Starting phenix.real_space_refine on Tue Oct 27 00:45:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lqy_23491/10_2026/7lqy_23491_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lqy_23491/10_2026/7lqy_23491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lqy_23491/10_2026/7lqy_23491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lqy_23491/10_2026/7lqy_23491.map" model { file = "/net/cci-nas-00/data/ceres_data/7lqy_23491/10_2026/7lqy_23491_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lqy_23491/10_2026/7lqy_23491_neut.cif" } resolution = 3.19 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= 0.004 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: 7 Type Number sf(0) Gaussians P 32 5.49 5 S 128 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 15132 2.51 5 N 3532 2.21 5 O 4128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22954 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "B" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "C" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "D" Number of atoms: 5320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5320 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 20, 'TRANS': 638} Chain breaks: 1 Chain: "A" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 420 Unusual residues: {' CL': 1, ' NA': 1, 'POV': 8, 'YBG': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 418 Unusual residues: {'POV': 8, 'YBG': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 4.94, per 1000 atoms: 0.22 Number of scatterers: 22954 At special positions: 0 Unit cell: (122.96, 124.02, 125.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cl 1 17.00 S 128 16.00 P 32 15.00 Na 1 11.00 O 4128 8.00 N 3532 7.00 C 15132 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 994.8 milliseconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4984 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 4 sheets defined 59.1% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 115 through 125 removed outlier: 3.869A pdb=" N ILE A 119 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.520A pdb=" N ASP A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 removed outlier: 3.524A pdb=" N ASN A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.694A pdb=" N ILE A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.861A pdb=" N ASN A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.550A pdb=" N ALA A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.688A pdb=" N LEU A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 297 Processing helix chain 'A' and resid 300 through 322 removed outlier: 3.670A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 337 through 345 Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.957A pdb=" N ARG A 422 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 456 Processing helix chain 'A' and resid 470 through 499 Processing helix chain 'A' and resid 512 through 534 removed outlier: 3.758A pdb=" N MET A 516 " --> pdb=" O SER A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.513A pdb=" N SER A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 556 No H-bonds generated for 'chain 'A' and resid 554 through 556' Processing helix chain 'A' and resid 561 through 578 removed outlier: 3.613A pdb=" N TYR A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.805A pdb=" N VAL A 585 " --> pdb=" O ARG A 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 587 " --> pdb=" O MET A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 645 removed outlier: 3.659A pdb=" N THR A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 672 Processing helix chain 'A' and resid 675 through 692 removed outlier: 3.613A pdb=" N ASN A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 3.539A pdb=" N SER A 713 " --> pdb=" O ASP A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 721 removed outlier: 3.853A pdb=" N ARG A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 125 removed outlier: 3.869A pdb=" N ILE B 119 " --> pdb=" O ASP B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 158 through 166 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.520A pdb=" N ASP B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.523A pdb=" N ASN B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 removed outlier: 3.694A pdb=" N ILE B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 225 removed outlier: 3.861A pdb=" N ASN B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.550A pdb=" N ALA B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.687A pdb=" N LEU B 270 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 300 through 322 removed outlier: 3.670A pdb=" N LYS B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'B' and resid 347 through 355 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 413 through 416 Processing helix chain 'B' and resid 417 through 429 removed outlier: 3.957A pdb=" N ARG B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 456 Processing helix chain 'B' and resid 470 through 499 Processing helix chain 'B' and resid 512 through 534 removed outlier: 3.759A pdb=" N MET B 516 " --> pdb=" O SER B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.513A pdb=" N SER B 542 " --> pdb=" O GLU B 538 