Starting phenix.real_space_refine on Fri Aug 7 17:19:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3v_65610/08_2026/9w3v_65610_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3v_65610/08_2026/9w3v_65610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w3v_65610/08_2026/9w3v_65610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3v_65610/08_2026/9w3v_65610.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3v_65610/08_2026/9w3v_65610_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3v_65610/08_2026/9w3v_65610_neut.cif" } resolution = 2.53 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= 0.001 sd= 0.095 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 24 5.49 5 S 96 5.16 5 C 14024 2.51 5 N 4112 2.21 5 O 4380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22636 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5527 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 710} Chain breaks: 8 Chain: "B" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5527 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 710} Chain breaks: 8 Chain: "C" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5527 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 710} Chain breaks: 8 Chain: "D" Number of atoms: 5527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 732, 5527 Classifications: {'peptide': 732} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 710} Chain breaks: 8 Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "F" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Chain: "H" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 132 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 6} Link IDs: {'rna2p': 5} Time building chain proxies: 4.65, per 1000 atoms: 0.21 Number of scatterers: 22636 At special positions: 0 Unit cell: (121.25, 115.43, 171.69, 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 96 16.00 P 24 15.00 O 4380 8.00 N 4112 7.00 C 14024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5272 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 8 sheets defined 57.9% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.568A pdb=" N LYS A 19 " --> pdb=" O ASP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 51 through 56 removed outlier: 3.985A pdb=" N LEU A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.715A pdb=" N GLU A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 174 through 189 removed outlier: 4.607A pdb=" N GLY A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP A 186 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 225 removed outlier: 6.462A pdb=" N ARG A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.598A pdb=" N SER A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 286 removed outlier: 3.827A pdb=" N LEU A 275 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.741A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.520A pdb=" N ARG A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 326 " --> pdb=" O VAL A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 326' Processing helix chain 'A' and resid 333 through 342 removed outlier: 3.821A pdb=" N MET A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.511A pdb=" N LEU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.514A pdb=" N ARG A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 458 through 471 Processing helix chain 'A' and resid 472 through 475 removed outlier: 3.642A pdb=" N THR A 475 " --> pdb=" O VAL A 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 475' Processing helix chain 'A' and resid 501 through 521 removed outlier: 3.717A pdb=" N GLU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 551 removed outlier: 3.584A pdb=" N VAL A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 548 " --> pdb=" O GLN A 544 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 582 through 595 removed outlier: 3.623A pdb=" N ALA A 592 " --> pdb=" O ALA A 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 607 removed outlier: 3.573A pdb=" N ALA A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 632 removed outlier: 4.221A pdb=" N GLN A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 632 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 Processing helix chain 'A' and resid 639 through 657 Processing helix chain 'A' and resid 662 through 672 removed outlier: 3.872A pdb=" N VAL A 666 " --> pdb=" O ASP A 662 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 667 " --> pdb=" O PRO A 663 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 727 removed outlier: 3.652A pdb=" N ARG A 727 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 746 removed outlier: 3.624A pdb=" N ARG A 746 " --> pdb=" O VAL A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 768 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'B' and resid 15 through 20 removed outlier: 3.567A pdb=" N LYS B 19 " --> pdb=" O ASP B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.985A pdb=" N LEU B 56 " --> pdb=" O VAL B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.715A pdb=" N GLU B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 109 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 174 through 189 removed outlier: 4.608A pdb=" N GLY B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 186 " --> pdb=" O MET B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 225 removed outlier: 6.462A pdb=" N ARG B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.599A pdb=" N SER B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.827A pdb=" N LEU B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 310 removed outlier: 3.741A pdb=" N VAL B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 removed outlier: 3.520A pdb=" N ARG B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 326 " --> pdb=" O VAL B 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 326' Processing helix chain 'B' and resid 333 through 342 removed outlier: 3.821A pdb=" N MET B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'B' and resid 375 through 383 removed outlier: 3.512A pdb=" N LEU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.514A pdb=" N ARG B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 427 Processing helix chain 'B' and resid 429 through 434 Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 472 through 475 removed outlier: 3.643A pdb=" N THR B 475 " --> pdb=" O VAL B 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 475' Processing helix chain 'B' and resid 501 through 521 removed outlier: 3.717A pdb=" N GLU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 551 removed outlier: 3.585A pdb=" N VAL B 536 " --> pdb=" O GLN B 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 548 " --> pdb=" O GLN B 544 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 595 removed outlier: 3.621A pdb=" N ALA B 592 " --> pdb=" O ALA B 588 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 607 removed outlier: 3.572A pdb=" N ALA B 602 " --> pdb=" O ASN B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 632 removed outlier: 4.220A pdb=" N GLN B 616 " --> pdb=" O ASP B 612 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 638 Processing helix chain 'B' and resid 639 through 657 Processing helix chain 'B' and resid 662 through 672 removed outlier: 3.873A pdb=" N VAL B 666 " --> pdb=" O ASP B 662 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 667 " --> pdb=" O PRO B 663 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 668 " --> pdb=" O ARG B 664 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 672 " --> pdb=" O VAL B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 727 removed outlier: 3.649A pdb=" N ARG B 727 " --> pdb=" O ALA B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 746 removed outlier: 3.621A pdb=" N ARG B 746 " --> pdb=" O VAL B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 768 Processing helix