Starting phenix.real_space_refine on Tue Aug 26 12:24:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypi_34001/08_2025/7ypi_34001.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypi_34001/08_2025/7ypi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypi_34001/08_2025/7ypi_34001.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypi_34001/08_2025/7ypi_34001.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypi_34001/08_2025/7ypi_34001.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypi_34001/08_2025/7ypi_34001.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.87, per 1000 atoms: 0.22 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: 2.47 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 9252 Ramachandran restraints generated. 4626 Oldfield, 0 Emsley, 4626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8616 Finding SS restraints... Secondary structure from input PDB file: 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: 1.26 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: 6.95 Time building geometry restraints manager: 3.22 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: 21997 25.17 - 50.34: 867 50.34 - 75.50: 72 75.50 - 100.67: 16 100.67 - 125.84: 2 Dihedral angle restraints: 22954 sinusoidal: 9574 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 22951 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: 0.02 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: 5.360 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: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 29.140 Find NCS groups from input model: 0.760 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: 0.010 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: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 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 : 13.340 125.839 14338 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 aren 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 covalent geometry : bond 0.00735 (37128) covalent geometry : angle 1.25952 (50324) hydrogen bonds : bond 0.15784 ( 1505) hydrogen bonds : angle 7.76416 ( 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 : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.4275 (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: 0.2202 time to fit residues: 106.8798 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 : 1.426 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.125914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084508 restraints weight = 138214.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084505 restraints weight = 187581.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084505 restraints weight = 187684.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084505 restraints weight = 187685.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.084505 restraints weight = 187685.453| |-----------------------------------------------------------------------------| r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37128 Z= 0.189 Angle : 0.752 12.148 50324 Z= 0.388 Chirality : 0.046 0.213 5736 Planarity : 0.006 0.060 6548 Dihedral : 7.314 126.598 5144 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.72 % Allowed : 7.09 % Favored : 92.19 % 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 aren not related in a simple way. whole: -2.24 (0.11), residues: 4626 helix: -0.90 (0.11), residues: 1995 sheet: -1.89 (0.21), residues: 528 loop : -1.88 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 374 TYR 0.040 0.002 TYR C 577 PHE 0.032 0.002 PHE F 203 TRP 0.027 0.002 TRP C 431 HIS 0.013 0.002 HIS C 454 Details of bonding type rmsd covalent geometry : bond 0.00404 (37128) covalent geometry : angle 0.75167 (50324) hydrogen bonds : bond 0.04718 ( 1505) hydrogen bonds : angle 6.01854 ( 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 291 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 1.714 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 160 MET cc_start: -0.0553 (mtm) cc_final: -0.0899 (mmt) REVERT: A 381 LEU cc_start: 0.9595 (mt) cc_final: 0.8954 (tt) REVERT: A 427 MET cc_start: 0.6524 (ptt) cc_final: 0.6128 (tmm) REVERT: A 650 ASP cc_start: 0.8220 (m-30) cc_final: 0.7934 (t70) REVERT: B 38 MET cc_start: 0.4108 (mpp) cc_final: 0.3666 (mpp) REVERT: B 218 ASP cc_start: 0.9117 (t70) cc_final: 0.8885 (m-30) REVERT: B 409 MET cc_start: 0.4088 (ppp) cc_final: 0.3863 (ppp) REVERT: B 496 MET cc_start: 0.8529 (tmm) cc_final: 0.8325 (tmm) REVERT: C 401 MET cc_start: 0.6450 (mmm) cc_final: 0.5755 (mmm) REVERT: D 75 MET cc_start: 0.6554 (pmm) cc_final: 0.5807 (ptt) REVERT: D 160 MET cc_start: 0.7673 (ppp) cc_final: 0.7457 (ppp) REVERT: D 276 MET cc_start: -0.0428 (mpp) cc_final: -0.0777 (mpp) REVERT: D 427 MET cc_start: 0.8158 (tpt) cc_final: 0.7945 (mmm) REVERT: D 439 MET cc_start: 0.9244 (ppp) cc_final: 0.9025 (ppp) REVERT: D 691 LEU cc_start: 0.6138 (mp) cc_final: 0.5771 (tp) REVERT: E 75 MET cc_start: -0.0690 (mpp) cc_final: -0.0902 (mpp) REVERT: E 85 MET cc_start: 0.1414 (tpt) cc_final: 0.1158 (ptp) REVERT: E 401 MET cc_start: 0.8346 (tpp) cc_final: 0.7438 (ppp) REVERT: E 431 TRP cc_start: 0.7479 (t60) cc_final: 0.7257 (t60) REVERT: E 633 MET cc_start: 0.8236 (mmm) cc_final: 0.7930 (mmm) REVERT: E 698 MET cc_start: -0.1171 (mtt) cc_final: -0.1563 (mmm) REVERT: E 713 MET cc_start: 0.7527 (ppp) cc_final: 0.7054 (ppp) REVERT: F 427 MET cc_start: 0.5782 (tpt) cc_final: 0.5033 (tpt) REVERT: F 635 GLU cc_start: 0.9233 (mp0) cc_final: 0.8983 (mp0) REVERT: F 698 MET cc_start: 0.1405 (mmt) cc_final: 0.1201 (mmt) outliers start: 28 outliers final: 20 residues processed: 278 average time/residue: 0.2196 time to fit residues: 99.8825 Evaluate side-chains 248 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 228 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 468 ILE 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 626 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain E residue 230 MET 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: 5.9990 chunk 59 optimal weight: 6.9990 chunk 347 optimal weight: 0.0010 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 266 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 331 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS B 49 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.123333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.082397 restraints weight = 139184.