Starting phenix.real_space_refine on Sat Jul 4 19:26:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w3v_65610/07_2026/9w3v_65610_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w3v_65610/07_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_65610/07_2026/9w3v_65610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w3v_65610/07_2026/9w3v_65610.map" model { file = "/net/cci-nas-00/data/ceres_data/9w3v_65610/07_2026/9w3v_65610_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w3v_65610/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.13, per 1000 atoms: 0.23 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: 1.75 Conformation dependent library (CDL) restraints added in 1.0 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: 0.61 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: 4.37 Time building geometry restraints manager: 2.37 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 1.50e-02 4.44e+03 6.52e+00 bond pdb=" O3' A E 4 " pdb=" P A E 5 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.50e-02 4.44e+03 6.13e+00 bond pdb=" O3' A G 4 " pdb=" P A G 5 " ideal model delta sigma weight residual 1.607 1.570 0.037 1.50e-02 4.44e+03 6.13e+00 bond pdb=" O5' A E 3 " pdb=" C5' A E 3 " ideal model delta sigma weight residual 1.424 1.455 -0.031 1.50e-02 4.44e+03 4.21e+00 bond pdb=" O5' A G 3 " pdb=" C5' A G 3 " ideal model delta sigma weight residual 1.424 1.455 -0.031 1.50e-02 4.44e+03 4.21e+00 ... (remaining 23035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 29573 1.40 - 2.81: 1341 2.81 - 4.21: 273 4.21 - 5.62: 62 5.62 - 7.02: 27 Bond angle restraints: 31276 Sorted by residual: angle pdb=" C4' A G 2 " pdb=" C3' A G 2 " pdb=" O3' A G 2 " ideal model delta sigma weight residual 109.40 115.76 -6.36 1.50e+00 4.44e-01 1.80e+01 angle pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 109.40 115.76 -6.36 1.50e+00 4.44e-01 1.80e+01 angle pdb=" C4' A H 2 " pdb=" C3' A H 2 " pdb=" O3' A H 2 " ideal model delta sigma weight residual 109.40 115.74 -6.34 1.50e+00 4.44e-01 1.79e+01 angle pdb=" C PHE A 218 " pdb=" N TYR A 219 " pdb=" CA TYR A 219 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C PHE D 218 " pdb=" N TYR D 219 " pdb=" CA TYR D 219 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+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: 2593 0.048 - 0.095: 785 0.095 - 0.143: 150 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: 0.08 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- 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= 0.215 Angle : 0.727 7.020 31276 Z= 0.413 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 / 0.21 (23040) covalent geometry : angle 0.72731 / 0.41 (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 : 0.899 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: 0.7369 time to fit residues: 203.6952 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 : 0.825 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.196095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.162622 restraints weight = 19893.560| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.30 r_work: 0.3237 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0567 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= 0.170 Angle : 0.623 7.253 31276 Z= 0.338 Chirality : 0.042 0.186 3540 Planarity : 0.004 0.034 4008 Dihedral : 9.748 108.216 3499 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.50 % Favored : 95.38 % 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: -0.04 (0.16), residues: 2856 helix: 0.95 (0.13), residues: 1560 sheet: 0.34 (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 B 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 0.62343 / 0.34 (31276) hydrogen bonds : bond 0.07853 / 5.27 ( 1048) hydrogen bonds : angle 4.07092 / 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 : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7064 (mmm-85) REVERT: A 341 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: A 448 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: A 655 GLN cc_start: 0.6542 (mt0) cc_final: 0.6298 (tt0) REVERT: B 12 ASP cc_start: 0.6906 (OUTLIER) cc_final: 0.6698 (t0) REVERT: B 70 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7071 (mmm-85) REVERT: B 341 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: B 448 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: B 655 GLN cc_start: 0.6547 (mt0) cc_final: 0.6302 (tt0) REVERT: C 12 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6687 (t0) REVERT: C 70 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7062 (mmm-85) REVERT: C 341 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: C 448 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: C 655 GLN cc_start: 0.6542 (mt0) cc_final: 0.6297 (tt0) REVERT: D 12 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6703 (t0) REVERT: D 70 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7065 (mmm-85) REVERT: D 341 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: D 448 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.7403 (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: 0.7107 time to fit residues: 247.6124 Evaluate side-chains 274 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 277 optimal weight: 0.6980 chunk 284 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 203 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.4137 r_free = 0.4137 target = 0.196031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.162591 restraints weight = 19861.408| |-----------------------------------------------------------------------------| r_work (start): 0.3795 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: 0.8040 moved from start: 0.0721 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= 0.162 Angle : 0.599 7.040 31276 Z= 0.324 Chirality : 0.042 0.160 3540 Planarity : 