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 561 through 578 removed outlier: 3.612A pdb=" N TYR B 567 " --> pdb=" O GLN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.805A pdb=" N VAL B 585 " --> pdb=" O ARG B 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 645 removed outlier: 3.659A pdb=" N THR B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 672 Processing helix chain 'B' and resid 675 through 692 removed outlier: 3.614A pdb=" N ASN B 689 " --> pdb=" O GLY B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 713 removed outlier: 3.539A pdb=" N SER B 713 " --> pdb=" O ASP B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 719 removed outlier: 3.853A pdb=" N ARG B 719 " --> pdb=" O LEU B 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 125 removed outlier: 3.869A pdb=" N ILE C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 142 Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.519A pdb=" N ASP C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.524A pdb=" N ASN C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 removed outlier: 3.693A pdb=" N ILE C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 225 removed outlier: 3.860A pdb=" N ASN C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.550A pdb=" N ALA C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 271 removed outlier: 3.687A pdb=" N LEU C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 300 through 322 removed outlier: 3.670A pdb=" N LYS C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 330 Processing helix chain 'C' and resid 337 through 345 Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 413 through 416 Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.956A pdb=" N ARG C 422 " --> pdb=" O GLU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 456 Processing helix chain 'C' and resid 470 through 499 Processing helix chain 'C' and resid 512 through 534 removed outlier: 3.759A pdb=" N MET C 516 " --> pdb=" O SER C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 553 removed outlier: 3.513A pdb=" N SER C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 556 No H-bonds generated for 'chain 'C' and resid 554 through 556' Processing helix chain 'C' and resid 561 through 578 removed outlier: 3.612A pdb=" N TYR C 567 " --> pdb=" O GLN C 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 601 removed outlier: 3.805A pdb=" N VAL C 585 " --> pdb=" O ARG C 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 587 " --> pdb=" O MET C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 645 removed outlier: 3.658A pdb=" N THR C 635 " --> pdb=" O SER C 631 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR C 643 " --> pdb=" O LEU C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 672 Processing helix chain 'C' and resid 675 through 692 removed outlier: 3.614A pdb=" N ASN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 713 removed outlier: 3.540A pdb=" N SER C 713 " --> pdb=" O ASP C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.853A pdb=" N ARG C 719 " --> pdb=" O LEU C 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 125 removed outlier: 3.869A pdb=" N ILE D 119 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 142 Processing helix chain 'D' and resid 158 through 166 Processing helix chain 'D' and resid 174 through 185 removed outlier: 3.519A pdb=" N ASP D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 removed outlier: 3.524A pdb=" N ASN D 193 " --> pdb=" O LYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 removed outlier: 3.694A pdb=" N ILE D 209 " --> pdb=" O THR D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 225 removed outlier: 3.861A pdb=" N ASN D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 removed outlier: 3.551A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 271 removed outlier: 3.688A pdb=" N LEU D 270 " --> pdb=" O VAL D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 300 through 322 removed outlier: 3.671A pdb=" N LYS D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N HIS D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 Processing helix chain 'D' and resid 337 through 345 Processing helix chain 'D' and resid 347 through 355 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 413 through 416 Processing helix chain 'D' and resid 417 through 429 removed outlier: 3.956A pdb=" N ARG D 422 " --> pdb=" O GLU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 456 Processing helix chain 'D' and resid 470 through 499 Processing helix chain 'D' and resid 512 through 534 removed outlier: 3.759A pdb=" N MET D 516 " --> pdb=" O SER D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 553 removed outlier: 3.513A pdb=" N SER D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 556 No H-bonds generated for 'chain 'D' and resid 554 through 556' Processing helix chain 'D' and resid 561 through 578 removed outlier: 3.613A pdb=" N TYR D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 601 removed outlier: 3.804A pdb=" N VAL D 585 " --> pdb=" O ARG D 581 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU D 587 " --> pdb=" O MET D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 645 removed outlier: 3.658A pdb=" N THR D 635 " --> pdb=" O SER