET cc_start: 0.9005 (mpp) cc_final: 0.8778 (mpp) REVERT: C 427 MET cc_start: 0.6678 (tmm) cc_final: 0.6252 (tpp) REVERT: D 75 MET cc_start: 0.3834 (pmm) cc_final: 0.2186 (ptt) REVERT: D 160 MET cc_start: 0.7609 (ppp) cc_final: 0.7328 (ppp) REVERT: D 258 MET cc_start: 0.4488 (mtt) cc_final: 0.3960 (mtt) REVERT: D 419 ILE cc_start: 0.3551 (mm) cc_final: 0.3214 (mt) REVERT: D 439 MET cc_start: 0.8762 (ppp) cc_final: 0.8534 (ppp) REVERT: D 634 LYS cc_start: 0.8177 (mttp) cc_final: 0.7977 (mmtt) REVERT: D 691 LEU cc_start: 0.6326 (mp) cc_final: 0.6064 (tp) REVERT: E 85 MET cc_start: 0.1712 (tpt) cc_final: 0.1268 (ptp) REVERT: E 421 LEU cc_start: 0.7659 (mm) cc_final: 0.7371 (mt) REVERT: E 713 MET cc_start: 0.7581 (ppp) cc_final: 0.7235 (ppp) REVERT: F 401 MET cc_start: 0.8127 (tpt) cc_final: 0.7629 (tmm) REVERT: F 427 MET cc_start: 0.5869 (tpt) cc_final: 0.4799 (tpt) REVERT: F 583 TYR cc_start: 0.7395 (m-80) cc_final: 0.7163 (m-10) REVERT: F 633 MET cc_start: 0.8580 (ttt) cc_final: 0.8127 (ptp) REVERT: F 698 MET cc_start: 0.0775 (mmt) cc_final: -0.1439 (mmt) outliers start: 5 outliers final: 2 residues processed: 300 average time/residue: 0.2104 time to fit residues: 103.3897 Evaluate side-chains 243 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain D residue 350 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 GLN A 407 HIS A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** B 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 666 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.125876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.084168 restraints weight = 138329.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084088 restraints weight = 193895.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084088 restraints weight = 192683.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084088 restraints weight = 192683.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084088 restraints weight = 192683.457| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6218 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 37128 Z= 0.186 Angle : 0.745 12.347 50324 Z= 0.383 Chirality : 0.046 0.217 5736 Planarity : 0.006 0.061 6548 Dihedral : 6.931 129.960 5122 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.94 % Favored : 94.03 % Rotamer: Outliers : 0.74 % Allowed : 7.09 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.11), residues: 4626 helix: -0.86 (0.11), residues: 1993 sheet: -1.91 (0.21), residues: 528 loop : -1.89 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 374 TYR 0.043 0.002 TYR C 577 PHE 0.029 0.002 PHE F 203 TRP 0.028 0.002 TRP C 431 HIS 0.013 0.002 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (37128) covalent geometry : angle 0.74526 / 0.38 (50324) hydrogen bonds : bond 0.04632 / 3.08 ( 1505) hydrogen bonds : angle 6.00196 / 4.27 ( 4395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: -0.0533 (mtm) cc_final: -0.0883 (mmt) REVERT: A 258 MET cc_start: 0.6296 (mpp) cc_final: 0.6063 (mpp) REVERT: A 381 LEU cc_start: 0.9599 (mt) cc_final: 0.8958 (tt) REVERT: A 427 MET cc_start: 0.6606 (ptt) cc_final: 0.6214 (tmm) REVERT: A 650 ASP cc_start: 0.8244 (m-30) cc_final: 0.7952 (t70) REVERT: B 38 MET cc_start: 0.3869 (mpp) cc_final: 0.3438 (mpp) REVERT: B 218 ASP cc_start: 0.9111 (t70) cc_final: 0.8878 (m-30) REVERT: B 409 MET cc_start: 0.4093 (ppp) cc_final: 0.3872 (ppp) REVERT: B 496 MET cc_start: 0.8656 (tmm) cc_final: 0.8429 (tmm) REVERT: C 401 MET cc_start: 0.6457 (mmm) cc_final: 0.5763 (mmm) REVERT: D 75 MET cc_start: 0.6534 (pmm) cc_final: 0.5757 (ptt) REVERT: D 160 MET cc_start: 0.7675 (ppp) cc_final: 0.7465 (ppp) REVERT: D 276 MET cc_start: -0.0679 (mpp) cc_final: -0.1034 (mpp) REVERT: D 427 MET cc_start: 0.8157 (tpt) cc_final: 0.7923 (mmm) REVERT: D 439 MET cc_start: 0.9257 (ppp) cc_final: 0.9034 (ppp) REVERT: D 691 LEU cc_start: 0.5975 (mp) cc_final: 0.5600 (tp) REVERT: E 75 MET cc_start: -0.0778 (mpp) cc_final: -0.0985 (mpp) REVERT: E 85 MET cc_start: 0.1407 (tpt) cc_final: 0.1143 (ptp) REVERT: E 401 MET cc_start: 0.8366 (tpp) cc_final: 0.7479 (ppp) REVERT: E 431 TRP cc_start: 0.7521 (t60) cc_final: 0.7309 (t60) REVERT: E 633 MET cc_start: 0.8227 (mmm) cc_final: 0.7920 (mmm) REVERT: E 698 MET cc_start: -0.1072 (mtt) cc_final: -0.1389 (mmm) REVERT: E 713 MET cc_start: 0.7512 (ppp) cc_final: 0.7260 (ppp) REVERT: F 276 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7701 (ppp) REVERT: F 427 MET cc_start: 0.5801 (tpt) cc_final: 0.5031 (tpt) REVERT: F 583 TYR cc_start: 0.7470 (m-80) cc_final: 0.7236 (m-10) REVERT: F 635 GLU cc_start: 0.9208 (mp0) cc_final: 0.8963 (mp0) REVERT: F 698 MET cc_start: 0.1349 (mmt) cc_final: 0.1135 (mmt) outliers start: 29 outliers final: 17 residues processed: 280 average time/residue: 0.2224 time to fit residues: 102.8137 Evaluate side-chains 245 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 276 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 329 optimal weight: 3.9990 chunk 59 optimal weight: 30.0000 chunk 347 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 chunk 331 optimal weight: 20.0000 chunk 114 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 HIS ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN E 664 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 742 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.124719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.084435 restraints weight = 139338.