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.081930 restraints weight = 197339.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.081930 restraints weight = 216268.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.081930 restraints weight = 216268.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.081930 restraints weight = 216268.491| |-----------------------------------------------------------------------------| r_work (final): 0.4231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37128 Z= 0.191 Angle : 0.723 11.028 50324 Z= 0.369 Chirality : 0.045 0.214 5736 Planarity : 0.006 0.062 6548 Dihedral : 7.072 122.308 5142 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.49 % Allowed : 10.17 % Favored : 88.34 % 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 aren not related in a simple way. whole: -1.95 (0.12), residues: 4626 helix: -0.52 (0.11), residues: 1991 sheet: -2.11 (0.21), residues: 526 loop : -1.77 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 552 TYR 0.021 0.002 TYR D 225 PHE 0.024 0.002 PHE F 203 TRP 0.030 0.002 TRP C 431 HIS 0.010 0.002 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00409 (37128) covalent geometry : angle 0.72274 (50324) hydrogen bonds : bond 0.04398 ( 1505) hydrogen bonds : angle 5.72638 ( 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 299 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 1.579 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: 0.9636 (mt) cc_final: 0.9201 (tt) REVERT: A 409 MET cc_start: 0.9448 (mmm) cc_final: 0.8183 (tmm) REVERT: A 427 MET cc_start: 0.6472 (ptt) cc_final: 0.5935 (tmm) REVERT: A 650 ASP cc_start: 0.8211 (m-30) cc_final: 0.7897 (t0) REVERT: B 38 MET cc_start: 0.4231 (mpp) cc_final: 0.3969 (mmm) REVERT: B 409 MET cc_start: 0.4183 (ppp) cc_final: 0.3931 (ppp) REVERT: B 439 MET cc_start: 0.8803 (mmt) cc_final: 0.8512 (mmt) REVERT: B 496 MET cc_start: 0.8697 (tmm) cc_final: 0.8407 (tmm) REVERT: C 217 MET cc_start: 0.7400 (tpt) cc_final: 0.6338 (mmm) REVERT: C 401 MET cc_start: 0.6441 (mmm) cc_final: 0.5821 (mmm) REVERT: D 75 MET cc_start: 0.6549 (pmm) cc_final: 0.6078 (pmm) REVERT: D 160 MET cc_start: 0.7732 (ppp) cc_final: 0.7518 (ppp) REVERT: D 361 LYS cc_start: 0.7721 (mttt) cc_final: 0.6990 (ptmm) REVERT: D 419 ILE cc_start: 0.3619 (mm) cc_final: 0.3292 (mt) REVERT: D 439 MET cc_start: 0.9247 (ppp) cc_final: 0.9036 (ppp) REVERT: D 552 ARG cc_start: 0.7320 (mmm160) cc_final: 0.6025 (mmp80) REVERT: D 713 MET cc_start: 0.8040 (tmm) cc_final: 0.7511 (tmm) REVERT: E 75 MET cc_start: -0.0667 (mpp) cc_final: -0.0874 (mpp) REVERT: E 401 MET cc_start: 0.8572 (tpp) cc_final: 0.7657 (ppp) REVERT: E 439 MET cc_start: 0.8853 (mmm) cc_final: 0.8578 (mmm) REVERT: E 683 MET cc_start: 0.3796 (mpp) cc_final: 0.3561 (mpp) REVERT: E 698 MET cc_start: -0.0904 (mtt) cc_final: -0.1133 (mmm) REVERT: E 713 MET cc_start: 0.7594 (ppp) cc_final: 0.7143 (ppp) REVERT: F 372 MET cc_start: 0.7056 (tmm) cc_final: 0.6431 (mmt) REVERT: F 427 MET cc_start: 0.6078 (tpt) cc_final: 0.5517 (tpt) REVERT: F 698 MET cc_start: 0.1758 (mmt) cc_final: 0.1489 (mmt) outliers start: 58 outliers final: 36 residues processed: 278 average time/residue: 0.2225 time to fit residues: 104.6607 Evaluate side-chains 260 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 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 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 372 MET Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 230 MET 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 85 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 319 HIS 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: 9.9990 chunk 200 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 0.0570 chunk 152 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 265 optimal weight: 8.9990 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4865 r_free = 0.4865 target = 0.125189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.083982 restraints weight = 137355.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.083982 restraints weight = 196411.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.083982 restraints weight = 196411.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.083982 restraints weight = 196411.