chain 'B' and resid 780 through 795 Processing helix chain 'C' and resid 15 through 20 removed outlier: 3.567A pdb=" N LYS C 19 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 51 through 56 removed outlier: 3.985A pdb=" N LEU C 56 " --> pdb=" O VAL C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 104 through 116 removed outlier: 3.715A pdb=" N GLU C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 174 through 189 removed outlier: 4.608A pdb=" N GLY C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP C 186 " --> pdb=" O MET C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 6.463A pdb=" N ARG C 222 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 239 through 243 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.599A pdb=" N SER C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.827A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 310 removed outlier: 3.741A pdb=" N VAL C 294 " --> pdb=" O ALA C 290 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C 299 " --> pdb=" O ARG C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 removed outlier: 3.520A pdb=" N ARG C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 326 " --> pdb=" O VAL C 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 326' Processing helix chain 'C' and resid 333 through 342 removed outlier: 3.821A pdb=" N MET C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'C' and resid 375 through 383 removed outlier: 3.512A pdb=" N LEU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.514A pdb=" N ARG C 390 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 427 Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 458 through 471 Processing helix chain 'C' and resid 472 through 475 removed outlier: 3.642A pdb=" N THR C 475 " --> pdb=" O VAL C 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 475' Processing helix chain 'C' and resid 501 through 521 removed outlier: 3.718A pdb=" N GLU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 551 removed outlier: 3.583A pdb=" N VAL C 536 " --> pdb=" O GLN C 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA C 548 " --> pdb=" O GLN C 544 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY C 549 " --> pdb=" O ALA C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 595 removed outlier: 3.622A pdb=" N ALA C 592 " --> pdb=" O ALA C 588 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 593 " --> pdb=" O ALA C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 607 removed outlier: 3.572A pdb=" N ALA C 602 " --> pdb=" O ASN C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 632 removed outlier: 4.220A pdb=" N GLN C 616 " --> pdb=" O ASP C 612 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 632 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 638 Processing helix chain 'C' and resid 639 through 657 Processing helix chain 'C' and resid 662 through 672 removed outlier: 3.873A pdb=" N VAL C 666 " --> pdb=" O ASP C 662 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL C 667 " --> pdb=" O PRO C 663 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 668 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 672 " --> pdb=" O VAL C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 727 removed outlier: 3.649A pdb=" N ARG C 727 " --> pdb=" O ALA C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 746 removed outlier: 3.621A pdb=" N ARG C 746 " --> pdb=" O VAL C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 768 Processing helix chain 'C' and resid 780 through 795 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.567A pdb=" N LYS D 19 " --> pdb=" O ASP D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 35 Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.985A pdb=" N LEU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 116 removed outlier: 3.715A pdb=" N GLU D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 125 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 174 through 189 removed outlier: 4.608A pdb=" N GLY D 183 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP D 186 " --> pdb=" O MET D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 removed outlier: 6.463A pdb=" N ARG D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 239 through 243 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.598A pdb=" N SER D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 286 removed outlier: 3.827A pdb=" N LEU D 275 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 310 removed outlier: 3.741A pdb=" N VAL D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 removed outlier: 3.520A pdb=" N ARG D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 326 " --> pdb=" O VAL D 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 326' Processing helix chain 'D' and resid 333 through 342 removed outlier: 3.822A pdb=" N MET D 337 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 360 Processing helix chain 'D' and resid 375 through 383 removed outlier: 3.511A pdb=" N LEU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 390 removed outlier: 3.514A pdb=" N ARG D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 427 Processing helix chain 'D' and resid 429 through 434 Processing helix chain 'D' and resid 458 through 471 Processing helix chain 'D' and resid 472 through 475 removed outlier: 3.643A pdb=" N THR D 475 " --> pdb=" O VAL D 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 475' Processing helix chain 'D' and resid 501 through 521 removed outlier: 3.717A pdb=" N GLU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 551 removed outlier: 3.584A pdb=" N VAL D 536 " --> pdb=" O GLN D 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA D 548 " --> pdb=" O GLN D 544 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY D 549 " --> pdb=" O ALA D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 595 removed outlier: 3.624A pdb=" N ALA D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER D 593 " --> pdb=" O ALA D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 607 removed outlier: 3.572A pdb=" N ALA D 602 " --> pdb=" O ASN D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 632 removed outlier: 4.220A pdb=" N GLN D 616 " --> pdb=" O ASP D 612 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 632 " --> pdb=" O LEU D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 638 Processing helix chain 'D' and resid 639 through 657 Processing helix chain 'D' and resid 662 through 672 removed outlier: 3.873A pdb=" N VAL D 666 " --> pdb=" O ASP D 662 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 667 " --> pdb=" O PRO D 663 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 668 " --> pdb=" O ARG D 664 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 672 " --> pdb=" O VAL D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 711 through 727 removed outlier: 3.649A pdb=" N ARG D 727 " --> pdb=" O ALA D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 746 removed outlier: 3.621A pdb=" N ARG D 746 " --> pdb=" O VAL D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 755 through 768 Processing helix chain 'D' and resid 780 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 136 removed outlier: 6.675A pdb=" N THR A 2 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 92 " --> pdb=" O THR A 2 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 4 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU A 94 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N HIS A 6 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL A 3 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER A 169 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL A 5 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL A 166 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA A 195 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 168 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 