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.082042 restraints weight = 207884.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.081555 restraints weight = 227529.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.081555 restraints weight = 230882.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.081555 restraints weight = 230882.598| |-----------------------------------------------------------------------------| r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37128 Z= 0.169 Angle : 0.699 11.040 50324 Z= 0.355 Chirality : 0.045 0.179 5736 Planarity : 0.005 0.062 6548 Dihedral : 6.574 125.617 5120 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.46 % Allowed : 10.02 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.12), residues: 4626 helix: -0.45 (0.11), residues: 1991 sheet: -2.08 (0.21), residues: 526 loop : -1.75 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 552 TYR 0.019 0.002 TYR C 577 PHE 0.024 0.002 PHE F 203 TRP 0.030 0.002 TRP C 431 HIS 0.009 0.001 HIS F 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (37128) covalent geometry : angle 0.69913 / 0.36 (50324) hydrogen bonds : bond 0.04265 / 2.88 ( 1505) hydrogen bonds : angle 5.63846 / 4.04 ( 4395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9624 (mt) cc_final: 0.9212 (tt) REVERT: A 409 MET cc_start: 0.9450 (mmm) cc_final: 0.8156 (tmm) REVERT: A 427 MET cc_start: 0.6276 (ptt) cc_final: 0.5799 (tmm) REVERT: A 650 ASP cc_start: 0.8238 (m-30) cc_final: 0.7911 (t0) REVERT: B 38 MET cc_start: 0.4265 (mpp) cc_final: 0.3975 (mmm) REVERT: B 439 MET cc_start: 0.8879 (mmt) cc_final: 0.8601 (mmt) REVERT: B 496 MET cc_start: 0.8331 (tmm) cc_final: 0.8066 (tmm) REVERT: C 217 MET cc_start: 0.7356 (tpt) cc_final: 0.6237 (mmm) REVERT: C 401 MET cc_start: 0.6292 (mmm) cc_final: 0.5671 (mmm) REVERT: D 75 MET cc_start: 0.6531 (pmm) cc_final: 0.6059 (pmm) REVERT: D 160 MET cc_start: 0.7744 (ppp) cc_final: 0.7534 (ppp) REVERT: D 439 MET cc_start: 0.9269 (ppp) cc_final: 0.8670 (ptt) REVERT: D 552 ARG cc_start: 0.7334 (mmm160) cc_final: 0.5977 (mmp80) REVERT: D 713 MET cc_start: 0.7986 (tmm) cc_final: 0.7497 (tmm) REVERT: E 75 MET cc_start: -0.0623 (mpp) cc_final: -0.0839 (mpp) REVERT: E 85 MET cc_start: 0.1631 (tpt) cc_final: 0.1428 (ptp) REVERT: E 401 MET cc_start: 0.8538 (tpp) cc_final: 0.7808 (ppp) REVERT: E 439 MET cc_start: 0.8768 (mmm) cc_final: 0.8493 (mmm) REVERT: E 683 MET cc_start: 0.3695 (mpp) cc_final: 0.3463 (mpp) REVERT: E 698 MET cc_start: -0.0950 (mtt) cc_final: -0.1171 (mmm) REVERT: E 713 MET cc_start: 0.7515 (ppp) cc_final: 0.7062 (ppp) REVERT: F 276 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7987 (ppp) REVERT: F 427 MET cc_start: 0.6200 (tpt) cc_final: 0.5690 (tpt) REVERT: F 583 TYR cc_start: 0.7526 (m-80) cc_final: 0.7306 (m-10) REVERT: F 698 MET cc_start: 0.1539 (mmt) cc_final: 0.1248 (mmt) outliers start: 57 outliers final: 33 residues processed: 276 average time/residue: 0.2198 time to fit residues: 102.1332 Evaluate side-chains 257 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 634 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 150 optimal weight: 0.9990 chunk 300 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 chunk 91 optimal weight: 40.0000 chunk 45 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 303 optimal weight: 0.8980 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 ASN ** F 510 GLN ** 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 = 0.4880 r_free = 0.4880 target = 0.126953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.084954 restraints weight = 134212.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.083965 restraints weight = 191317.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.083839 restraints weight = 201916.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.083839 restraints weight = 206405.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.083839 restraints weight = 206405.310| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37128 Z= 0.129 Angle : 0.648 12.559 50324 Z= 0.326 Chirality : 0.044 0.185 5736 Planarity : 0.005 0.059 6548 Dihedral : 6.269 125.367 5120 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.26 % Allowed : 12.22 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.12), residues: 4626 helix: -0.13 (0.11), residues: 1997 sheet: -1.88 (0.21), residues: 548 loop : -1.61 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 552 TYR 0.015 0.001 TYR B 320 PHE 0.019 0.001 PHE F 203 TRP 0.030 0.002 TRP C 431 HIS 0.008 0.001 HIS E 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (37128) covalent geometry : angle 0.64810 / 0.33 (50324) hydrogen bonds : bond 0.03816 / 2.57 ( 1505) hydrogen bonds : angle 5.29132 / 3.79 ( 4395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 233 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9592 (mt) cc_final: 0.9070 (tp) REVERT: A 409 MET cc_start: 