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.083982 restraints weight = 196411.254| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37128 Z= 0.141 Angle : 0.666 11.330 50324 Z= 0.335 Chirality : 0.044 0.187 5736 Planarity : 0.005 0.059 6548 Dihedral : 6.823 122.192 5142 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.49 % Allowed : 12.22 % Favored : 86.29 % 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 aren not related in a simple way. whole: -1.68 (0.12), residues: 4626 helix: -0.25 (0.11), residues: 1995 sheet: -1.99 (0.21), residues: 548 loop : -1.65 (0.14), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 552 TYR 0.014 0.001 TYR E 332 PHE 0.020 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 covalent geometry : bond 0.00309 (37128) covalent geometry : angle 0.66586 (50324) hydrogen bonds : bond 0.03951 ( 1505) hydrogen bonds : angle 5.43449 ( 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 290 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 1.494 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: 0.9573 (mt) cc_final: 0.9059 (tt) REVERT: A 409 MET cc_start: 0.9463 (mmm) cc_final: 0.8212 (tmm) REVERT: A 427 MET cc_start: 0.5935 (ptt) cc_final: 0.5509 (tmm) REVERT: A 650 ASP cc_start: 0.8203 (m-30) cc_final: 0.7830 (t0) REVERT: B 38 MET cc_start: 0.4474 (mpp) cc_final: 0.4088 (mmm) REVERT: B 439 MET cc_start: 0.8767 (mmt) cc_final: 0.8390 (mmt) REVERT: B 496 MET cc_start: 0.8629 (tmm) cc_final: 0.8272 (tmm) REVERT: B 683 MET cc_start: 0.7917 (mpp) cc_final: 0.7607 (mpp) REVERT: C 401 MET cc_start: 0.6438 (mmm) cc_final: 0.5948 (mmm) REVERT: D 75 MET cc_start: 0.6770 (pmm) cc_final: 0.6324 (pmm) REVERT: D 361 LYS cc_start: 0.7608 (mttt) cc_final: 0.6756 (ptmm) REVERT: D 419 ILE cc_start: 0.3751 (mm) cc_final: 0.3448 (mt) REVERT: D 427 MET cc_start: 0.8115 (mmm) cc_final: 0.7201 (tmm) REVERT: D 439 MET cc_start: 0.9370 (ppp) cc_final: 0.8992 (ppp) REVERT: D 633 MET cc_start: 0.8129 (mmm) cc_final: 0.7520 (mmm) REVERT: D 713 MET cc_start: 0.7959 (tmm) cc_final: 0.7325 (tmm) REVERT: E 401 MET cc_start: 0.8551 (tpp) cc_final: 0.7806 (ppp) REVERT: E 439 MET cc_start: 0.8938 (mmm) cc_final: 0.8543 (mmt) REVERT: E 698 MET cc_start: -0.1022 (mtt) cc_final: -0.1291 (mmm) REVERT: E 713 MET cc_start: 0.7417 (ppp) cc_final: 0.6961 (ppp) REVERT: F 372 MET cc_start: 0.7065 (tmm) cc_final: 0.6686 (mmp) REVERT: F 427 MET cc_start: 0.5899 (tpt) cc_final: 0.5254 (tpt) REVERT: F 496 MET cc_start: 0.6434 (pmm) cc_final: 0.6214 (pmm) REVERT: F 698 MET cc_start: 0.2009 (mmt) cc_final: 0.0848 (mmt) outliers start: 58 outliers final: 40 residues processed: 276 average time/residue: 0.2114 time to fit residues: 98.6181 Evaluate side-chains 263 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL 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 84 VAL Chi-restraints excluded: chain B residue 421 LEU 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 578 LEU Chi-restraints excluded: chain B residue 638 GLN 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 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 703 THR Chi-restraints excluded: chain D residue 204 GLU 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 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 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 319 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 305 optimal weight: 2.9990 chunk 327 optimal weight: 50.0000 chunk 220 optimal weight: 8.9990 chunk 168 optimal weight: 0.0020 chunk 93 optimal weight: 50.0000 chunk 70 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 447 optimal weight: 30.0000 chunk 296 optimal weight: 6.9990 chunk 1 optimal weight: 0.0670 chunk 130 optimal weight: 9.9990 overall best weight: 2.2132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 GLN ** C 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 GLN E 168 HIS ** 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 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.126482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.085054 restraints weight = 135033.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.085054 restraints weight = 192996.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.085054 restraints weight = 192996.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.085054 restraints weight = 192996.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.085054 restraints weight = 192996.900| |-----------------------------------------------------------------------------| r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6226 moved from start: 0.2425 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= 0.126 Angle : 0.649 12.500 50324 Z= 0.324 Chirality : 0.044 0.185 5736 Planarity : 0.005 0.056 6548 Dihedral : 6.622 120.736 5142 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.67 % Allowed : 12.92 % Favored : 85.41 % 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 aren not related in a simple way. whole: -1.46 (0.12), residues: 4626 helix: -0.04 (0.11), residues: 2007 sheet: -1.84 (0.21), residues: 538 loop : -1.59 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 552 TYR 0.020 0.001 TYR C 332 PHE 0.017 0.001 PHE F 203 TRP 0.032 0.002 TRP C 431 HIS 0.007 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00277 (37128) covalent geometry : angle 0.64905 (50324) hydrogen bonds : bond 0.03736 ( 1505) hydrogen bonds : angle 5.23993 ( 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 305 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 1.574 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: 0.9547 (mt) cc_final: 0.9036 (tp) REVERT: A 409 MET cc_start: 0.9515 (mmm) cc_final: 0.8322 (tmm) REVERT: A 415 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8297 (tt) REVERT: A 650 ASP cc_start: 0.8214 (m-30) cc_final: 0.7811 (t0) REVERT: B 38 MET cc_start: 0.3872 (mpp) cc_final: 0.3598 (mpp) REVERT: B 409 MET cc_start: 0.3777 (ppp) cc_final: 0.3154 (tmm) REVERT: B 439 MET cc_start: 0.8842 (mmt) cc_final: 0.8432 (mmt) REVERT: B 496 MET cc_start: 0.8745 (tmm) cc_final: 0.8366 (tmm) REVERT: B 683 MET cc_start: 0.8049 (mpp) cc_final: 0.7813 (mpp) REVERT: C 217 MET cc_start: 0.7339 (tpt) cc_final: 0.6220 (mmm) REVERT: C 401 MET cc_start: 0.6340 (mmm) cc_final: 0.5919 (mmm) REVERT: C 427 MET cc_start: 0.7233 (tmm) cc_final: 0.6755 (tmm) REVERT: D 75 MET cc_start: 0.6727 (pmm) cc_final: 0.6283 (pmm) REVERT: D 160 MET cc_start: 0.7451 (ppp) cc_final: 0.7241 (ppp) REVERT: D 361 LYS cc_start: 0.7597 (mttt) cc_final: 0.6767 (ptmm) REVERT: D 427 MET cc_start: 0.8166 (mmm) cc_final: 0.6813 (tmm) REVERT: D 439 MET cc_start: 