481 through 490 removed outlier: 6.380A pdb=" N GLY A 447 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER A 484 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 449 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 486 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 451 " --> pdb=" O VAL A 486 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE A 488 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 453 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP A 490 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A 455 " --> pdb=" O ASP A 490 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 404 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 525 " --> pdb=" O PHE A 555 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLU A 557 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A 527 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 572 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 130 through 136 removed outlier: 6.675A pdb=" N THR B 2 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU B 92 " --> pdb=" O THR B 2 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU B 4 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU B 94 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N HIS B 6 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL B 3 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER B 169 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL B 5 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 166 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA B 195 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 168 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 490 removed outlier: 6.380A pdb=" N GLY B 447 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER B 484 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL B 449 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 486 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 451 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE B 488 " --> pdb=" O PHE B 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 453 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP B 490 " --> pdb=" O LEU B 453 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS B 455 " --> pdb=" O ASP B 490 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL B 404 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 525 " --> pdb=" O PHE B 555 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N GLU B 557 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 527 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN B 572 " --> pdb=" O THR B 558 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 130 through 136 removed outlier: 6.675A pdb=" N THR C 2 " --> pdb=" O HIS C 90 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU C 92 " --> pdb=" O THR C 2 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU C 4 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU C 94 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N HIS C 6 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 3 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER C 169 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL C 5 " --> pdb=" O SER C 169 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 166 " --> pdb=" O ARG C 193 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA C 195 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 168 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 481 through 490 removed outlier: 6.380A pdb=" N GLY C 447 " --> pdb=" O ILE C 482 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 484 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL C 449 " --> pdb=" O SER C 484 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 486 " --> pdb=" O VAL C 449 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE C 451 " --> pdb=" O VAL C 486 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ILE C 488 " --> pdb=" O PHE C 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU C 453 " --> pdb=" O ILE C 488 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP C 490 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS C 455 " --> pdb=" O ASP C 490 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL C 404 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL C 525 " --> pdb=" O PHE C 555 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU C 557 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL C 527 " --> pdb=" O GLU C 557 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN C 572 " --> pdb=" O THR C 558 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 130 through 136 removed outlier: 6.675A pdb=" N THR D 2 " --> pdb=" O HIS D 90 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU D 92 " --> pdb=" O THR D 2 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 4 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 94 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N HIS D 6 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL D 3 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SER D 169 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 5 " --> pdb=" O SER D 169 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL D 166 " --> pdb=" O ARG D 193 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA D 195 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL D 168 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 481 through 490 removed outlier: 6.380A pdb=" N GLY D 447 " --> pdb=" O ILE D 482 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER D 484 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL D 449 " --> pdb=" O SER D 484 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 486 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE D 451 " --> pdb=" O VAL D 486 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE D 488 " --> pdb=" O PHE D 451 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 453 " --> pdb=" O ILE D 488 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ASP D 490 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS D 455 " --> pdb=" O ASP D 490 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL D 404 " --> pdb=" O GLU D 448 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL D 525 " --> pdb=" O PHE D 555 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLU D 557 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL D 527 " --> pdb=" O GLU D 557 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN D 572 " --> pdb=" O THR D 558 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3072 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: 4.24 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7799 1.34 - 1.46: 4520 1.46 - 1.58: 10524 1.58 - 1.70: 41 1.70 - 1.82: 156 Bond restraints: 23040 Sorted by residual: bond pdb=" O3' A H 4 " pdb=" P A H 5 " ideal model delta sigma weight residual 1.607 1.569 0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" O3' A E 4 " pdb=" P A E 5 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.20e-02 6.94e+03 9.58e+00 bond pdb=" O3' A G 4 " pdb=" P A G 5 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.20e-02 6.94e+03 9.58e+00 bond pdb=" O5' A E 3 " pdb=" C5' A E 3 " ideal model delta sigma weight residual 1.424 1.455 -0.031 1.60e-02 3.91e+03 3.70e+00 bond pdb=" O5' A G 3 " pdb=" C5' A G 3 " ideal model delta sigma weight residual 1.424 1.455 -0.031 1.60e-02 3.91e+03 3.70e+00 ... (remaining 23035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 29575 1.40 - 2.81: 1330 2.81 - 4.21: 281 4.21 - 5.62: 63 5.62 - 7.02: 27 Bond angle restraints: 31276 Sorted by residual: angle pdb=" O5' A E 3 " pdb=" C5' A E 3 " pdb=" C4' A E 3 " ideal model delta sigma weight residual 109.40 113.59 -4.19 8.00e-01 1.56e+00 2.74e+01 angle pdb=" O5' A G 3 " pdb=" C5' A G 3 " pdb=" C4' A G 3 " ideal model delta sigma weight residual 109.40 113.59 -4.19 8.00e-01 1.56e+00 2.74e+01 angle pdb=" O5' A H 3 " pdb=" C5' A H 3 " pdb=" C4' A H 3 " ideal model delta sigma weight residual 109.40 113.58 -4.18 8.00e-01 1.56e+00 2.73e+01 angle pdb=" O5' A F 2 " pdb=" C5' A F 2 " pdb=" C4' A F 2 " ideal model delta sigma weight residual 109.40 112.66 -3.26 8.00e-01 1.56e+00 1.66e+01 angle pdb=" O5' A F 3 " pdb=" C5' A F 3 " pdb=" C4' A F 3 " ideal model delta sigma weight residual 109.40 112.52 -3.12 8.00e-01 1.56e+00 1.52e+01 ... (remaining 31271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.09: 12168 21.09 - 42.17: 1160 42.17 - 63.26: 308 63.26 - 84.35: 48 84.35 - 105.43: 12 Dihedral angle restraints: 13696 sinusoidal: 5472 harmonic: 8224 Sorted by residual: dihedral pdb=" C5' A H 6 " pdb=" C4' A H 6 " pdb=" C3' A H 6 " pdb=" O3' A H 6 " ideal model delta sinusoidal sigma weight residual 147.00 100.16 46.84 1 8.00e+00 1.56e-02 4.74e+01 dihedral pdb=" O4' A H 6 " pdb=" C4' A H 6 " pdb=" C3' A H 6 " pdb=" C2' A H 6 " ideal model delta sinusoidal sigma weight residual 24.00 -20.18 44.18 1 8.00e+00 1.56e-02 4.24e+01 dihedral pdb=" C3' A H 6 " pdb=" C4' A H 6 " pdb=" O4' A H 6 " pdb=" C1' A H 6 " ideal model delta sinusoidal sigma weight residual -2.00 35.34 -37.34 1 8.00e+00 1.56e-02 3.07e+01 ... (remaining 13693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2596 0.048 - 0.095: 783 0.095 - 0.143: 149 0.143 - 0.191: 9 0.191 - 0.238: 3 Chirality restraints: 3540 Sorted by residual: chirality pdb=" C3' A H 1 " pdb=" C4' A H 1 " pdb=" O3' A H 1 " pdb=" C2' A H 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3' A G 1 " pdb=" C4' A G 1 " pdb=" O3' A G 1 " pdb=" C2' A G 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" C3' A E 1 " pdb=" C4' A E 1 " pdb=" O3' A E 1 " pdb=" C2' A E 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 3537 not shown) Planarity restraints: 4008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 183 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C GLY C 183 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY C 183 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL C 184 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 183 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C GLY B 183 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 183 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 184 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 183 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.64e+00 pdb=" C GLY D 183 " 0.041 2.00e-02 2.50e+03 pdb=" O GLY D 183 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL D 184 " -0.014 2.00e-02 2.50e+03 ... (remaining 4005 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 1 2.25 - 2.91: 8458 2.91 - 3.57: 29693 3.57 - 4.24: 50003 4.24 - 4.90: 84627 Nonbonded interactions: 172782 Sorted by model distance: nonbonded pdb=" P A H 1 " pdb=" O3' A H 6 " model vdw 1.582 3.400 nonbonded pdb=" OP2 A H 1 " pdb=" O3' A H 6 " model vdw 2.464 3.040 nonbonded pdb=" OP1 A H 1 " pdb=" O3' A H 6 " model vdw 2.479 3.040 nonbonded pdb=" O5' A H 1 " pdb=" O3' A H 6 " model vdw 2.487 3.040 nonbonded pdb=" O5' A H 4 " pdb=" O4' A H 4 " model vdw 2.491 2.432 ... (remaining 172777 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.240 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.070 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 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 : 0.004 0.038 23040 Z= 0.218 Angle : 0.729 7.020 31276 Z= 0.417 Chirality : 0.045 0.238 3540 Planarity : 0.005 0.050 4008 Dihedral : 17.796 105.434 8424 Min Nonbonded Distance : 1.582 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.64 % Favored : 95.24 % Rotamer: Outliers : 2.24 % Allowed : 22.05 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 2856 helix: 0.51 (0.13), residues: 1528 sheet: 0.36 (0.27), residues: 352 loop : -1.89 (0.18), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 209 TYR 0.018 0.002 TYR A 491 PHE 0.012 0.002 PHE B 218 TRP 0.012 0.002 TRP A 693 HIS 0.008 0.002 HIS D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.22 (23040) covalent geometry : angle 0.72939 / 0.42 (31276) hydrogen bonds : bond 0.20117 / 13.87 ( 1048) hydrogen bonds : angle 5.26716 / 3.70 ( 3072) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: A 341 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: B 236 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: B 341 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7429 (mp0) REVERT: C 236 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: C 341 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: D 236 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7011 (tt0) REVERT: D 341 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7420 (mp0) outliers start: 50 outliers final: 27 residues processed: 246 average time/residue: 0.6710 time to fit residues: 185.3995 Evaluate side-chains 238 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 347 SER Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 347 SER Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 654 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 HIS B 90 HIS C 90 HIS D 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.196169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.162738 restraints weight = 19901.385| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.29 r_work: 0.3237 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23040 Z= 0.169 Angle : 0.626 7.239 31276 Z= 0.338 Chirality : 0.042 0.161 3540 Planarity : 0.004 0.034 4008 Dihedral : 9.656 104.168 3499 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.40 % Favored : 95.48 % Rotamer: Outliers : 5.32 % Allowed : 18.11 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.16), residues: 2856 helix: 0.96 (0.13), residues: 1560 sheet: 0.35 (0.27), residues: 352 loop : -1.81 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 434 TYR 0.015 0.002 TYR D 491 PHE 0.010 0.002 PHE D 499 TRP 0.012 0.002 TRP B 395 HIS 0.007 0.002 HIS C 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (23040) covalent geometry : angle 0.62635 / 0.34 (31276) hydrogen bonds : bond 0.07805 / 5.24 ( 1048) hydrogen bonds : angle 4.07035 / 2.83 ( 3072) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 224 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6689 (t0) REVERT: A 70 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7068 (mmm-85) REVERT: A 341 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: A 448 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: A 655 GLN cc_start: 0.6534 (mt0) cc_final: 0.6291 (tt0) REVERT: B 12 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6692 (t0) REVERT: B 70 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7075 (mmm-85) REVERT: B 341 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 448 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: B 655 GLN cc_start: 0.6543 (mt0) cc_final: 0.6297 (tt0) REVERT: C 12 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6681 (t0) REVERT: C 70 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7063 (mmm-85) REVERT: C 341 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: C 448 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: C 655 GLN cc_start: 0.6539 (mt0) cc_final: 0.6294 (tt0) REVERT: D 12 ASP cc_start: 0.6908 (OUTLIER) cc_final: 0.6700 (t0) REVERT: D 70 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7067 (mmm-85) REVERT: D 341 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7319 (mp0) REVERT: D 448 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: D 655 GLN cc_start: 0.6537 (mt0) cc_final: 0.6292 (tt0) outliers start: 119 outliers final: 43 residues processed: 309 average time/residue: 0.6610 time to fit residues: 230.2991 Evaluate side-chains 275 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 171 