0.9448 (mmm) cc_final: 0.8179 (tmm) REVERT: A 427 MET cc_start: 0.5974 (ptt) cc_final: 0.5623 (tmm) REVERT: A 650 ASP cc_start: 0.8037 (m-30) cc_final: 0.7650 (t0) REVERT: A 698 MET cc_start: 0.4133 (tpt) cc_final: 0.2763 (mmm) REVERT: B 38 MET cc_start: 0.4270 (mpp) cc_final: 0.3890 (mmm) REVERT: B 409 MET cc_start: 0.4184 (ppp) cc_final: 0.3925 (ppp) REVERT: B 439 MET cc_start: 0.8810 (mmt) cc_final: 0.8453 (mmt) REVERT: B 496 MET cc_start: 0.8631 (tmm) cc_final: 0.8289 (tmm) REVERT: C 401 MET cc_start: 0.6462 (mmm) cc_final: 0.5947 (mmm) REVERT: C 427 MET cc_start: 0.7154 (tmm) cc_final: 0.6620 (tmm) REVERT: D 75 MET cc_start: 0.6574 (pmm) cc_final: 0.6116 (pmm) REVERT: D 361 LYS cc_start: 0.7697 (mttt) cc_final: 0.6820 (pptt) REVERT: D 427 MET cc_start: 0.8108 (mmm) cc_final: 0.7506 (tmm) REVERT: D 439 MET cc_start: 0.9331 (ppp) cc_final: 0.8938 (ppp) REVERT: D 713 MET cc_start: 0.7892 (tmm) cc_final: 0.7257 (tmm) REVERT: E 75 MET cc_start: -0.0645 (mpp) cc_final: -0.0869 (mpp) REVERT: E 401 MET cc_start: 0.8677 (tpp) cc_final: 0.7964 (ppp) REVERT: E 439 MET cc_start: 0.8913 (mmm) cc_final: 0.8521 (mmt) REVERT: E 633 MET cc_start: 0.8128 (mmm) cc_final: 0.7928 (mmm) REVERT: E 698 MET cc_start: -0.1134 (mtt) cc_final: -0.1395 (mmm) REVERT: E 713 MET cc_start: 0.7434 (ppp) cc_final: 0.6966 (ppp) REVERT: F 427 MET cc_start: 0.5880 (tpt) cc_final: 0.5264 (tpt) REVERT: F 496 MET cc_start: 0.6350 (pmm) cc_final: 0.6132 (pmm) REVERT: F 583 TYR cc_start: 0.7531 (m-80) cc_final: 0.7320 (m-10) REVERT: F 698 MET cc_start: 0.1912 (mmt) cc_final: 0.0706 (mmt) outliers start: 49 outliers final: 30 residues processed: 269 average time/residue: 0.2227 time to fit residues: 99.8774 Evaluate side-chains 249 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 516 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 635 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 305 optimal weight: 7.9990 chunk 327 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 93 optimal weight: 50.0000 chunk 70 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 447 optimal weight: 30.0000 chunk 296 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 340 GLN ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN D 499 GLN E 168 HIS ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 726 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.119423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.080496 restraints weight = 140253.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.080496 restraints weight = 206835.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.080496 restraints weight = 206836.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.080496 restraints weight = 206837.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.080496 restraints weight = 206837.020| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37128 Z= 0.216 Angle : 0.743 12.035 50324 Z= 0.376 Chirality : 0.046 0.246 5736 Planarity : 0.006 0.066 6548 Dihedral : 6.449 120.462 5120 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 26.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.93 % Allowed : 13.53 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.12), residues: 4626 helix: -0.26 (0.11), residues: 2010 sheet: -2.01 (0.21), residues: 550 loop : -1.67 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 484 TYR 0.030 0.002 TYR D 225 PHE 0.024 0.002 PHE F 451 TRP 0.033 0.002 TRP C 431 HIS 0.011 0.002 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.22 (37128) covalent geometry : angle 0.74314 / 0.38 (50324) hydrogen bonds : bond 0.04278 / 2.88 ( 1505) hydrogen bonds : angle 5.52389 / 3.96 ( 4395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9600 (mt) cc_final: 0.9081 (tt) REVERT: A 409 MET cc_start: 0.9523 (mmm) cc_final: 0.8454 (tmm) REVERT: A 427 MET cc_start: 0.6286 (ptt) cc_final: 0.5828 (tmm) REVERT: A 462 LEU cc_start: 0.7997 (mp) cc_final: 0.7442 (tp) REVERT: A 541 ARG cc_start: 0.8256 (tpt170) cc_final: 0.8025 (tpt170) REVERT: A 650 ASP cc_start: 0.8348 (m-30) cc_final: 0.8040 (t0) REVERT: B 38 MET cc_start: 0.4281 (mpp) cc_final: 0.3986 (mpp) REVERT: B 160 MET cc_start: 0.8121 (tmm) cc_final: 0.7918 (tpt) REVERT: B 409 MET cc_start: 0.4089 (ppp) cc_final: 0.3839 (ppp) REVERT: B 439 MET cc_start: 0.8856 (mmt) cc_final: 0.8476 (mmt) REVERT: B 496 MET cc_start: 0.8718 (tmm) cc_final: 0.8374 (tmm) REVERT: B 698 MET cc_start: 0.7835 (ptm) cc_final: 0.7400 (pmm) REVERT: C 217 MET cc_start: 0.7397 (tpt) cc_final: 0.6246 (mmm) REVERT: D 75 MET cc_start: 0.6764 (pmm) cc_final: 0.6328 (pmm) REVERT: D 160 MET cc_start: 0.7520 (ppp) cc_final: 0.7308 (ppp) REVERT: D 361 LYS cc_start: 0.7715 (mttt) cc_final: 0.6940 (pptt) REVERT: D 419 ILE cc_start: 0.4204 (mm) cc_final: 0.3995 (mm) REVERT: D 439 MET cc_start: 0.9366 (ppp) cc_final: 0.9042 (ppp) REVERT: D 691 LEU cc_start: 0.6504 (mp) cc_final: 0.6104 (mt) REVERT: E 75 MET cc_start: 0.1227 (mpp) cc_final: 0.1007 (mpp) REVERT: E 401 MET cc_start: 0.8718 (tpp) cc_final: 0.7942 (ppp) REVERT: E 439 MET cc_start: 0.9003 (mmm) cc_final: 0.8692 (mmt) REVERT: E 698 MET cc_start: -0.0162 (mtt) cc_final: -0.0540 (mtt) REVERT: E 713 MET cc_start: 