0.004 0.049 4008 Dihedral : 9.096 107.356 3472 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.92 % Favored : 94.96 % Rotamer: Outliers : 6.04 % Allowed : 17.71 % Favored : 76.25 % 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: 1.13 (0.14), residues: 1560 sheet: 0.34 (0.27), residues: 352 loop : -1.80 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 762 TYR 0.015 0.002 TYR A 491 PHE 0.009 0.002 PHE C 499 TRP 0.011 0.002 TRP B 395 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (23040) covalent geometry : angle 0.59898 / 0.32 (31276) hydrogen bonds : bond 0.07350 / 4.94 ( 1048) hydrogen bonds : angle 3.84235 / 2.68 ( 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 363 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 228 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.8751 (mmm) cc_final: 0.8344 (mmp) REVERT: A 448 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7397 (mm-30) REVERT: A 655 GLN cc_start: 0.6460 (mt0) cc_final: 0.6246 (tt0) REVERT: A 725 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: B 12 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6688 (t0) REVERT: B 424 MET cc_start: 0.8798 (mmm) cc_final: 0.8408 (mmp) REVERT: B 448 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: B 655 GLN cc_start: 0.6455 (mt0) cc_final: 0.6241 (tt0) REVERT: C 12 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6684 (t0) REVERT: C 424 MET cc_start: 0.8756 (mmm) cc_final: 0.8348 (mmp) REVERT: C 448 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: C 655 GLN cc_start: 0.6452 (mt0) cc_final: 0.6238 (tt0) REVERT: D 12 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6706 (t0) REVERT: D 424 MET cc_start: 0.8759 (mmm) cc_final: 0.8352 (mmp) REVERT: D 448 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: D 655 GLN cc_start: 0.6447 (mt0) cc_final: 0.6233 (tt0) outliers start: 135 outliers final: 61 residues processed: 343 average time/residue: 0.7000 time to fit residues: 271.4576 Evaluate side-chains 297 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASP 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 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 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 B residue 12 ASP Chi-restraints excluded: chain B residue 16 ASP 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 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 707 VAL Chi-restraints excluded: chain B residue 710 CYS Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 16 ASP 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 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 707 VAL Chi-restraints excluded: chain C residue 710 CYS Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain D residue 16 ASP 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 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 707 VAL Chi-restraints excluded: chain D residue 710 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 142 optimal weight: 7.9990 chunk 133 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 262 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.192335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158990 restraints weight = 19713.008| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.28 r_work: 0.3197 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23040 Z= 0.273 Angle : 0.798 8.048 31276 Z= 0.429 Chirality : 0.051 0.201 3540 Planarity : 0.006 0.042 4008 Dihedral : 9.266 103.426 3464 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 1.12 % Allowed : 4.06 % Favored : 94.82 % Rotamer: Outliers : 7.16 % Allowed : 17.53 % Favored : 75.31 % 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 (0.15), residues: 2856 helix: 0.67 (0.13), residues: 1568 sheet: 0.44 (0.27), residues: 344 loop : -1.93 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 209 TYR 0.019 0.003 TYR C 491 PHE 0.015 0.003 PHE D 218 TRP 0.015 0.003 TRP D 220 HIS 0.010 0.002 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.27 (23040) covalent geometry : angle 0.79820 / 0.43 (31276) hydrogen bonds : bond 0.10264 / 6.87 ( 1048) hydrogen bonds : angle 4.09965 / 2.87 ( 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 378 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 218 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: 0.7417 (OUTLIER) cc_final: 0.6987 (mmm-85) REVERT: A 235 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.5920 (mp10) REVERT: A 236 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6858 (tm-30) REVERT: A 424 MET cc_start: 0.8823 (mmm) cc_final: 0.8437 (mmp) REVERT: A 448 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: A 504 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 655 GLN cc_start: 0.6660 (mt0) cc_final: 0.6393 (tt0) REVERT: A 706 GLU cc_start: 0.6082 (OUTLIER) cc_final: 0.5821 (pt0) REVERT: A 725 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: A 749 ARG cc_start: 0.5985 (OUTLIER) cc_final: 0.5710 (mmt-90) REVERT: B 70 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6981 (mmm-85) REVERT: B 235 GLN cc_start: 0.6412 (OUTLIER) cc_final: 0.5934 (mp10) REVERT: B 236 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6879 (tm-30) REVERT: B 424 MET cc_start: 0.8818 (mmm) cc_final: 0.8435 (mmp) REVERT: B 448 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: B 504 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: B 655 GLN cc_start: 0.6659 (mt0) cc_final: 0.6392 (tt0) REVERT: B 725 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: B 749 ARG cc_start: 0.5991 (OUTLIER) cc_final: 0.5711 (mmt-90) REVERT: C 70 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6981 (mmm-85) REVERT: C 235 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.5823 (mp10) REVERT: C 236 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6863 (tm-30) REVERT: C 424 MET cc_start: 0.8827 (mmm) cc_final: 0.8441 (mmp) REVERT: C 448 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: C 504 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: C 655 GLN cc_start: 0.6663 (mt0) cc_final: 0.6395 (tt0) REVERT: C 725 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7072 (tm-30) REVERT: C 749 ARG cc_start: 0.5984 (OUTLIER) cc_final: 0.5705 (mmt-90) REVERT: D 70 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.6986 (mmm-85) REVERT: D 235 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.5928 (mp10) REVERT: D 236 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6867 (tm-30) REVERT: D 424 MET cc_start: 0.8831 (mmm) cc_final: 0.8449 (mmp) REVERT: D 448 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7577 (mm-30) REVERT: D 504 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: D 655 GLN cc_start: 0.6642 (mt0) cc_final: 0.6376 (tt0) REVERT: D 725 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: D 749 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5715 (mmt-90) outliers start: 160 outliers final: 88 residues processed: 355 average time/residue: 0.6820 time to fit residues: 274.1233 Evaluate side-chains 333 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 216 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 484 SER Chi-restraints excluded: chain A residue 504 GLU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 544 GLN 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 A residue 749 ARG 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 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 484 SER Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 544 GLN 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 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 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 484 SER Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 544 GLN 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 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 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 484 SER Chi-restraints excluded: chain D residue 504 GLU Chi-restraints excluded: chain D residue 530 LEU Chi-restraints excluded: chain D residue 544 GLN 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: 1.9990 chunk 271 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 257 optimal weight: 0.0770 chunk 87 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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 = 0.4158 r_free = 0.4158 target = 0.198106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.158862 restraints weight = 19846.032| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.43 r_work: 0.3258 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 23040 Z= 0.131 Angle : 0.538 7.614 31276 Z= 0.294 Chirality : 0.039 0.151 3540 Planarity : 0.004 0.031 4008 Dihedral : 9.083 108.274 3464 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.22 % Favored : 95.66 % Rotamer: Outliers : 5.55 % Allowed : 19.23 % 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: 0.25 (0.16), residues: 2856 helix: 1.27 (0.14), residues: 1568 sheet: 0.27 (0.27), residues: 352 loop : -1.80 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 463 TYR 0.012 0.001 TYR B 491 PHE 0.010 0.001 PHE B 499 TRP 0.013 0.001 TRP D 395 HIS 0.004 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.13 (23040) covalent geometry : angle 0.53823 / 0.29 (31276) hydrogen bonds : bond 0.05957 / 4.02 ( 1048) hydrogen bonds : angle 3.71855 / 2.59 ( 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 337 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 213 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6887 (mmm-85) REVERT: A 235 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5761 (mp10) REVERT: A 330 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6640 (pp20) REVERT: A 448 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.7367 (mm-30) REVERT: A 725 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: B 70 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6903 (mmm-85) REVERT: B 235 GLN cc_start: 0.6190 (OUTLIER) cc_final: 0.5768 (mp10) REVERT: B 448 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7362 (mm-30) REVERT: B 706 GLU cc_start: 0.5959 (OUTLIER) cc_final: 0.5721 (pt0) REVERT: B 725 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: C 70 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6881 (mmm-85) REVERT: C 235 GLN cc_start: 0.6182 (OUTLIER) cc_final: 0.5759 (mp10) REVERT: C 448 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: C 706 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5682 (pt0) REVERT: C 725 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6770 (tm-30) REVERT: D 70 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6893 (mmm-85) REVERT: D 235 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5761 (mp10) REVERT: D 448 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7371 (mm-30) REVERT: D 706 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5683 (pt0) REVERT: D 725 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6763 (tm-30) outliers start: 124 outliers final: 59 residues processed: 315 average time/residue: 0.7347 time to fit residues: 259.8454 Evaluate side-chains 298 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 330 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 654 CYS 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 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 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 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 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 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 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 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 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 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: 9.