D 631 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR D 643 " --> pdb=" O LEU D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 672 Processing helix chain 'D' and resid 675 through 692 removed outlier: 3.613A pdb=" N ASN D 689 " --> pdb=" O GLY D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 693 through 713 removed outlier: 3.539A pdb=" N SER D 713 " --> pdb=" O ASP D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 719 removed outlier: 3.853A pdb=" N ARG D 719 " --> pdb=" O LEU D 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 376 removed outlier: 6.907A pdb=" N SER A 381 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 370 through 376 removed outlier: 6.907A pdb=" N SER B 381 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA B 375 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 370 through 376 removed outlier: 6.907A pdb=" N SER C 381 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA C 375 " --> pdb=" O VAL C 379 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 370 through 376 removed outlier: 6.907A pdb=" N SER D 381 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA D 375 " --> pdb=" O VAL D 379 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 3039 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: 3.59 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3452 1.31 - 1.43: 6271 1.43 - 1.56: 13349 1.56 - 1.69: 124 1.69 - 1.81: 204 Bond restraints: 23400 Sorted by residual: bond pdb=" C31 POV B 902 " pdb=" O31 POV B 902 " ideal model delta sigma weight residual 1.327 1.425 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" C31 POV D 905 " pdb=" O31 POV D 905 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C31 POV C 902 " pdb=" O31 POV C 902 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C21 POV D 902 " pdb=" O21 POV D 902 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 23395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 30040 2.77 - 5.55: 888 5.55 - 8.32: 267 8.32 - 11.09: 107 11.09 - 13.87: 54 Bond angle restraints: 31356 Sorted by residual: angle pdb=" C ARG A 430 " pdb=" N PHE A 431 " pdb=" CA PHE A 431 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 angle pdb=" C ARG B 430 " pdb=" N PHE B 431 " pdb=" CA PHE B 431 " ideal model delta sigma weight residual 121.54 133.11 -11.57 1.91e+00 2.74e-01 3.67e+01 angle pdb=" C ARG C 430 " pdb=" N PHE C 431 " pdb=" CA PHE C 431 " ideal model delta sigma weight residual 121.54 133.11 -11.57 1.91e+00 2.74e-01 3.67e+01 angle pdb=" C ARG D 430 " pdb=" N PHE D 431 " pdb=" CA PHE D 431 " ideal model delta sigma weight residual 121.54 133.07 -11.53 1.91e+00 2.74e-01 3.64e+01 angle pdb=" C PRO C 362 " pdb=" N GLU C 363 " pdb=" CA GLU C 363 " ideal model delta sigma weight residual 121.54 131.90 -10.36 1.91e+00 2.74e-01 2.94e+01 ... (remaining 31351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 13567 35.80 - 71.59: 595 71.59 - 107.39: 143 107.39 - 143.19: 79 143.19 - 178.98: 36 Dihedral angle restraints: 14420 sinusoidal: 6672 harmonic: 7748 Sorted by residual: dihedral pdb=" CA ARG A 624 " pdb=" C ARG A 624 " pdb=" N PRO A 625 " pdb=" CA PRO A 625 " ideal model delta harmonic sigma weight residual 180.00 147.28 32.72 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA ARG B 624 " pdb=" C ARG B 624 " pdb=" N PRO B 625 " pdb=" CA PRO B 625 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.27e+01 dihedral pdb=" CA ARG D 624 " pdb=" C ARG D 624 " pdb=" N PRO D 625 " pdb=" CA PRO D 625 " ideal model delta harmonic sigma weight residual 180.00 147.32 32.68 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 14417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 2679 0.058 - 0.115: 556 0.115 - 0.173: 96 0.173 - 0.230: 17 0.230 - 0.288: 12 Chirality restraints: 3360 Sorted by residual: chirality pdb=" CB VAL D 397 " pdb=" CA VAL D 397 " pdb=" CG1 VAL D 397 " pdb=" CG2 VAL D 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB VAL A 397 " pdb=" CA VAL A 397 " pdb=" CG1 VAL A 397 " pdb=" CG2 VAL A 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB VAL C 397 " pdb=" CA VAL C 397 " pdb=" CG1 VAL C 397 " pdb=" CG2 VAL C 397 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 3357 not shown) Planarity restraints: 3796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 624 " -0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO C 625 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 625 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 625 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 624 " 0.056 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 625 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 625 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 624 " 0.056 5.00e-02 4.00e+02 8.38e-02 1.12e+01 pdb=" N PRO A 625 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO A 625 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 625 " 0.046 5.00e-02 4.00e+02 ... (remaining 3793 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1943 2.73 - 3.27: 21682 3.27 - 3.81: 37209 3.81 - 4.36: 48189 4.36 - 4.90: 80810 Nonbonded interactions: 189833 Sorted by model distance: nonbonded pdb=" O PRO A 765 " pdb=" OH TYR B 201 " model vdw 2.186 3.040 nonbonded pdb=" O PRO C 765 " pdb=" OH