0.7574 (ppp) cc_final: 0.7043 (ppp) REVERT: F 328 ARG cc_start: 0.7883 (mpt180) cc_final: 0.7359 (tpt170) REVERT: F 427 MET cc_start: 0.6193 (tpt) cc_final: 0.5720 (tpt) REVERT: F 583 TYR cc_start: 0.7523 (m-80) cc_final: 0.7322 (m-10) outliers start: 75 outliers final: 50 residues processed: 285 average time/residue: 0.2092 time to fit residues: 100.4459 Evaluate side-chains 273 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 638 GLN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 431 TRP Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 634 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 287 optimal weight: 8.9990 chunk 433 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 422 optimal weight: 1.9990 chunk 375 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 311 optimal weight: 50.0000 chunk 77 optimal weight: 50.0000 chunk 338 optimal weight: 10.0000 chunk 319 optimal weight: 50.0000 chunk 108 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.117489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.082763 restraints weight = 120853.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.082763 restraints weight = 172259.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.082763 restraints weight = 172259.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.082763 restraints weight = 172259.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.082763 restraints weight = 172259.175| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37128 Z= 0.185 Angle : 0.714 11.216 50324 Z= 0.360 Chirality : 0.046 0.196 5736 Planarity : 0.005 0.058 6548 Dihedral : 6.402 118.280 5120 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.34 % Allowed : 14.46 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.12), residues: 4626 helix: -0.19 (0.11), residues: 2006 sheet: -2.11 (0.21), residues: 562 loop : -1.68 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 395 TYR 0.037 0.002 TYR D 225 PHE 0.017 0.002 PHE F 203 TRP 0.029 0.002 TRP C 431 HIS 0.011 0.002 HIS E 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (37128) covalent geometry : angle 0.71374 / 0.36 (50324) hydrogen bonds : bond 0.04041 / 2.71 ( 1505) hydrogen bonds : angle 5.43218 / 3.90 ( 4395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 230 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9599 (mt) cc_final: 0.9085 (tp) REVERT: A 409 MET cc_start: 0.9466 (mmm) cc_final: 0.8365 (tmm) REVERT: A 650 ASP cc_start: 0.8292 (m-30) cc_final: 0.7979 (t0) REVERT: B 38 MET cc_start: 0.3234 (mpp) cc_final: 0.3023 (mpp) REVERT: B 409 MET cc_start: 0.4013 (ppp) cc_final: 0.3658 (ppp) REVERT: B 439 MET cc_start: 0.8997 (mmt) cc_final: 0.8605 (mmt) REVERT: B 470 THR cc_start: 0.8121 (p) cc_final: 0.7712 (p) REVERT: B 496 MET cc_start: 0.8520 (tmm) cc_final: 0.8240 (tmm) REVERT: D 75 MET cc_start: 0.5621 (pmm) cc_final: 0.5209 (pmm) REVERT: D 160 MET cc_start: 0.7318 (ppp) cc_final: 0.7047 (ppp) REVERT: D 230 MET cc_start: 0.4263 (ptm) cc_final: 0.4016 (ptm) REVERT: D 258 MET cc_start: 0.2647 (mtt) cc_final: 0.1998 (mtm) REVERT: D 361 LYS cc_start: 0.7561 (mttt) cc_final: 0.6818 (pptt) REVERT: D 439 MET cc_start: 0.9373 (ppp) cc_final: 0.9045 (ppp) REVERT: D 713 MET cc_start: 0.8190 (tmm) cc_final: 0.7552 (tmm) REVERT: E 85 MET cc_start: 0.2639 (tpt) cc_final: 0.1920 (ptp) REVERT: E 401 MET cc_start: 0.8769 (tpp) cc_final: 0.8007 (ppp) REVERT: E 439 MET cc_start: 0.8879 (mmm) cc_final: 0.8616 (mmm) REVERT: E 683 MET cc_start: 0.4777 (OUTLIER) cc_final: 0.4350 (mtp) REVERT: E 698 MET cc_start: -0.0300 (mtt) cc_final: -0.0738 (mtt) REVERT: E 713 MET cc_start: 0.7100 (ppp) cc_final: 0.6410 (ppp) REVERT: F 328 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7538 (tpt170) REVERT: F 350 ILE cc_start: 0.4030 (pt) cc_final: 0.3784 (mp) REVERT: F 427 MET cc_start: 0.5805 (tpt) cc_final: 0.5329 (tpt) REVERT: F 485 MET cc_start: 0.6912 (mmm) cc_final: 0.6638 (mmm) REVERT: F 496 MET cc_start: 0.6004 (pmm) cc_final: 0.5788 (pmm) REVERT: F 583 TYR cc_start: 0.7516 (m-80) cc_final: 0.7274 (m-10) outliers start: 91 outliers final: 59 residues processed: 299 average time/residue: 0.2287 time to fit residues: 114.5582 Evaluate side-chains 287 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 227 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 635 GLU Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 634 LYS Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 259 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 174 optimal weight: 50.0000 chunk 442 optimal weight: 10.0000 chunk 436 optimal weight: 30.0000 chunk 367 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 666 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** 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 = 0.4780 r_free = 0.4780 target = 0.114470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.078254 restraints weight = 133108.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.078254 restraints weight = 179754.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.078254 restraints weight = 179754.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.078254 restraints weight = 179754.