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.193839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157159 restraints weight = 19835.969| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.37 r_work: 0.3200 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23040 Z= 0.217 Angle : 0.707 7.422 31276 Z= 0.379 Chirality : 0.047 0.174 3540 Planarity : 0.005 0.044 4008 Dihedral : 9.148 99.991 3472 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.92 % Favored : 94.96 % Rotamer: Outliers : 6.80 % Allowed : 17.08 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 2856 helix: 0.86 (0.13), residues: 1560 sheet: 0.29 (0.27), residues: 352 loop : -1.89 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 762 TYR 0.018 0.002 TYR A 491 PHE 0.012 0.002 PHE B 218 TRP 0.013 0.002 TRP D 395 HIS 0.007 0.002 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.22 (23040) covalent geometry : angle 0.70672 / 0.38 (31276) hydrogen bonds : bond 0.09049 / 6.06 ( 1048) hydrogen bonds : angle 4.02233 / 2.82 ( 3072) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 224 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6936 (OUTLIER) cc_final: 0.6701 (t0) REVERT: A 70 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7025 (mmm-85) REVERT: A 236 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: A 424 MET cc_start: 0.8780 (mmm) cc_final: 0.8389 (mmp) REVERT: A 448 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7512 (mm-30) REVERT: A 504 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: A 655 GLN cc_start: 0.6560 (mt0) cc_final: 0.6337 (tt0) REVERT: A 725 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: A 749 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5665 (mmt180) REVERT: B 12 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6686 (t0) REVERT: B 70 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7022 (mmm-85) REVERT: B 236 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: B 424 MET cc_start: 0.8806 (mmm) cc_final: 0.8425 (mmp) REVERT: B 448 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: B 504 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: B 655 GLN cc_start: 0.6546 (mt0) cc_final: 0.6323 (tt0) REVERT: B 749 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5674 (mmt180) REVERT: C 12 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6703 (t0) REVERT: C 70 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7028 (mmm-85) REVERT: C 236 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: C 424 MET cc_start: 0.8785 (mmm) cc_final: 0.8392 (mmp) REVERT: C 448 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: C 504 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: C 655 GLN cc_start: 0.6551 (mt0) cc_final: 0.6328 (tt0) REVERT: C 749 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5668 (mmt180) REVERT: D 12 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6685 (t0) REVERT: D 70 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7032 (mmm-85) REVERT: D 236 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6736 (tm-30) REVERT: D 424 MET cc_start: 0.8788 (mmm) cc_final: 0.8395 (mmp) REVERT: D 448 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7511 (mm-30) REVERT: D 504 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: D 655 GLN cc_start: 0.6543 (mt0) cc_final: 0.6321 (tt0) REVERT: D 749 ARG cc_start: 0.5980 (OUTLIER) cc_final: 0.5673 (mmt180) outliers start: 152 outliers final: 72 residues processed: 356 average time/residue: 0.7005 time to fit residues: 281.5921 Evaluate side-chains 317 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 220 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 749 ARG Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 749 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 142 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.194140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158561 restraints weight = 19807.984| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.36 r_work: 0.3201 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23040 Z= 0.207 Angle : 0.688 7.381 31276 Z= 0.370 Chirality : 0.046 0.180 3540 Planarity : 0.005 0.035 4008 Dihedral : 9.219 100.766 3472 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.92 % Favored : 94.96 % Rotamer: Outliers : 7.11 % Allowed : 17.35 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2856 helix: 0.89 (0.13), residues: 1568 sheet: 0.25 (0.27), residues: 352 loop : -1.90 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 136 TYR 0.017 0.002 TYR A 491 PHE 0.010 0.002 PHE D 555 TRP 0.013 0.002 TRP A 395 HIS 0.008 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (23040) covalent geometry : angle 0.68830 / 0.37 (31276) hydrogen bonds : bond 0.08585 / 5.75 ( 1048) hydrogen bonds : angle 3.97086 / 2.78 ( 3072) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 232 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6728 (t0) REVERT: A 70 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6888 (mmm-85) REVERT: A 235 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5847 (mp10) REVERT: A 236 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 424 MET cc_start: 0.8797 (mmm) cc_final: 0.8396 (mmp) REVERT: A 448 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: A 504 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: A 655 GLN cc_start: 0.6551 (mt0) cc_final: 0.6322 (tt0) REVERT: A 725 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: A 749 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5623 (mmt180) REVERT: B 12 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6730 (t0) REVERT: B 70 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6895 (mmm-85) REVERT: B 235 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.5846 (mp10) REVERT: B 236 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6620 (tt0) REVERT: B 424 MET cc_start: 0.8795 (mmm) cc_final: 0.8396 (mmp) REVERT: B 448 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.7530 (mm-30) REVERT: B 504 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: B 655 GLN cc_start: 0.6548 (mt0) cc_final: 0.6320 (tt0) REVERT: B 725 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7103 (tm-30) REVERT: B 749 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5627 (mmt180) REVERT: C 12 ASP cc_start: 0.6964 (OUTLIER) cc_final: 0.6729 (t0) REVERT: C 70 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6886 (mmm-85) REVERT: C 235 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5849 (mp10) REVERT: C 236 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: C 424 MET cc_start: 0.8801 (mmm) cc_final: 0.8400 (mmp) REVERT: C 448 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: C 504 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: C 655 GLN cc_start: 0.6550 (mt0) cc_final: 0.6322 (tt0) REVERT: C 725 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: C 749 ARG cc_start: 0.5971 (OUTLIER) cc_final: 0.5624 (mmt180) REVERT: D 12 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6707 (t0) REVERT: D 70 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6907 (mmm-85) REVERT: D 235 GLN cc_start: 0.6336 (OUTLIER) cc_final: 0.5845 (mp10) REVERT: D 236 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6620 (tt0) REVERT: D 424 MET cc_start: 0.8805 (mmm) cc_final: 0.8405 (mmp) REVERT: D 448 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7536 (mm-30) REVERT: D 504 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: D 655 GLN cc_start: 0.6547 (mt0) cc_final: 0.6318 (tt0) REVERT: D 725 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7089 (tm-30) REVERT: D 749 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5628 (mmt180) outliers start: 159 outliers final: 72 residues processed: 365 average time/residue: 0.6643 time to fit residues: 273.9120 Evaluate side-chains 330 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 226 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain A residue 749 ARG Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 484 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 749 ARG Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 749 ARG Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 484 SER Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 725 GLU Chi-restraints excluded: chain D residue 749 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 272 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 267 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 240 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.198182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.159544 restraints weight = 19780.229| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.43 r_work: 0.3264 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23040 Z= 0.129 Angle : 0.538 7.455 31276 Z= 0.292 Chirality : 0.039 0.159 3540 Planarity : 0.003 0.030 4008 Dihedral : 9.011 105.618 3464 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.43 % Favored : 95.45 % Rotamer: Outliers : 5.37 % Allowed : 19.45 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 2856 helix: 1.31 (0.14), residues: 1572 sheet: 0.30 (0.27), residues: 352 loop : -1.76 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 136 TYR 0.012 0.001 TYR B 491 PHE 0.010 0.001 PHE C 499 TRP 0.012 0.001 TRP D 395 HIS 0.004 0.001 HIS C 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.13 (23040) covalent geometry : angle 0.53751 / 0.29 (31276) hydrogen bonds : bond 0.05883 / 3.97 ( 1048) hydrogen bonds : angle 3.70228 / 2.58 ( 3072) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 224 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6917 (mmm-85) REVERT: A 235 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5709 (mp10) REVERT: A 236 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: A 448 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: A 655 GLN cc_start: 0.6409 (mt0) cc_final: 0.6207 (tt0) REVERT: A 706 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5716 (pt0) REVERT: A 725 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: B 70 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6907 (mmm-85) REVERT: B 235 GLN cc_start: 0.6151 (OUTLIER) cc_final: 0.5712 (mp10) REVERT: B 236 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: B 448 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7334 (mm-30) REVERT: B 655 GLN cc_start: 0.6418 (mt0) cc_final: 0.6215 (tt0) REVERT: B 706 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5718 (pt0) REVERT: B 725 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6820 (tm-30) REVERT: C 70 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6902 (mmm-85) REVERT: C 235 GLN cc_start: 0.6147 (OUTLIER) cc_final: 0.5708 (mp10) REVERT: C 236 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: C 448 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7339 (mm-30) REVERT: C 655 GLN cc_start: 0.6415 (mt0) cc_final: 0.6210 (tt0) REVERT: C 706 GLU cc_start: 0.5937 (OUTLIER) cc_final: 0.5715 (pt0) REVERT: C 725 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: D 70 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6924 (mmm-85) REVERT: D 235 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5703 (mp10) REVERT: D 236 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: D 448 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: D 655 GLN cc_start: 0.6425 (mt0) cc_final: 0.6222 (tt0) REVERT: D 706 GLU cc_start: 0.5942 (OUTLIER) cc_final: 0.5718 (pt0) REVERT: D 725 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6801 (tm-30) outliers start: 120 outliers final: 72 residues processed: 324 average time/residue: 0.7188 time to fit residues: 262.5283 Evaluate side-chains 316 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 220 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 725 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 181 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 113 optimal weight: 0.0770 chunk 68 optimal weight: 20.0000 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.194656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.161545 restraints weight = 19734.048| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.30 r_work: 0.3229 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23040 Z= 0.206 Angle : 0.683 7.437 31276 Z= 0.366 Chirality : 0.046 0.173 3540 Planarity : 0.005 0.059 4008 Dihedral : 9.082 100.483 3464 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.92 % Favored : 94.96 % Rotamer: Outliers : 6.57 % Allowed : 18.25 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2856 helix: 1.05 (0.13), residues: 1568 sheet: 0.29 (0.27), residues: 352 loop : -1.85 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 762 TYR 0.017 0.002 TYR A 491 PHE 0.011 0.002 PHE A 218 TRP 0.011 0.002 TRP D 395 HIS 0.008 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.21 (23040) covalent geometry : angle 0.68298 / 0.37 (31276) hydrogen bonds : bond 0.08409 / 5.63 ( 1048) hydrogen bonds : angle 3.87105 / 2.70 ( 3072) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 228 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6893 (mmm-85) REVERT: A 235 GLN cc_start: 0.6328 (OUTLIER) cc_final: 0.5823 (mp10) REVERT: A 236 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6819 (tt0) REVERT: A 448 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: A 655 GLN cc_start: 0.6578 (mt0) cc_final: 0.6337 (tt0) REVERT: A 706 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5732 (pt0) REVERT: A 725 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: A 743 MET cc_start: 0.7351 (mmt) cc_final: 0.7042 (mtt) REVERT: B 70 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6905 (mmm-85) REVERT: B 235 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5832 (mp10) REVERT: B 236 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: B 448 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: B 655 GLN cc_start: 0.6581 (mt0) cc_final: 0.6339 (tt0) REVERT: B 706 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5734 (pt0) REVERT: B 725 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: B 743 MET cc_start: 0.7361 (mmt) cc_final: 0.7051 (mtt) REVERT: C 70 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6897 (mmm-85) REVERT: C 235 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: C 236 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: C 448 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7477 (mm-30) REVERT: C 655 GLN cc_start: 0.6576 (mt0) cc_final: 0.6333 (tt0) REVERT: C 706 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5729 (pt0) REVERT: C 725 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7125 (tm-30) REVERT: C 743 MET cc_start: 0.7354 (mmt) cc_final: 0.7045 (mtt) REVERT: D 70 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6919 (mmm-85) REVERT: D 235 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5832 (mp10) REVERT: D 236 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: D 448 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: D 655 GLN cc_start: 0.6575 (mt0) cc_final: 0.6333 (tt0) REVERT: D 706 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5736 (pt0) REVERT: D 725 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: D 743 MET cc_start: 0.7351 (mmt) cc_final: 0.7041 (mtt) outliers start: 147 outliers final: 76 residues processed: 356 average time/residue: 0.6687 time to fit residues: 269.6431 Evaluate side-chains 322 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 222 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 725 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 136 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.199953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164975 restraints weight = 19937.354| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.32 r_work: 0.3305 