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.193396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.157880 restraints weight = 19719.713| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.36 r_work: 0.3186 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 23040 Z= 0.260 Angle : 0.764 7.734 31276 Z= 0.411 Chirality : 0.050 0.197 3540 Planarity : 0.005 0.039 4008 Dihedral : 9.264 104.168 3464 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 1.12 % Allowed : 4.06 % Favored : 94.82 % Rotamer: Outliers : 7.25 % Allowed : 17.89 % Favored : 74.87 % 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: -0.20 (0.15), residues: 2856 helix: 0.81 (0.13), residues: 1568 sheet: 0.26 (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 B 209 TYR 0.019 0.003 TYR B 491 PHE 0.014 0.003 PHE B 218 TRP 0.014 0.003 TRP D 220 HIS 0.009 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.26 (23040) covalent geometry : angle 0.76378 / 0.41 (31276) hydrogen bonds : bond 0.09605 / 6.42 ( 1048) hydrogen bonds : angle 3.99132 / 2.79 ( 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 372 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 210 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6918 (mmm-85) REVERT: A 235 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.5920 (mp10) REVERT: A 236 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6888 (tm-30) REVERT: A 330 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: A 424 MET cc_start: 0.8830 (mmm) cc_final: 0.8437 (mmp) REVERT: A 448 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: A 504 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: A 706 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5806 (pt0) REVERT: A 725 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: A 743 MET cc_start: 0.7198 (mmt) cc_final: 0.6879 (mtt) REVERT: A 749 ARG cc_start: 0.5963 (OUTLIER) cc_final: 0.5644 (mmt180) REVERT: B 70 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6905 (mmm-85) REVERT: B 235 GLN cc_start: 0.6417 (OUTLIER) cc_final: 0.5932 (mp10) REVERT: B 236 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: B 424 MET cc_start: 0.8830 (mmm) cc_final: 0.8437 (mmp) REVERT: B 448 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: B 504 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 706 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5801 (pt0) REVERT: B 725 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: B 743 MET cc_start: 0.7208 (mmt) cc_final: 0.6888 (mtt) REVERT: B 749 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.5650 (mmt180) REVERT: C 70 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6918 (mmm-85) REVERT: C 235 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.5930 (mp10) REVERT: C 236 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: C 424 MET cc_start: 0.8839 (mmm) cc_final: 0.8445 (mmp) REVERT: C 448 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: C 504 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: C 706 GLU cc_start: 0.6022 (OUTLIER) cc_final: 0.5790 (pt0) REVERT: C 725 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: C 743 MET cc_start: 0.7203 (mmt) cc_final: 0.6883 (mtt) REVERT: C 749 ARG cc_start: 0.5961 (OUTLIER) cc_final: 0.5642 (mmt180) REVERT: D 70 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6920 (mmm-85) REVERT: D 235 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5932 (mp10) REVERT: D 236 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6895 (tm-30) REVERT: D 424 MET cc_start: 0.8840 (mmm) cc_final: 0.8445 (mmp) REVERT: D 448 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: D 504 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: D 706 GLU cc_start: 0.6025 (OUTLIER) cc_final: 0.5804 (pt0) REVERT: D 725 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: D 743 MET cc_start: 0.7202 (mmt) cc_final: 0.6881 (mtt) REVERT: D 749 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5648 (mmt180) outliers start: 162 outliers final: 84 residues processed: 357 average time/residue: 0.6929 time to fit residues: 280.0255 Evaluate side-chains 333 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 216 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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 330 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 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 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 A residue 749 ARG 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 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 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 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 B residue 749 ARG 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 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 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 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 C residue 749 ARG 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 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 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 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 Chi-restraints excluded: chain D residue 749 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 39 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 274 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 282 optimal weight: 20.0000 chunk 172 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4168 r_free = 0.4168 target = 0.199294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164579 restraints weight = 19923.869| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 1.35 r_work: 0.3287 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1073 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= 0.118 Angle : 0.515 