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.078254 restraints weight = 179754.130| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 37128 Z= 0.213 Angle : 0.761 11.551 50324 Z= 0.384 Chirality : 0.047 0.222 5736 Planarity : 0.005 0.056 6548 Dihedral : 6.510 115.858 5120 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 28.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.41 % Allowed : 15.49 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.12), residues: 4626 helix: -0.27 (0.11), residues: 2002 sheet: -2.19 (0.21), residues: 558 loop : -1.70 (0.14), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 584 TYR 0.026 0.002 TYR C 332 PHE 0.022 0.002 PHE F 451 TRP 0.032 0.002 TRP C 431 HIS 0.009 0.002 HIS E 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 (37128) covalent geometry : angle 0.76126 / 0.38 (50324) hydrogen bonds : bond 0.04257 / 2.87 ( 1505) hydrogen bonds : angle 5.59642 / 4.01 ( 4395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 238 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9605 (mt) cc_final: 0.9077 (tt) REVERT: A 409 MET cc_start: 0.9491 (mmm) cc_final: 0.8323 (tmm) REVERT: A 427 MET cc_start: 0.6064 (ptt) cc_final: 0.5603 (tmm) REVERT: A 534 TYR cc_start: 0.6350 (OUTLIER) cc_final: 0.5355 (m-10) REVERT: A 650 ASP cc_start: 0.8381 (m-30) cc_final: 0.8058 (t0) REVERT: B 38 MET cc_start: 0.3695 (mpp) cc_final: 0.3387 (mpp) REVERT: B 409 MET cc_start: 0.4368 (ppp) cc_final: 0.4017 (ppp) REVERT: B 439 MET cc_start: 0.8981 (mmt) cc_final: 0.8630 (mmt) REVERT: B 496 MET cc_start: 0.8523 (tmm) cc_final: 0.8255 (tmm) REVERT: B 545 ARG cc_start: 0.7594 (mmt180) cc_final: 0.6928 (ptt-90) REVERT: D 75 MET cc_start: 0.6208 (pmm) cc_final: 0.5760 (pmm) REVERT: D 160 MET cc_start: 0.7394 (ppp) cc_final: 0.7153 (ppp) REVERT: D 230 MET cc_start: 0.4472 (ptm) cc_final: 0.4102 (ptm) REVERT: D 258 MET cc_start: 0.2754 (mtt) cc_final: 0.2091 (mtm) REVERT: D 361 LYS cc_start: 0.7629 (mttt) cc_final: 0.6756 (ptmm) REVERT: D 439 MET cc_start: 0.9369 (ppp) cc_final: 0.9034 (ppp) REVERT: D 516 MET cc_start: 0.4045 (mmm) cc_final: 0.3837 (tpt) REVERT: D 691 LEU cc_start: 0.7057 (mp) cc_final: 0.6640 (mt) REVERT: E 85 MET cc_start: 0.2470 (tpt) cc_final: 0.1793 (ptp) REVERT: E 276 MET cc_start: 0.7989 (mpp) cc_final: 0.7680 (mpp) REVERT: E 401 MET cc_start: 0.8856 (tpp) cc_final: 0.8029 (ppp) REVERT: E 439 MET cc_start: 0.9050 (mmm) cc_final: 0.8779 (mmm) REVERT: E 683 MET cc_start: 0.4987 (OUTLIER) cc_final: 0.4746 (mtp) REVERT: E 698 MET cc_start: -0.0003 (mtt) cc_final: -0.0310 (mtt) REVERT: E 713 MET cc_start: 0.6676 (ppp) cc_final: 0.6337 (ppp) REVERT: F 328 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7325 (tpt90) REVERT: F 350 ILE cc_start: 0.4444 (pt) cc_final: 0.4237 (mp) REVERT: F 427 MET cc_start: 0.6542 (tpt) cc_final: 0.6191 (tpt) REVERT: F 475 GLN cc_start: 0.7675 (mp10) cc_final: 0.7164 (pm20) REVERT: F 485 MET cc_start: 0.7260 (mmm) cc_final: 0.6949 (mmm) REVERT: F 583 TYR cc_start: 0.7571 (m-80) cc_final: 0.7318 (m-10) REVERT: F 698 MET cc_start: 0.1594 (mmp) cc_final: 0.1278 (mmp) outliers start: 94 outliers final: 68 residues processed: 314 average time/residue: 0.2046 time to fit residues: 107.0512 Evaluate side-chains 300 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 230 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 537 GLU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 529 ARG Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 231 LYS Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 332 TYR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 708 LEU Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 770 LEU Chi-restraints excluded: chain E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 634 LYS Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 304 optimal weight: 8.9990 chunk 333 optimal weight: 0.0980 chunk 187 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 410 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.120472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.086790 restraints weight = 117956.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.083469 restraints weight = 172504.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.083236 restraints weight = 203240.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.083236 restraints weight = 211946.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.083236 restraints weight = 211945.482| |-----------------------------------------------------------------------------| r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37128 Z= 0.131 Angle : 0.700 12.721 50324 Z= 0.349 Chirality : 0.045 0.206 5736 Planarity : 0.005 0.053 6548 Dihedral : 6.204 117.047 5120 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.00 % Allowed : 16.31 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.12), residues: 4626 helix: 0.01 (0.11), residues: 2007 sheet: -1.95 (0.21), residues: 556 loop : -1.64 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 395 TYR 0.028 0.001 TYR D 225 PHE 0.014 0.001 PHE B 132 TRP 0.024 0.001 TRP D 602 HIS 0.008 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (37128) covalent geometry : angle 0.69991 / 0.35 (50324) hydrogen bonds : bond 0.03755 / 2.52 ( 1505) hydrogen bonds : angle 5.21266 / 3.73 ( 4395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 247 time to evaluate : 1.121 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 381 LEU cc_start: 0.9580 (mt) cc_final: 0.9015 (tp) REVERT: A 409 MET cc_start: 0.9454 (mmm) cc_final: 0.8369 (tmm) REVERT: A 427 MET cc_start: 0.5964 (ptt) cc_final: 0.5589 (tmm) REVERT: A 534 TYR cc_start: 0.5951 (OUTLIER) cc_final: 0.5205 (m-10) REVERT: A 650 ASP cc_start: 0.8321 (m-30) cc_final: 0.7921 (t0) REVERT: A 698 MET cc_start: 0.4364 (tpt) cc_final: 0.3194 (mmm) REVERT: A 702 MET cc_start: 0.5081 (tmm) cc_final: 0.3941 (tmm) REVERT: B 38 MET cc_start: 0.3300 (mpp) cc_final: 0.3078 (mpp) REVERT: B 276 MET cc_start: 0.6707 (tpt) cc_final: 0.6491 (tpt) REVERT: B 409 MET cc_start: 0.4251 (ppp) cc_final: 0.3842 (ppp) REVERT: B 432 ARG cc_start: 0.3919 (OUTLIER) cc_final: 0.3052 (tpt90) REVERT: B 439 MET cc_start: 0.9019 (mmt) cc_final: 0.8621 (mmt) REVERT: B 496 MET cc_start: 0.8560 (tmm) cc_final: 0.8260 (tmm) REVERT: B 545 ARG cc_start: 0.7483 (mmt180) cc_final: 0.6836 (ptt-90) REVERT: B 635 GLU cc_start: 0.7600 (tp30) cc_final: 0.7266 (tp30) REVERT: C 217 MET cc_start: 0.7486 (tpt) cc_final: 0.6306 (mmm) REVERT: C 254 GLU cc_start: 0.2844 (OUTLIER) cc_final: 0.2096 (mt-10) REVERT: C 427 MET cc_start: 0.7320 (tmm) cc_final: 0.6815 (tpp) REVERT: C 447 GLN cc_start: 0.6563 (OUTLIER) cc_final: 0.5688 (pm20) REVERT: C 713 MET cc_start: 0.8234 (mpp) cc_final: 0.7507 (mpp) REVERT: D 75 MET cc_start: 0.5857 (pmm) cc_final: 0.5434 (pmm) REVERT: D 160 MET cc_start: 0.7368 (ppp) cc_final: 0.7134 (ppp) REVERT: D 258 MET cc_start: 0.3236 (mtt) cc_final: 0.1784 (ttm) REVERT: D 361 LYS cc_start: 0.7533 (mttt) cc_final: 0.6649 (ptmm) REVERT: D 427 MET cc_start: 0.7944 (mmm) cc_final: 0.6624 (tmm) REVERT: D 439 MET cc_start: 0.9407 (ppp) cc_final: 0.8874 (ptt) REVERT: D 633 MET cc_start: 0.7665 (mmm) cc_final: 0.7242 (mmm) REVERT: D 663 LEU cc_start: 0.7383 (tt) cc_final: 0.6973 (tp) REVERT: D 713 MET cc_start: 0.8060 (tmm) cc_final: 0.7480 (tmm) REVERT: E 85 MET cc_start: 0.2902 (tpt) cc_final: 0.2301 (ptp) REVERT: E 258 MET cc_start: 0.3094 (mmt) cc_final: 0.2579 (mmp) REVERT: E 276 MET cc_start: 0.7709 (mpp) cc_final: 0.7419 (mpp) REVERT: E 401 MET cc_start: 0.8930 (tpp) cc_final: 0.8212 (ppp) REVERT: E 439 MET cc_start: 0.8737 (mmm) cc_final: 0.8505 (mmm) REVERT: E 683 MET cc_start: 0.4815 (OUTLIER) cc_final: 0.4468 (mtp) REVERT: E 698 MET cc_start: -0.0644 (mtt) cc_final: -0.1498 (mmm) REVERT: F 222 ARG cc_start: 0.9233 (mmp-170) cc_final: 0.9021 (mmp80) REVERT: F 233 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6927 (tt) REVERT: F 328 ARG cc_start: 0.7877 (mpt180) cc_final: 0.7379 (tpt90) REVERT: F 350 ILE cc_start: 0.3755 (pt) cc_final: 0.3543 (mp) REVERT: F 427 MET cc_start: 0.5896 (tpt) cc_final: 0.5473 (tpt) REVERT: F 475 GLN cc_start: 0.7621 (mp10) cc_final: 0.7122 (pm20) REVERT: F 485 MET cc_start: 0.6942 (mmm) cc_final: 0.6672 (mmm) REVERT: F 496 MET cc_start: 0.6144 (pmm) cc_final: 0.5909 (pmm) REVERT: F 583 TYR cc_start: 0.7613 (m-80) cc_final: 0.7388 (m-10) outliers start: 78 outliers final: 52 residues processed: 309 average time/residue: 0.1986 time to fit residues: 102.3621 Evaluate side-chains 284 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 332 TYR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 319 HIS Chi-restraints excluded: chain F residue 368 ILE Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 134 optimal weight: 8.9990 chunk 209 optimal weight: 8.9990 chunk 0 optimal weight: 90.0000 chunk 293 optimal weight: 8.9990 chunk 402 optimal weight: 50.0000 chunk 399 optimal weight: 3.9990 chunk 150 optimal weight: 9.9990 chunk 42 optimal weight: 30.0000 chunk 237 optimal weight: 30.0000 chunk 305 optimal weight: 5.9990 chunk 279 optimal weight: 0.3980 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.114534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.082076 restraints weight = 127024.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.079369 restraints weight = 181312.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.079141 restraints weight = 211100.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.079139 restraints weight = 216068.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.079139 restraints weight = 216174.153| |-----------------------------------------------------------------------------| r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37128 Z= 0.199 Angle : 0.763 12.338 50324 Z= 0.382 Chirality : 0.047 0.221 5736 Planarity : 0.005 0.060 6548 Dihedral : 6.329 116.239 5120 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 27.