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 23040 Z= 0.116 Angle : 0.506 7.600 31276 Z= 0.276 Chirality : 0.039 0.150 3540 Planarity : 0.003 0.046 4008 Dihedral : 8.951 107.143 3464 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.36 % Favored : 95.52 % Rotamer: Outliers : 5.14 % Allowed : 19.63 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2856 helix: 1.50 (0.14), residues: 1560 sheet: 0.51 (0.28), residues: 328 loop : -1.71 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 136 TYR 0.009 0.001 TYR C 491 PHE 0.010 0.001 PHE B 499 TRP 0.012 0.001 TRP D 395 HIS 0.004 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.12 (23040) covalent geometry : angle 0.50619 / 0.28 (31276) hydrogen bonds : bond 0.04980 / 3.38 ( 1048) hydrogen bonds : angle 3.58456 / 2.48 ( 3072) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 220 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6876 (mmm-85) REVERT: A 193 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6935 (mtp180) REVERT: A 235 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.5665 (mp10) REVERT: A 448 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: A 706 GLU cc_start: 0.5916 (OUTLIER) cc_final: 0.5694 (pt0) REVERT: A 725 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: B 70 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6864 (mmm-85) REVERT: B 193 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6942 (mtp180) REVERT: B 235 GLN cc_start: 0.6089 (OUTLIER) cc_final: 0.5662 (mp10) REVERT: B 448 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: B 706 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5694 (pt0) REVERT: B 725 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: C 70 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6865 (mmm-85) REVERT: C 193 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6945 (mtp180) REVERT: C 235 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5660 (mp10) REVERT: C 448 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7259 (mm-30) REVERT: C 706 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5694 (pt0) REVERT: C 725 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: D 70 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6894 (mmm-85) REVERT: D 193 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6940 (mtp180) REVERT: D 235 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5659 (mp10) REVERT: D 448 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: D 706 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5696 (pt0) REVERT: D 725 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6832 (tm-30) outliers start: 115 outliers final: 56 residues processed: 308 average time/residue: 0.6656 time to fit residues: 231.1449 Evaluate side-chains 288 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 208 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 333 LYS Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 725 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 258 optimal weight: 3.9990 chunk 287 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 232 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.196495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159356 restraints weight = 19536.476| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.38 r_work: 0.3236 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23040 Z= 0.168 Angle : 0.611 7.197 31276 Z= 0.327 Chirality : 0.042 0.156 3540 Planarity : 0.004 0.058 4008 Dihedral : 8.974 102.557 3464 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.50 % Favored : 95.38 % Rotamer: Outliers : 5.05 % Allowed : 20.17 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.16), residues: 2856 helix: 1.32 (0.13), residues: 1564 sheet: 0.35 (0.27), residues: 352 loop : -1.72 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 762 TYR 0.015 0.002 TYR C 491 PHE 0.010 0.002 PHE B 555 TRP 0.010 0.002 TRP D 395 HIS 0.007 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (23040) covalent geometry : angle 0.61145 / 0.33 (31276) hydrogen bonds : bond 0.07143 / 4.79 ( 1048) hydrogen bonds : angle 3.68824 / 2.57 ( 3072) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 205 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6923 (mmm-85) REVERT: A 235 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.5802 (mp10) REVERT: A 236 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: A 448 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: A 706 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5755 (pt0) REVERT: A 725 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.7037 (tm-30) REVERT: B 70 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6916 (mmm-85) REVERT: B 235 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.5810 (mp10) REVERT: B 236 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: B 448 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7447 (mm-30) REVERT: B 706 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5758 (pt0) REVERT: B 725 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: C 70 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6926 (mmm-85) REVERT: C 235 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.5808 (mp10) REVERT: C 236 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: C 448 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7441 (mm-30) REVERT: C 706 GLU cc_start: 0.5994 (OUTLIER) cc_final: 0.5757 (pt0) REVERT: C 725 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7082 (tm-30) REVERT: D 70 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6940 (mmm-85) REVERT: D 235 GLN cc_start: 0.6300 (OUTLIER) cc_final: 0.5804 (mp10) REVERT: D 236 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: D 448 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: D 706 GLU cc_start: 0.5989 (OUTLIER) cc_final: 0.5756 (pt0) REVERT: D 725 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7073 (tm-30) outliers start: 113 outliers final: 66 residues processed: 302 average time/residue: 0.6081 time to fit residues: 206.9948 Evaluate side-chains 292 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 202 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 507 ARG Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 236 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 507 ARG Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 236 GLU Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 507 ARG Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 725 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.194485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.157632 restraints weight = 19646.016| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.41 r_work: 0.3207 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.0918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23040 Z= 0.213 Angle : 0.700 7.737 31276 Z= 0.376 Chirality : 0.046 0.168 3540 Planarity : 0.005 0.061 4008 Dihedral : 9.057 99.960 3464 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.98 % Allowed : 4.24 % Favored : 94.78 % Rotamer: Outliers : 5.68 % Allowed : 19.59 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2856 helix: 1.07 (0.13), residues: 1564 sheet: 0.30 (0.27), residues: 352 loop : -1.80 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 762 TYR 0.018 0.002 TYR A 219 PHE 0.012 0.002 PHE D 218 TRP 0.011 0.002 TRP A 220 HIS 0.009 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (23040) covalent geometry : angle 0.69994 / 0.38 (31276) hydrogen bonds : bond 0.08577 / 5.74 ( 1048) hydrogen bonds : angle 3.83422 / 2.68 ( 3072) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 192 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6855 (mmm-85) REVERT: A 235 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5875 (mp10) REVERT: A 448 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: A 706 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5770 (pt0) REVERT: A 725 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7113 (tm-30) REVERT: B 70 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6868 (mmm-85) REVERT: B 235 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5880 (mp10) REVERT: B 448 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: B 706 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5771 (pt0) REVERT: B 725 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: C 70 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6862 (mmm-85) REVERT: C 235 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.5883 (mp10) REVERT: C 448 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7542 (mm-30) REVERT: C 706 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5769 (pt0) REVERT: C 725 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: D 70 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6880 (mmm-85) REVERT: D 235 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.5884 (mp10) REVERT: D 448 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: D 706 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5766 (pt0) REVERT: D 725 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7137 (tm-30) outliers start: 127 outliers final: 61 residues processed: 303 average time/residue: 0.6282 time to fit residues: 215.3258 Evaluate side-chains 275 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 194 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 725 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 220 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 277 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.195077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158885 restraints weight = 19808.206| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.37 r_work: 0.3219 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23040 Z= 0.173 Angle : 0.623 7.376 31276 Z= 0.336 Chirality : 0.043 0.168 3540 Planarity : 0.005 0.059 4008 Dihedral : 9.041 102.391 3464 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.50 % Favored : 95.52 % Rotamer: Outliers : 4.74 % Allowed : 20.66 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.16), residues: 2856 helix: 1.16 (0.13), residues: 1564 sheet: 0.29 (0.27), residues: 352 loop : -1.78 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 762 TYR 0.015 0.002 TYR A 491 PHE 0.010 0.002 PHE D 555 TRP 0.012 0.002 TRP A 395 HIS 0.007 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (23040) covalent geometry : angle 0.62340 / 0.34 (31276) hydrogen bonds : bond 0.07478 / 5.01 ( 1048) hydrogen bonds : angle 3.74512 / 2.61 ( 3072) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5712 Ramachandran restraints generated. 2856 Oldfield, 0 Emsley, 2856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 197 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6926 (mmm-85) REVERT: A 235 GLN cc_start: 0.6305 (OUTLIER) cc_final: 0.5851 (mp10) REVERT: A 309 GLU cc_start: 0.5457 (OUTLIER) cc_final: 0.5248 (mt-10) REVERT: A 448 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: A 706 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5783 (pt0) REVERT: A 725 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: B 70 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6925 (mmm-85) REVERT: B 235 GLN cc_start: 0.6305 (OUTLIER) cc_final: 0.5851 (mp10) REVERT: B 309 GLU cc_start: 0.5468 (OUTLIER) cc_final: 0.5258 (mt-10) REVERT: B 448 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: B 706 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5785 (pt0) REVERT: B 725 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: C 70 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6914 (mmm-85) REVERT: C 235 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5848 (mp10) REVERT: C 309 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.5242 (mt-10) REVERT: C 448 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: C 706 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5781 (pt0) REVERT: C 725 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: D 70 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6941 (mmm-85) REVERT: D 235 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5847 (mp10) REVERT: D 309 GLU cc_start: 0.5454 (OUTLIER) cc_final: 0.5242 (mt-10) REVERT: D 448 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7493 (mm-30) REVERT: D 706 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5785 (pt0) REVERT: D 725 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7083 (tm-30) outliers start: 106 outliers final: 68 residues processed: 294 average time/residue: 0.6469 time to fit residues: 215.2278 Evaluate side-chains 281 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 189 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 70 ARG Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 193 ARG Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 448 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 654 CYS Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 GLU Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 710 CYS Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 70 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 193 ARG Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 235 GLN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 341 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 448 GLU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 601 SER Chi-restraints excluded: chain B residue 654 CYS Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 70 ARG Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 448 GLU Chi-restraints excluded: chain C residue 472 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 601 SER Chi-restraints excluded: chain C residue 654 CYS Chi-restraints excluded: chain C residue 705 SER Chi-restraints excluded: chain C residue 706 GLU Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 132 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 193 ARG Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 235 GLN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 381 THR Chi-restraints excluded: chain D residue 448 GLU Chi-restraints excluded: chain D residue 472 VAL Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 601 SER Chi-restraints excluded: chain D residue 654 CYS Chi-restraints excluded: chain D residue 705 SER Chi-restraints excluded: chain D residue 706 GLU Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 710 CYS Chi-restraints excluded: chain D residue 725 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 66 optimal weight: 0.0980 chunk 191 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 HIS A 730 HIS B 6 HIS C 6 HIS D 6 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.194107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.159087 restraints weight = 19764.498| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.34 r_work: 0.3211 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23040 Z= 0.199 Angle : 0.670 7.738 31276 Z= 0.360 Chirality : 0.045 0.173 3540 Planarity : 0.005 0.068 4008 Dihedral : 9.072 100.607 3464 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.92 % Favored : 95.10 % Rotamer: Outliers : 4.79 % Allowed : 20.84 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2856 helix: 0.95 (0.13), residues: 1588 sheet: 0.26 (0.27), residues: 352 loop : -1.74 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 762 TYR 0.017 0.002 TYR A 219 PHE 0.011 0.002 PHE D 555 TRP 0.012 0.002 TRP A 395 HIS 0.008 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (23040) covalent geometry : angle 0.67011 / 0.36 (31276) hydrogen bonds : bond 0.08269 / 5.53 ( 1048) hydrogen bonds : angle 3.80197 / 2.65 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9295.05 seconds wall clock time: 158 minutes 16.98 seconds (9496.98 seconds total)