0.9405 (ppp) cc_final: 0.9033 (ppp) REVERT: D 691 LEU cc_start: 0.5918 (mp) cc_final: 0.5543 (mt) REVERT: D 713 MET cc_start: 0.8026 (tmm) cc_final: 0.7286 (tmm) REVERT: E 85 MET cc_start: 0.1473 (tpt) cc_final: 0.0889 (ptp) REVERT: E 401 MET cc_start: 0.8595 (tpp) cc_final: 0.7927 (ppp) REVERT: E 439 MET cc_start: 0.8871 (mmm) cc_final: 0.8635 (mmm) REVERT: E 633 MET cc_start: 0.7828 (mmm) cc_final: 0.7410 (mmm) REVERT: E 698 MET cc_start: -0.1084 (mtt) cc_final: -0.1414 (mmm) REVERT: E 713 MET cc_start: 0.7349 (ppp) cc_final: 0.6833 (ppp) REVERT: F 328 ARG cc_start: 0.7718 (mpt180) cc_final: 0.7238 (tpt170) REVERT: F 372 MET cc_start: 0.7018 (tmm) cc_final: 0.6743 (mmp) REVERT: F 427 MET cc_start: 0.5557 (tpt) cc_final: 0.4913 (tpt) REVERT: F 698 MET cc_start: 0.1872 (mmt) cc_final: 0.0777 (mmt) outliers start: 65 outliers final: 45 residues processed: 284 average time/residue: 0.2397 time to fit residues: 113.4641 Evaluate side-chains 274 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 421 LEU 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 468 ILE Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 638 GLN 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 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 626 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 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 708 LEU Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 309 ASN Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 574 ILE 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 634 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 287 optimal weight: 1.9990 chunk 433 optimal weight: 0.0070 chunk 161 optimal weight: 30.0000 chunk 422 optimal weight: 10.0000 chunk 375 optimal weight: 6.9990 chunk 193 optimal weight: 0.3980 chunk 311 optimal weight: 40.0000 chunk 77 optimal weight: 50.0000 chunk 338 optimal weight: 8.9990 chunk 319 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 411 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** E 726 HIS ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.126234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.086508 restraints weight = 135837.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.082521 restraints weight = 196335.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.082521 restraints weight = 215310.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.082521 restraints weight = 215309.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.082521 restraints weight = 215309.772| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37128 Z= 0.124 Angle : 0.647 11.775 50324 Z= 0.322 Chirality : 0.044 0.240 5736 Planarity : 0.005 0.052 6548 Dihedral : 6.497 119.456 5142 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.59 % Allowed : 14.18 % Favored : 84.23 % 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 aren not related in a simple way. whole: -1.28 (0.12), residues: 4626 helix: 0.13 (0.11), residues: 1999 sheet: -1.71 (0.22), residues: 522 loop : -1.55 (0.14), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 552 TYR 0.019 0.001 TYR C 332 PHE 0.015 0.001 PHE F 203 TRP 0.033 0.001 TRP C 431 HIS 0.008 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00274 (37128) covalent geometry : angle 0.64697 (50324) hydrogen bonds : bond 0.03636 ( 1505) hydrogen bonds : angle 5.14260 ( 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 298 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 236 time to evaluate : 1.613 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: 0.9558 (mt) cc_final: 0.9031 (tp) REVERT: A 427 MET cc_start: 0.6046 (ptt) cc_final: 0.5678 (tmm) REVERT: A 650 ASP cc_start: 0.8162 (m-30) cc_final: 0.7729 (t0) REVERT: B 38 MET cc_start: 0.4094 (mpp) cc_final: 0.3783 (mpp) REVERT: B 409 MET cc_start: 0.3836 (ppp) cc_final: 0.3293 (tmm) REVERT: B 439 MET cc_start: 0.8798 (mmt) cc_final: 0.8397 (mmt) REVERT: B 496 MET cc_start: 0.8699 (tmm) cc_final: 0.8398 (tmm) REVERT: B 698 MET cc_start: 0.6495 (ptm) cc_final: 0.6125 (pmm) REVERT: C 217 MET cc_start: 0.7373 (tpt) cc_final: 0.6250 (mmm) REVERT: C 401 MET cc_start: 0.6264 (mmm) cc_final: 0.5906 (mmm) REVERT: D 75 MET cc_start: 0.6626 (pmm) cc_final: 0.6196 (pmm) REVERT: D 160 MET cc_start: 0.7463 (ppp) cc_final: 0.7249 (ppp) REVERT: D 361 LYS cc_start: 0.7630 (mttt) cc_final: 0.6826 (ptmm) REVERT: D 439 MET cc_start: 0.9386 (ppp) cc_final: 0.9117 (ppp) REVERT: D 663 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6986 (tp) REVERT: D 713 MET cc_start: 0.7969 (tmm) cc_final: 0.7176 (tmm) REVERT: E 85 MET cc_start: 0.1966 (tpt) cc_final: 0.1460 (ptp) REVERT: E 401 MET cc_start: 0.8730 (tpp) cc_final: 0.8077 (ppp) REVERT: E 439 MET cc_start: 0.8885 (mmm) cc_final: 0.8666 (mmm) REVERT: E 698 MET cc_start: -0.1049 (mtt) cc_final: -0.1446 (mmm) REVERT: E 713 MET cc_start: 0.7079 (ppp) cc_final: 0.6653 (ppp) REVERT: F 328 ARG cc_start: 0.7706 (mpt180) cc_final: 0.7212 (tpt170) REVERT: F 372 MET cc_start: 0.7038 (tmm) cc_final: 0.6712 (mmp) REVERT: F 427 MET cc_start: 0.5853 (tpt) cc_final: 0.5278 (tpt) REVERT: F 698 MET cc_start: 0.1614 (mmt) cc_final: 0.0462 (mmt) outliers start: 62 outliers final: 45 residues processed: 280 average time/residue: 0.2454 time to fit residues: 113.2662 Evaluate side-chains 272 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET 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 516 MET Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 638 GLN 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 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 626 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 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 543 LEU Chi-restraints excluded: chain D residue 584 ARG 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 663 LEU Chi-restraints excluded: chain D residue 681 ILE 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 230 MET 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 E residue 635 GLU Chi-restraints excluded: chain F residue 296 VAL 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: 7.9990 chunk 360 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 283 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 376 optimal weight: 6.9990 chunk 174 optimal weight: 50.0000 chunk 442 optimal weight: 0.0980 chunk 436 optimal weight: 0.0770 chunk 367 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 overall best weight: 4.