7.709 31276 Z= 0.281 Chirality : 0.039 0.158 3540 Planarity : 0.003 0.031 4008 Dihedral : 9.050 108.848 3464 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.36 % Favored : 95.52 % Rotamer: Outliers : 4.65 % Allowed : 20.08 % Favored : 75.27 % 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: 0.41 (0.16), residues: 2856 helix: 1.42 (0.14), residues: 1560 sheet: 0.29 (0.27), residues: 352 loop : -1.73 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 136 TYR 0.009 0.001 TYR A 491 PHE 0.010 0.001 PHE C 499 TRP 0.013 0.002 TRP C 395 HIS 0.004 0.001 HIS C 730 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 (23040) covalent geometry : angle 0.51466 / 0.28 (31276) hydrogen bonds : bond 0.05263 / 3.56 ( 1048) hydrogen bonds : angle 3.64826 / 2.53 ( 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 323 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 219 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6890 (mmm-85) REVERT: A 193 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6939 (mtp180) REVERT: A 235 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5718 (mp10) REVERT: A 236 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: A 330 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6656 (pp20) REVERT: A 448 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: A 725 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: B 70 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6874 (mmm-85) REVERT: B 235 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5722 (mp10) REVERT: B 236 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6819 (tm-30) REVERT: B 448 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: B 725 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: C 70 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6882 (mmm-85) REVERT: C 193 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6952 (mtp180) REVERT: C 235 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5714 (mp10) REVERT: C 236 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6806 (tm-30) REVERT: C 448 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.7303 (mm-30) REVERT: C 725 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: D 70 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6899 (mmm-85) REVERT: D 193 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6944 (mtp180) REVERT: D 235 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5714 (mp10) REVERT: D 236 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: D 448 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7308 (mm-30) REVERT: D 725 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7036 (tm-30) outliers start: 104 outliers final: 54 residues processed: 303 average time/residue: 0.7423 time to fit residues: 252.6015 Evaluate side-chains 277 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 199 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET 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 236 GLU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 330 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 484 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 654 CYS 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 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 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 484 SER 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 C residue 1 MET 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 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 484 SER 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 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 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 484 SER 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 258 optimal weight: 7.9990 chunk 287 optimal weight: 20.0000 chunk 257 optimal weight: 0.0670 chunk 204 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 232 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.196278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.158166 restraints weight = 19521.760| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.39 r_work: 0.3236 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23040 Z= 0.169 Angle : 0.613 7.142 31276 Z= 0.329 Chirality : 0.042 0.159 3540 Planarity : 0.004 0.062 4008 Dihedral : 9.083 106.700 3464 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.50 % Favored : 95.38 % Rotamer: Outliers : 4.79 % Allowed : 20.26 % Favored : 74.96 % 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: 0.27 (0.16), residues: 2856 helix: 1.25 (0.13), residues: 1572 sheet: 0.32 (0.27), residues: 352 loop : -1.76 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 762 TYR 0.016 0.002 TYR A 491 PHE 0.011 0.002 PHE D 555 TRP 0.011 0.002 TRP D 395 HIS 0.007 0.001 HIS D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (23040) covalent geometry : angle 0.61282 / 0.33 (31276) hydrogen bonds : bond 0.07164 / 4.80 ( 1048) hydrogen bonds : angle 3.70659 / 2.58 ( 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 309 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 202 time to evaluate : 0.819 Fit side-chains REVERT: A 70 ARG cc_start: 0.7373 (OUTLIER) cc_final: 0.6924 (mmm-85) REVERT: A 235 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: A 236 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6915 (tm-30) REVERT: A 330 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: A 448 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.7438 (mm-30) REVERT: A 725 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 743 MET cc_start: 0.6966 (mmt) cc_final: 0.6705 (mtt) REVERT: B 70 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6924 (mmm-85) REVERT: B 235 GLN cc_start: 0.6276 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: B 236 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: B 448 