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.05 % Allowed : 16.80 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.12), residues: 4626 helix: -0.12 (0.11), residues: 2000 sheet: -2.09 (0.21), residues: 578 loop : -1.64 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 529 TYR 0.034 0.002 TYR D 225 PHE 0.020 0.002 PHE F 451 TRP 0.022 0.002 TRP C 602 HIS 0.009 0.002 HIS E 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.20 (37128) covalent geometry : angle 0.76255 / 0.38 (50324) hydrogen bonds : bond 0.04098 / 2.77 ( 1505) hydrogen bonds : angle 5.42892 / 3.89 ( 4395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 239 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9624 (mt) cc_final: 0.9095 (tt) REVERT: A 409 MET cc_start: 0.9434 (mmm) cc_final: 0.8446 (tmm) REVERT: A 427 MET cc_start: 0.6146 (ptt) cc_final: 0.5738 (tmm) REVERT: A 534 TYR cc_start: 0.6254 (OUTLIER) cc_final: 0.5279 (m-10) REVERT: A 650 ASP cc_start: 0.8401 (m-30) cc_final: 0.8034 (t0) REVERT: A 698 MET cc_start: 0.4673 (tpt) cc_final: 0.3293 (mmm) REVERT: A 702 MET cc_start: 0.5152 (tmm) cc_final: 0.4048 (tmm) REVERT: B 38 MET cc_start: 0.3502 (mpp) cc_final: 0.3208 (mpp) REVERT: B 409 MET cc_start: 0.4531 (ppp) cc_final: 0.4155 (ppp) REVERT: B 432 ARG cc_start: 0.4260 (OUTLIER) cc_final: 0.3548 (tpt90) REVERT: B 439 MET cc_start: 0.9140 (mmt) cc_final: 0.8725 (mmt) REVERT: B 470 THR cc_start: 0.8315 (p) cc_final: 0.8113 (p) REVERT: B 496 MET cc_start: 0.8729 (tmm) cc_final: 0.8451 (tmm) REVERT: C 217 MET cc_start: 0.7387 (tpt) cc_final: 0.6191 (mmm) REVERT: C 254 GLU cc_start: 0.2899 (OUTLIER) cc_final: 0.2143 (mt-10) REVERT: C 524 ASP cc_start: 0.9213 (p0) cc_final: 0.8558 (m-30) REVERT: D 75 MET cc_start: 0.6014 (pmm) cc_final: 0.5762 (pmm) REVERT: D 160 MET cc_start: 0.7395 (ppp) cc_final: 0.7167 (ppp) REVERT: D 258 MET cc_start: 0.2245 (mtt) cc_final: 0.0868 (ttm) REVERT: D 361 LYS cc_start: 0.7529 (mttt) cc_final: 0.6711 (ptmm) REVERT: D 427 MET cc_start: 0.7975 (mmm) cc_final: 0.6922 (tpp) REVERT: D 439 MET cc_start: 0.9432 (ppp) cc_final: 0.8839 (ptt) REVERT: D 516 MET cc_start: 0.4147 (mmm) cc_final: 0.3913 (tpt) REVERT: D 702 MET cc_start: 0.6248 (mpp) cc_final: 0.5591 (mmm) REVERT: D 713 MET cc_start: 0.8147 (tmm) cc_final: 0.7487 (tmm) REVERT: E 85 MET cc_start: 0.2956 (tpt) cc_final: 0.2367 (ptp) REVERT: E 276 MET cc_start: 0.7677 (mpp) cc_final: 0.7339 (mpp) REVERT: E 401 MET cc_start: 0.8980 (tpp) cc_final: 0.8208 (ppp) REVERT: E 439 MET cc_start: 0.8781 (mmm) cc_final: 0.8569 (mmm) REVERT: E 683 MET cc_start: 0.4947 (OUTLIER) cc_final: 0.4650 (mtp) REVERT: E 713 MET cc_start: 0.6316 (ppp) cc_final: 0.6026 (ppp) REVERT: F 328 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7597 (tpt90) REVERT: F 350 ILE cc_start: 0.4266 (pt) cc_final: 0.3993 (mp) REVERT: F 427 MET cc_start: 0.6218 (tpt) cc_final: 0.5903 (tpt) REVERT: F 475 GLN cc_start: 0.7727 (mp10) cc_final: 0.7267 (pm20) REVERT: F 485 MET cc_start: 0.7137 (mmm) cc_final: 0.6769 (mmm) REVERT: F 496 MET cc_start: 0.6202 (pmm) cc_final: 0.5874 (pmm) REVERT: F 583 TYR cc_start: 0.7680 (m-80) cc_final: 0.7439 (m-10) REVERT: F 698 MET cc_start: 0.1346 (mmp) cc_final: 0.1094 (mmp) outliers start: 80 outliers final: 59 residues processed: 301 average time/residue: 0.2081 time to fit residues: 104.8666 Evaluate side-chains 297 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 234 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 527 ILE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 332 TYR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 594 VAL Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 29 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 265 optimal weight: 0.0470 chunk 166 optimal weight: 50.0000 chunk 425 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 263 optimal weight: 4.9990 chunk 300 optimal weight: 0.3980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** 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 = 0.4845 r_free = 0.4845 target = 0.122626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.084366 restraints weight = 135533.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.080696 restraints weight = 200814.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.080615 restraints weight = 216454.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.080615 restraints weight = 221873.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.080615 restraints weight = 221873.674| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37128 Z= 0.128 Angle : 0.717 13.261 50324 Z= 0.356 Chirality : 0.046 0.254 5736 Planarity : 0.005 0.063 6548 Dihedral : 6.074 117.005 5120 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.67 % Allowed : 17.31 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.12), residues: 4626 helix: 0.10 (0.11), residues: 1996 sheet: -1.88 (0.22), residues: 540 loop : -1.57 (0.14), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 697 TYR 0.035 0.001 TYR D 225 PHE 0.013 0.001 PHE B 132 TRP 0.023 0.001 TRP D 602 HIS 0.009 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (37128) covalent geometry : angle 0.71671 / 0.36 (50324) hydrogen bonds : bond 0.03679 / 2.46 ( 1505) hydrogen bonds : angle 5.13311 / 3.67 ( 4395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 238 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 381 LEU cc_start: 0.9551 (mt) cc_final: 0.9216 (mm) REVERT: A 409 MET cc_start: 0.9471 (mmm) cc_final: 0.8448 (tmm) REVERT: A 427 MET cc_start: 0.6217 (ptt) cc_final: 0.5627 (mmm) REVERT: A 534 TYR cc_start: 0.5668 (OUTLIER) cc_final: 0.4923 (m-10) REVERT: A 650 ASP cc_start: 0.8189 (m-30) cc_final: 0.7709 (t0) REVERT: A 698 MET cc_start: 0.4130 (tpt) cc_final: 0.3000 (mmm) REVERT: A 702 MET cc_start: 0.4926 (tmm) cc_final: 0.4017 (tmm) REVERT: B 38 MET cc_start: 0.4112 (mpp) cc_final: 0.3745 (mpp) REVERT: B 207 LYS cc_start: 0.9255 (tptp) cc_final: 0.8805 (mmtt) REVERT: B 409 MET cc_start: 0.4413 (ppp) cc_final: 0.4050 (ppp) REVERT: B 432 ARG cc_start: 0.3890 (OUTLIER) cc_final: 0.2840 (tpt90) REVERT: B 439 MET cc_start: 0.9061 (mmt) cc_final: 0.8662 (mmt) REVERT: B 496 MET cc_start: 0.8647 (tmm) cc_final: 0.8296 (tmm) REVERT: B 635 GLU cc_start: 0.7651 (tp30) cc_final: 0.7244 (tp30) REVERT: C 254 GLU cc_start: 0.2561 (OUTLIER) cc_final: 0.2068 (mt-10) REVERT: C 427 MET cc_start: 0.7273 (tmm) cc_final: 0.6728 (tpp) REVERT: C 447 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.5583 (pm20) REVERT: D 75 MET cc_start: 0.6920 (pmm) cc_final: 0.6700 (pmm) REVERT: D 160 MET cc_start: 0.7482 (ppp) cc_final: 0.7271 (ppp) REVERT: D 258 MET cc_start: 0.3241 (mtt) cc_final: 0.1865 (ttm) REVERT: D 361 LYS cc_start: 0.7548 (mttt) cc_final: 0.6738 (ptmm) REVERT: D 516 MET cc_start: 0.3935 (mmm) cc_final: 0.3729 (tpt) REVERT: D 633 MET cc_start: 0.7796 (mmm) cc_final: 0.7526 (mmm) REVERT: D 663 LEU cc_start: 0.7343 (tt) cc_final: 0.6956 (tp) REVERT: D 702 MET cc_start: 0.6289 (mpp) cc_final: 0.5764 (mmm) REVERT: D 713 MET cc_start: 0.8072 (tmm) cc_final: 0.7447 (tmm) REVERT: E 85 MET cc_start: 0.2901 (tpt) cc_final: 0.2487 (ptp) REVERT: E 237 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6833 (mm) REVERT: E 401 MET cc_start: 0.8925 (tpp) cc_final: 0.8173 (ppp) REVERT: E 683 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.4446 (mtp) REVERT: F 222 ARG cc_start: 0.9219 (mmp-170) cc_final: 0.9004 (mmp80) REVERT: F 328 ARG cc_start: 0.7862 (mpt180) cc_final: 0.7428 (tpt90) REVERT: F 427 MET cc_start: 0.5993 (tpt) cc_final: 0.5632 (tpt) REVERT: F 475 GLN cc_start: 0.7736 (mp10) cc_final: 0.7240 (pm20) REVERT: F 485 MET cc_start: 0.7014 (mmm) cc_final: 0.6703 (mmm) REVERT: F 496 MET cc_start: 0.6654 (pmm) cc_final: 0.6453 (pmm) REVERT: F 698 MET cc_start: 0.1740 (mmp) cc_final: 0.1455 (mmp) outliers start: 65 outliers final: 53 residues processed: 289 average time/residue: 0.2066 time to fit residues: 99.2854 Evaluate side-chains 288 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 432 ARG Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 447 GLN Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 550 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 583 TYR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 332 TYR Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 407 HIS Chi-restraints excluded: chain D residue 431 TRP Chi-restraints excluded: chain D residue 472 ASN Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 632 VAL Chi-restraints excluded: chain D residue 638 GLN Chi-restraints excluded: chain D residue 664 HIS Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 750 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 328 ARG Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 683 MET Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 700 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 319 optimal weight: 0.9990 chunk 85 optimal weight: 50.0000 chunk 40 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 443 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 173 optimal weight: 50.0000 chunk 411 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 351 optimal weight: 0.0670 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 447 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 510 GLN ** 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 = 0.4840 r_free = 0.4840 target = 0.121392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.087007 restraints weight = 116184.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.086976 restraints weight = 177094.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.085056 restraints weight = 178163.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.085055 restraints weight = 217941.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.085055 restraints weight = 217942.861| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.225 37128 Z= 0.190 Angle : 0.805 59.186 50324 Z= 0.419 Chirality : 0.046 0.398 5736 Planarity : 0.005 0.060 6548 Dihedral : 6.070 117.040 5120 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.67 % Allowed : 17.28 % Favored : 81.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.12), residues: 4626 helix: 0.12 (0.11), residues: 1996 sheet: -1.89 (0.21), residues: 546 loop : -1.56 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.001 ARG D 227 TYR 0.033 0.001 TYR D 225 PHE 0.013 0.001 PHE B 132 TRP 0.021 0.001 TRP D 602 HIS 0.007 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (37128) covalent geometry : angle 0.80516 / 0.42 (50324) hydrogen bonds : bond 0.03696 / 2.47 ( 1505) hydrogen bonds : angle 5.14600 / 3.67 ( 4395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9504.73 seconds wall clock time: 163 minutes 48.67 seconds (9828.67 seconds total)