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN ** B 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 ** 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** ** 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 = 0.4838 r_free = 0.4838 target = 0.122363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.082391 restraints weight = 139110.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.082391 restraints weight = 176338.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.082391 restraints weight = 176338.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.082391 restraints weight = 176338.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.082391 restraints weight = 176338.014| |-----------------------------------------------------------------------------| r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37128 Z= 0.158 Angle : 0.684 11.443 50324 Z= 0.342 Chirality : 0.045 0.200 5736 Planarity : 0.005 0.057 6548 Dihedral : 6.547 116.452 5142 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.72 % Allowed : 14.89 % Favored : 83.38 % 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 aren not related in a simple way. whole: -1.32 (0.12), residues: 4626 helix: 0.09 (0.11), residues: 2007 sheet: -1.84 (0.22), residues: 522 loop : -1.52 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 143 TYR 0.024 0.002 TYR C 332 PHE 0.017 0.002 PHE D 203 TRP 0.043 0.002 TRP C 431 HIS 0.009 0.001 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00348 (37128) covalent geometry : angle 0.68350 (50324) hydrogen bonds : bond 0.03739 ( 1505) hydrogen bonds : angle 5.22181 ( 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 301 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 234 time to evaluate : 1.205 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: 0.9519 (mt) cc_final: 0.8986 (tt) REVERT: A 409 MET cc_start: 0.9315 (mmm) cc_final: 0.8434 (tmm) REVERT: A 411 GLN cc_start: 0.8834 (tp40) cc_final: 0.8598 (pp30) REVERT: A 427 MET cc_start: 0.5586 (ptt) cc_final: 0.5326 (tmm) REVERT: A 650 ASP cc_start: 0.8075 (m-30) cc_final: 0.7665 (t0) REVERT: A 698 MET cc_start: 0.4702 (tpt) cc_final: 0.3085 (mmm) REVERT: B 38 MET cc_start: 0.5567 (mpp) cc_final: 0.5135 (mpp) REVERT: B 409 MET cc_start: 0.3745 (ppp) cc_final: 0.3451 (ppp) REVERT: B 439 MET cc_start: 0.9015 (mmt) cc_final: 0.8644 (mmt) REVERT: B 496 MET cc_start: 0.8409 (tmm) cc_final: 0.8179 (tmm) REVERT: C 401 MET cc_start: 0.6342 (mmm) cc_final: 0.5992 (mmm) REVERT: C 427 MET cc_start: 0.6877 (tmm) cc_final: 0.6241 (tpp) REVERT: C 622 LYS cc_start: 0.6830 (ptpp) cc_final: 0.6609 (ptpp) REVERT: D 75 MET cc_start: 0.6724 (pmm) cc_final: 0.6300 (pmm) REVERT: D 258 MET cc_start: 0.3976 (mtt) cc_final: 0.3061 (mtt) REVERT: D 361 LYS cc_start: 0.7816 (mttt) cc_final: 0.6906 (ptmm) REVERT: D 427 MET cc_start: 0.7900 (mmm) cc_final: 0.7473 (tmm) REVERT: D 439 MET cc_start: 0.9354 (ppp) cc_final: 0.8965 (ppp) REVERT: D 663 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6952 (tp) REVERT: D 691 LEU cc_start: 0.6690 (mp) cc_final: 0.6312 (mt) REVERT: D 702 MET cc_start: 0.6650 (mpp) cc_final: 0.6268 (mmm) REVERT: E 85 MET cc_start: 0.2026 (tpt) cc_final: 0.1606 (ptp) REVERT: E 401 MET cc_start: 0.8810 (tpp) cc_final: 0.8074 (ppp) REVERT: E 439 MET cc_start: 0.9114 (mmm) cc_final: 0.8831 (mmm) REVERT: E 534 TYR cc_start: 0.5915 (m-80) cc_final: 0.5686 (m-80) REVERT: E 698 MET cc_start: -0.0477 (mtt) cc_final: -0.0847 (mtt) REVERT: E 713 MET cc_start: 0.7067 (ppp) cc_final: 0.6612 (ppp) REVERT: F 328 ARG cc_start: 0.7819 (mpt180) cc_final: 0.7336 (tpt170) REVERT: F 427 MET cc_start: 0.6041 (tpt) cc_final: 0.5516 (tpt) outliers start: 67 outliers final: 50 residues processed: 285 average time/residue: 0.1972 time to fit residues: 93.4227 Evaluate side-chains 279 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 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 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 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 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 703 THR Chi-restraints excluded: chain D residue 204 GLU 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 584 ARG 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 663 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 708 LEU 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 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN 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 F residue 233 ILE Chi-restraints excluded: chain F residue 296 VAL 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: 9.9990 chunk 333 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 410 optimal weight: 1.9990 chunk 352 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 67 optimal weight: 30.0000 chunk 278 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** 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 ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.122712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.084801 restraints weight = 131410.