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: B 706 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5800 (pt0) REVERT: B 725 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: B 743 MET cc_start: 0.6972 (mmt) cc_final: 0.6712 (mtt) REVERT: C 70 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6930 (mmm-85) REVERT: C 235 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: C 236 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6919 (tm-30) REVERT: C 448 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: C 706 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5798 (pt0) REVERT: C 725 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: C 743 MET cc_start: 0.6968 (mmt) cc_final: 0.6707 (mtt) REVERT: D 70 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6937 (mmm-85) REVERT: D 235 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5823 (mp10) REVERT: D 236 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: D 448 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7433 (mm-30) REVERT: D 706 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5801 (pt0) REVERT: D 725 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7059 (tm-30) REVERT: D 743 MET cc_start: 0.6962 (mmt) cc_final: 0.6702 (mtt) outliers start: 107 outliers final: 67 residues processed: 297 average time/residue: 0.7135 time to fit residues: 239.2785 Evaluate side-chains 293 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 202 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 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 283 MET Chi-restraints excluded: chain A residue 330 GLU 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 484 SER 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 707 VAL 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 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 484 SER 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 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 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 484 SER 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 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 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 484 SER 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 725 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 256 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 240 optimal weight: 0.9980 chunk 278 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 = 0.194401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.160817 restraints weight = 19590.273| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.28 r_work: 0.3223 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23040 Z= 0.213 Angle : 0.694 7.610 31276 Z= 0.372 Chirality : 0.046 0.164 3540 Planarity : 0.006 0.081 4008 Dihedral : 9.182 104.927 3464 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.92 % Favored : 94.96 % Rotamer: Outliers : 4.74 % Allowed : 20.53 % 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: 0.06 (0.16), residues: 2856 helix: 1.06 (0.13), residues: 1556 sheet: 0.25 (0.27), residues: 352 loop : -1.75 (0.19), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 762 TYR 0.018 0.002 TYR B 219 PHE 0.012 0.002 PHE C 218 TRP 0.011 0.002 TRP B 220 HIS 0.009 0.002 HIS D 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.21 (23040) covalent geometry : angle 0.69403 / 0.37 (31276) hydrogen bonds : bond 0.08507 / 5.69 ( 1048) hydrogen bonds : angle 3.83249 / 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 302 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 196 time to evaluate : 0.824 Fit side-chains REVERT: A 70 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6848 (mmm-85) REVERT: A 235 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5901 (mp10) REVERT: A 236 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: A 330 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6744 (pp20) REVERT: A 448 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: A 725 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: B 70 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6869 (mmm-85) REVERT: B 235 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5892 (mp10) REVERT: B 236 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: B 448 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: B 706 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5832 (pt0) REVERT: B 725 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: C 70 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6860 (mmm-85) REVERT: C 235 GLN cc_start: 0.6351 (OUTLIER) cc_final: 0.5897 (mp10) REVERT: C 236 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: C 448 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: C 706 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5833 (pt0) REVERT: C 725 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7151 (tm-30) REVERT: D 70 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6873 (mmm-85) REVERT: D 235 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5897 (mp10) REVERT: D 236 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: D 448 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.7514 (mm-30) REVERT: D 706 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5843 (pt0) REVERT: D 725 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7126 (tm-30) outliers start: 106 outliers final: 69 residues processed: 294 average time/residue: 0.7129 time to fit residues: 236.0667 Evaluate side-chains 292 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 199 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 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 330 GLU 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 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 707 VAL Chi-restraints excluded: chain A residue 725 