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.081888 restraints weight = 194645.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.081374 restraints weight = 251436.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.081374 restraints weight = 239736.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.081374 restraints weight = 239736.334| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37128 Z= 0.141 Angle : 0.678 12.709 50324 Z= 0.336 Chirality : 0.045 0.269 5736 Planarity : 0.005 0.050 6548 Dihedral : 6.480 116.438 5142 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.64 % Allowed : 15.51 % Favored : 82.85 % 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 aren not related in a simple way. whole: -1.25 (0.12), residues: 4626 helix: 0.17 (0.11), residues: 2009 sheet: -1.82 (0.22), residues: 523 loop : -1.50 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 552 TYR 0.025 0.001 TYR C 332 PHE 0.015 0.001 PHE D 203 TRP 0.033 0.002 TRP C 431 HIS 0.007 0.001 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00312 (37128) covalent geometry : angle 0.67826 (50324) hydrogen bonds : bond 0.03654 ( 1505) hydrogen bonds : angle 5.14085 ( 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 301 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 237 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.5074 (mmp) cc_final: 0.4529 (mmt) REVERT: A 381 LEU cc_start: 0.9533 (mt) cc_final: 0.8951 (tp) REVERT: A 427 MET cc_start: 0.6389 (ptt) cc_final: 0.5980 (tmm) REVERT: A 650 ASP cc_start: 0.8267 (m-30) cc_final: 0.7850 (t0) REVERT: A 698 MET cc_start: 0.4399 (tpt) cc_final: 0.2840 (mmm) REVERT: A 702 MET cc_start: 0.5034 (tmm) cc_final: 0.4134 (tmm) REVERT: B 38 MET cc_start: 0.4169 (mpp) cc_final: 0.3796 (mpp) REVERT: B 207 LYS cc_start: 0.9187 (tptt) cc_final: 0.8771 (mmtt) REVERT: B 409 MET cc_start: 0.4032 (ppp) cc_final: 0.3723 (ppp) REVERT: B 439 MET cc_start: 0.8905 (mmt) cc_final: 0.8509 (mmt) REVERT: B 496 MET cc_start: 0.8687 (tmm) cc_final: 0.8369 (tmm) REVERT: C 217 MET cc_start: 0.7471 (tpt) cc_final: 0.6400 (mmm) REVERT: C 401 MET cc_start: 0.6156 (mmm) cc_final: 0.5804 (mmm) REVERT: C 427 MET cc_start: 0.7122 (tmm) cc_final: 0.6639 (tmm) REVERT: C 713 MET cc_start: 0.8229 (mpp) cc_final: 0.7505 (mpp) REVERT: D 75 MET cc_start: 0.6565 (pmm) cc_final: 0.6136 (pmm) REVERT: D 258 MET cc_start: 0.3434 (mtt) cc_final: 0.2573 (mtt) REVERT: D 361 LYS cc_start: 0.7621 (mttt) cc_final: 0.6888 (ptmm) REVERT: D 439 MET cc_start: 0.9424 (ppp) cc_final: 0.9103 (ppp) REVERT: D 633 MET cc_start: 0.7670 (mmm) cc_final: 0.7335 (mmm) REVERT: D 663 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7042 (tp) REVERT: D 691 LEU cc_start: 0.6654 (mp) cc_final: 0.6268 (mt) REVERT: D 702 MET cc_start: 0.6650 (mpp) cc_final: 0.6243 (mmm) REVERT: D 713 MET cc_start: 0.7999 (tmm) cc_final: 0.7341 (tmm) REVERT: E 85 MET cc_start: 0.2022 (tpt) cc_final: 0.1555 (ptp) REVERT: E 236 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8028 (mm-30) REVERT: E 401 MET cc_start: 0.8873 (tpp) cc_final: 0.8162 (ppp) REVERT: E 439 MET cc_start: 0.8857 (mmm) cc_final: 0.8634 (mmm) REVERT: E 698 MET cc_start: -0.0694 (mtt) cc_final: -0.1076 (mtt) REVERT: E 713 MET cc_start: 0.7028 (ppp) cc_final: 0.6559 (ppp) REVERT: F 85 MET cc_start: 0.2040 (mmp) cc_final: 0.1223 (tmm) REVERT: F 328 ARG cc_start: 0.7844 (mpt180) cc_final: 0.7425 (tpt170) REVERT: F 427 MET cc_start: 0.5894 (tpt) cc_final: 0.5387 (tpt) outliers start: 64 outliers final: 54 residues processed: 283 average time/residue: 0.2172 time to fit residues: 101.7262 Evaluate side-chains 285 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 230 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 516 MET 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 290 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 499 GLN Chi-restraints excluded: chain B residue 530 VAL 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 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 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 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 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 663 LEU 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 E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 309 ASN 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 F residue 233 ILE Chi-restraints excluded: chain F residue 296 VAL 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: 6.9990 chunk 209 optimal weight: 0.1980 chunk 0 optimal weight: 90.0000 chunk 293 optimal weight: 5.9990 chunk 402 optimal weight: 50.0000 chunk 399 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 40.0000 chunk 237 optimal weight: 50.0000 chunk 305 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 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 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 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** F 319 HIS ** 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 = 0.4821 r_free = 0.4821 target = 0.120382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.080826 restraints weight = 141918.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.078770 restraints weight = 204646.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.078650 restraints weight = 233791.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.078650 restraints weight = 233951.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.078650 restraints weight = 233951.560| |-----------------------------------------------------------------------------| r_work (final): 0.4182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37128 Z= 0.168 Angle : 0.715 13.615 50324 Z= 0.356 Chirality : 0.045 0.205 5736 Planarity : 0.005 0.052 6548 Dihedral : 6.560 114.151 5142 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.00 % Allowed : 15.67 % Favored : 82.33 % 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 aren not related in a simple way. whole: -1.33 (0.12), residues: 4626 helix: 0.08 (0.11), residues: 2009 sheet: -1.93 (0.22), residues: 520 loop : -1.51 (0.14), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 552 TYR 0.027 0.002 TYR C 332 PHE 0.015 0.002 PHE F 203 TRP 0.033 0.002 TRP C 431 HIS 0.008 0.001 HIS E 666 Details of bonding type rmsd covalent geometry : bond 0.00369 (37128) covalent geometry : angle 0.71544 (50324) hydrogen bonds : bond 0.03827 ( 1505) hydrogen bonds : angle 5.22818 ( 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 317 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 1.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.5046 (mmp) cc_final: 0.4617 (mmm) REVERT: A 313 GLN cc_start: 0.6876 (OUTLIER) cc_final: 0.6527 (pt0) REVERT: A 381 LEU cc_start: 0.9545 (mt) cc_final: 0.8953 (tp) REVERT: A 427 MET cc_start: 0.6141 (ptt) cc_final: 0.5795 (tmm) REVERT: A 534 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.5174 (m-10) REVERT: A 541 ARG cc_start: 0.8222 (tpt170) cc_final: 0.8002 (tpt170) REVERT: A 650 ASP cc_start: 0.8218 (m-30) cc_final: 0.7827 (t0) REVERT: A 702 MET cc_start: 0.4925 (tmm) cc_final: 0.3966 (tmm) REVERT: B 38 MET cc_start: 0.4703 (mpp) cc_final: 0.4293 (mpp) REVERT: B 409 MET cc_start: 0.4018 (ppp) cc_final: 0.3677 (ppp) REVERT: B 439 MET cc_start: 0.9020 (mmt) cc_final: 0.8623 (mmt) REVERT: B 496 MET cc_start: 0.8517 (tmm) cc_final: 0.8262 (tmm) REVERT: C 217 MET cc_start: 0.7529 (tpt) cc_final: 0.6363 (mmm) REVERT: C 276 MET cc_start: 0.1537 (mpp) cc_final: 0.1187 (mmm) REVERT: C 401 MET cc_start: 0.5936 (mmm) cc_final: 0.5564 (mmm) REVERT: C 713 MET cc_start: 0.8229 (mpp) cc_final: 0.7501 (mpp) REVERT: D 75 MET cc_start: 0.6809 (pmm) cc_final: 0.6396 (pmm) REVERT: D 258 MET cc_start: 0.3294 (mtt) cc_final: 0.2632 (mtm) REVERT: D 361 LYS cc_start: 0.7709 (mttt) cc_final: 0.6949 (ptmm) REVERT: D 439 MET cc_start: 0.9413 (ppp) cc_final: 0.9082 (ppp) REVERT: D 663 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7064 (tp) REVERT: D 702 MET cc_start: 0.6669 (mpp) cc_final: 0.6188 (mmm) REVERT: D 713 MET cc_start: 0.8107 (tmm) cc_final: 0.7441 (tmm) REVERT: E 85 MET cc_start: 0.2086 (tpt) cc_final: 0.1692 (ptp) REVERT: E 236 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8180 (mm-30) REVERT: E 276 MET cc_start: 0.7663 (mpp) cc_final: 0.7421 (mpp) REVERT: E 401 MET cc_start: 0.8876 (tpp) cc_final: 0.8150 (ppp) REVERT: E 439 MET cc_start: 0.8869 (mmm) cc_final: 0.8646 (mmm) REVERT: E 698 MET cc_start: -0.0209 (mtt) cc_final: -0.0615 (mtt) REVERT: E 713 MET cc_start: 0.6813 (ppp) cc_final: 0.6202 (ppp) REVERT: F 233 ILE cc_start: 0.6468 (OUTLIER) cc_final: 0.6243 (tt) REVERT: F 328 ARG cc_start: 0.7883 (mpt180) cc_final: 0.7389 (tpt90) REVERT: F 350 ILE cc_start: 0.4596 (pt) cc_final: 0.4309 (mp) REVERT: F 427 MET cc_start: 0.6304 (tpt) cc_final: 0.5898 (tpt) REVERT: F 475 GLN cc_start: 0.7716 (mp10) cc_final: 0.7157 (pm20) outliers start: 78 outliers final: 58 residues processed: 296 average time/residue: 0.2286 time to fit residues: 112.2445 Evaluate side-chains 296 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 313 GLN 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 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 499 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 530 VAL 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 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 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 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 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 663 LEU 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 E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET 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 522 VAL Chi-restraints excluded: chain E residue 574 ILE 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 700 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 29 optimal weight: 0.6980 chunk 201 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 166 optimal weight: 50.0000 chunk 425 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 300 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 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 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** 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 = 0.4821 r_free = 0.4821 target = 0.120024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.082271 restraints weight = 136766.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.079241 restraints weight = 210007.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.079252 restraints weight = 224806.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.079258 restraints weight = 226435.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.079258 restraints weight = 226522.358| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37128 Z= 0.158 Angle : 0.722 12.135 50324 Z= 0.359 Chirality : 0.045 0.214 5736 Planarity : 0.005 0.070 6548 Dihedral : 6.552 113.679 5142 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 22.