GLU Chi-restraints excluded: chain B residue 7 ILE 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 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 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 725 GLU Chi-restraints excluded: chain C residue 7 ILE 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 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 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 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 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 484 SER 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 725 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 220 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 179 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 174 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 overall best weight: 1.8582 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.196561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157093 restraints weight = 19732.203| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.35 r_work: 0.3248 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23040 Z= 0.144 Angle : 0.566 7.134 31276 Z= 0.307 Chirality : 0.040 0.164 3540 Planarity : 0.004 0.053 4008 Dihedral : 9.097 107.778 3464 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.54 % Favored : 95.34 % Rotamer: Outliers : 4.47 % Allowed : 20.97 % Favored : 74.55 % 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: 0.39 (0.16), residues: 2856 helix: 1.40 (0.14), residues: 1548 sheet: 0.25 (0.27), residues: 352 loop : -1.67 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 762 TYR 0.012 0.002 TYR A 491 PHE 0.010 0.001 PHE C 499 TRP 0.013 0.002 TRP A 395 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (23040) covalent geometry : angle 0.56581 / 0.31 (31276) hydrogen bonds : bond 0.06459 / 4.34 ( 1048) hydrogen bonds : angle 3.65283 / 2.54 ( 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 296 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 196 time to evaluate : 0.804 Fit side-chains REVERT: A 70 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6908 (mmm-85) REVERT: A 235 GLN cc_start: 0.6273 (OUTLIER) cc_final: 0.5842 (mp10) REVERT: A 330 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6736 (pp20) REVERT: A 448 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.7383 (mm-30) REVERT: A 725 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: B 70 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6912 (mmm-85) REVERT: B 235 GLN cc_start: 0.6269 (OUTLIER) cc_final: 0.5837 (mp10) REVERT: B 448 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: B 706 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5805 (pt0) REVERT: B 725 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: C 70 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6903 (mmm-85) REVERT: C 235 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.5839 (mp10) REVERT: C 448 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: C 706 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5805 (pt0) REVERT: C 725 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: D 70 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6920 (mmm-85) REVERT: D 235 GLN cc_start: 0.6268 (OUTLIER) cc_final: 0.5838 (mp10) REVERT: D 448 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7387 (mm-30) REVERT: D 706 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5811 (pt0) REVERT: D 725 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7067 (tm-30) outliers start: 100 outliers final: 69 residues processed: 285 average time/residue: 0.6213 time to fit residues: 201.5456 Evaluate side-chains 285 residues out of total 2236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 196 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain A residue 235 GLN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 330 GLU 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 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 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 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 484 SER 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 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 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 484 SER 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 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 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 484 SER 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 725 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 66 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 213 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.196542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.160185 restraints weight = 19679.091| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.33 r_work: 0.3241 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23040 Z= 0.147 Angle : 0.575 7.023 31276 Z= 0.310 Chirality : 0.041 0.169 3540 Planarity : 0.004 0.051 4008 Dihedral : 9.050 107.429 3464 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 1.12 % Allowed : 3.64 % Favored : 95.24 % Rotamer: Outliers : 4.70 % Allowed : 20.75 % Favored : 74.55 % 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: 0.44 (0.16), residues: 2856 helix: 1.44 (0.14), residues: 1548 sheet: 0.27 (0.27), residues: 352 loop : -1.65 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 762 TYR 0.014 0.002 TYR C 491 PHE 0.010 0.002 PHE B 555 TRP 0.012 0.002 TRP D 395 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (23040) covalent geometry : angle 0.57489 / 0.31 (31276) hydrogen bonds : bond 0.06544 / 4.39 ( 1048) hydrogen bonds : angle 3.61743 / 2.52 ( 3072) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9366.56 seconds wall clock time: 159 minutes 41.29 seconds (9581.29 seconds total)