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.72 % Allowed : 16.18 % 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 aren not related in a simple way. whole: -1.32 (0.12), residues: 4626 helix: 0.10 (0.11), residues: 2007 sheet: -1.87 (0.22), residues: 524 loop : -1.52 (0.14), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 529 TYR 0.037 0.002 TYR C 332 PHE 0.015 0.001 PHE F 203 TRP 0.030 0.002 TRP C 431 HIS 0.013 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00351 (37128) covalent geometry : angle 0.72190 (50324) hydrogen bonds : bond 0.03787 ( 1505) hydrogen bonds : angle 5.19703 ( 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 308 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 241 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.5433 (mmp) cc_final: 0.4846 (mmm) REVERT: A 313 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6552 (pt0) REVERT: A 381 LEU cc_start: 0.9529 (mt) cc_final: 0.8927 (tp) REVERT: A 409 MET cc_start: 0.9468 (mmm) cc_final: 0.8428 (tmm) REVERT: A 427 MET cc_start: 0.6489 (ptt) cc_final: 0.6147 (tmm) REVERT: A 534 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.5092 (m-10) REVERT: A 541 ARG cc_start: 0.8169 (tpt170) cc_final: 0.7940 (tpt170) REVERT: A 650 ASP cc_start: 0.8268 (m-30) cc_final: 0.7866 (t0) REVERT: A 698 MET cc_start: 0.4630 (tpt) cc_final: 0.3320 (mmm) REVERT: A 702 MET cc_start: 0.5159 (tmm) cc_final: 0.4252 (tmm) REVERT: B 38 MET cc_start: 0.4201 (mpp) cc_final: 0.3838 (mpp) REVERT: B 409 MET cc_start: 0.4180 (ppp) cc_final: 0.3827 (ppp) REVERT: B 439 MET cc_start: 0.8917 (mmt) cc_final: 0.8485 (mmt) REVERT: B 470 THR cc_start: 0.8242 (p) cc_final: 0.8010 (p) REVERT: B 496 MET cc_start: 0.8657 (tmm) cc_final: 0.8351 (tmm) REVERT: B 635 GLU cc_start: 0.7924 (tp30) cc_final: 0.7666 (tp30) REVERT: C 217 MET cc_start: 0.7459 (tpt) cc_final: 0.6252 (mmm) REVERT: C 276 MET cc_start: 0.1476 (mpp) cc_final: 0.1071 (mmm) REVERT: C 401 MET cc_start: 0.6196 (mmm) cc_final: 0.5791 (mmm) REVERT: C 427 MET cc_start: 0.7256 (tmm) cc_final: 0.6793 (tpp) REVERT: C 713 MET cc_start: 0.8246 (mpp) cc_final: 0.7484 (mpp) REVERT: D 75 MET cc_start: 0.6597 (pmm) cc_final: 0.6176 (pmm) REVERT: D 258 MET cc_start: 0.3006 (mtt) cc_final: 0.2341 (mtm) REVERT: D 361 LYS cc_start: 0.7551 (mttt) cc_final: 0.6882 (ptmm) REVERT: D 439 MET cc_start: 0.9423 (ppp) cc_final: 0.8759 (ptt) REVERT: D 633 MET cc_start: 0.7694 (mmm) cc_final: 0.7174 (mmm) REVERT: D 663 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7059 (tp) REVERT: D 702 MET cc_start: 0.6715 (mpp) cc_final: 0.6238 (mmm) REVERT: D 713 MET cc_start: 0.8109 (tmm) cc_final: 0.7430 (tmm) REVERT: E 85 MET cc_start: 0.2262 (tpt) cc_final: 0.1811 (ptp) REVERT: E 276 MET cc_start: 0.8134 (mpp) cc_final: 0.7779 (mpp) REVERT: E 351 LEU cc_start: 0.8542 (tp) cc_final: 0.8326 (mt) REVERT: E 401 MET cc_start: 0.8872 (tpp) cc_final: 0.8156 (ppp) REVERT: E 698 MET cc_start: -0.0354 (mtt) cc_final: -0.0755 (mtt) REVERT: E 713 MET cc_start: 0.6404 (ppp) cc_final: 0.6073 (ppp) REVERT: F 328 ARG cc_start: 0.7888 (mpt180) cc_final: 0.7452 (tpt90) REVERT: F 427 MET cc_start: 0.6007 (tpt) cc_final: 0.5592 (tpt) REVERT: F 475 GLN cc_start: 0.7790 (mp10) cc_final: 0.7247 (pm20) outliers start: 67 outliers final: 59 residues processed: 289 average time/residue: 0.2313 time to fit residues: 111.5530 Evaluate side-chains 295 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 233 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 313 GLN 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 516 MET 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 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 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 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 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 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 325 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 431 TRP 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 663 LEU 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 E residue 223 GLU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 230 MET 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 522 VAL Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 379 ILE 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: 6.9990 chunk 85 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 251 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 443 optimal weight: 5.9990 chunk 379 optimal weight: 9.9990 chunk 173 optimal weight: 40.0000 chunk 411 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 351 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 664 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 727 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** ** F 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 598 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.119522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.080395 restraints weight = 136778.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.080395 restraints weight = 179896.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.080395 restraints weight = 179896.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.080395 restraints weight = 179896.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.080395 restraints weight = 179896.199| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37128 Z= 0.161 Angle : 0.728 12.646 50324 Z= 0.363 Chirality : 0.046 0.207 5736 Planarity : 0.005 0.052 6548 Dihedral : 6.562 112.078 5142 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.75 % Allowed : 16.33 % Favored : 81.92 % 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 aren not related in a simple way. whole: -1.34 (0.12), residues: 4626 helix: 0.11 (0.11), residues: 1996 sheet: -1.87 (0.22), residues: 527 loop : -1.56 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 529 TYR 0.019 0.001 TYR E 225 PHE 0.015 0.001 PHE F 203 TRP 0.030 0.002 TRP C 431 HIS 0.008 0.001 HIS A 666 Details of bonding type rmsd covalent geometry : bond 0.00357 (37128) covalent geometry : angle 0.72777 (50324) hydrogen bonds : bond 0.03857 ( 1505) hydrogen bonds : angle 5.22908 ( 4395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11713.45 seconds wall clock time: 200 minutes 55.65 seconds (12055.65 seconds total)