TYR D 201 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 201 " pdb=" O PRO D 765 " model vdw 2.250 3.040 nonbonded pdb=" O PRO B 765 " pdb=" OH TYR C 201 " model vdw 2.251 3.040 nonbonded pdb=" N SER B 514 " pdb=" O6 YBG B 903 " model vdw 2.342 3.120 ... (remaining 189828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 111 through 902 or (resid 904 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 905 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or resid 907 through 908 or \ (resid 909 and (name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216 or name C217 or name C218)))) selection = (chain 'B' and (resid 111 through 902 or (resid 904 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 905 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or resid 907 through 908 or \ (resid 909 and (name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216 or name C217 or name C218)))) selection = (chain 'C' and (resid 111 through 902 or (resid 904 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 905 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or resid 907 through 908 or \ (resid 909 and (name C22 or name C23 or name C24 or name C25 or name C26 or name \ C27 or name C28 or name C29 or name C210 or name C211 or name C212 or name C213 \ or name C214 or name C215 or name C216 or name C217 or name C218)))) selection = (chain 'D' and (resid 111 through 779 or (resid 901 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218)) or (resid 902 and (name N or name C1 or name C11 or na \ me C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C36 or name C37 or name C38 or name C39 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P or name C210 \ or name C211 or name C212 or name C213 or name C214 or name C215 or name C216 or \ name C217 or name C218 or name C310 or name C311)) or resid 904 through 905 or \ resid 907 through 909)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.011 0.098 23404 Z= 0.523 Angle : 1.408 13.868 31356 Z= 0.659 Chirality : 0.053 0.288 3360 Planarity : 0.007 0.084 3796 Dihedral : 24.599 178.984 9436 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.56 % Favored : 93.28 % Rotamer: Outliers : 0.69 % Allowed : 5.32 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -5.23 (0.12), residues: 2620 helix: -4.09 (0.06), residues: 1456 sheet: -0.93 (0.60), residues: 96 loop : -2.52 (0.16), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 357 TYR 0.014 0.002 TYR D 201 PHE 0.045 0.003 PHE A 431 TRP 0.023 0.003 TRP C 699 HIS 0.008 0.002 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.01094 / 0.52 (23400) covalent geometry : angle 1.40802 / 0.66 (31356) hydrogen bonds : bond 0.28409 / 18.50 ( 1033) hydrogen bonds : angle 9.62200 / 6.70 ( 3039) Misc. bond : bond 0.00062 / 0.03 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 502 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8340 (m) cc_final: 0.7955 (t) REVERT: A 772 LYS cc_start: 0.7963 (tppp) cc_final: 0.7739 (tppt) REVERT: B 131 LEU cc_start: 0.8422 (tt) cc_final: 0.8116 (tp) REVERT: B 162 LYS cc_start: 0.8908 (tptm) cc_final: 0.8700 (tppp) REVERT: B 180 ASP cc_start: 0.8262 (m-30) cc_final: 0.8054 (m-30) REVERT: B 189 LYS cc_start: 0.8032 (mmmt) cc_final: 0.7777 (tppt) REVERT: B 506 LYS cc_start: 0.7798 (mmtm) cc_final: 0.7272 (tttm) REVERT: B 525 MET cc_start: 0.8359 (tpt) cc_final: 0.7917 (tpp) REVERT: B 772 LYS cc_start: 0.8038 (tppp) cc_final: 0.7808 (tppt) REVERT: C 133 SER cc_start: 0.8409 (m) cc_final: 0.7955 (t) REVERT: C 180 ASP cc_start: 0.7927 (m-30) cc_final: 0.7685 (m-30) REVERT: C 195 SER cc_start: 0.8130 (p) cc_final: 0.7618 (t) REVERT: C 506 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7359 (tttm) REVERT: C 525 MET cc_start: 0.8293 (tpt) cc_final: 0.7858 (tpp) REVERT: C 772 LYS cc_start: 0.8130 (tppp) cc_final: 0.7875 (tppt) REVERT: D 133 SER cc_start: 0.8367 (m) cc_final: 0.8021 (t) REVERT: D 180 ASP cc_start: 0.7813 (m-30) cc_final: 0.7530 (m-30) REVERT: D 506 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7524 (tttm) REVERT: D 619 ARG cc_start: 0.6047 (tpm-80) cc_final: 0.5818 (tpt170) REVERT: D 772 LYS cc_start: 0.8032 (tppp) cc_final: 0.7667 (tppt) outliers start: 16 outliers final: 5 residues processed: 510 average time/residue: 0.1871 time to fit residues: 141.8770 Evaluate side-chains 282 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 277 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 258] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.0270 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 258 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN A 169 ASN A 225 ASN A 230 GLN A 261 ASN A 291 HIS A 312 ASN A 366 HIS A 421 ASN A 697 ASN B 126 ASN B 129 GLN B 166 ASN B 169 ASN B 225 ASN B 230 GLN B 261 ASN B 291 HIS B 312 ASN B 366 HIS B 421 ASN B 697 ASN C 129 GLN C 166 ASN C 169 ASN C 225 ASN C 230 GLN C 261 ASN C 291 HIS C 312 ASN C 380 HIS C 421 ASN ** C 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 697 ASN C 702 GLN D 129 GLN D 166 ASN D 169 ASN D 225 ASN D 230 GLN D 261 ASN D 291 HIS D 312 ASN D 360 GLN D 380 HIS D 421 ASN D 697 ASN D 702 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.127458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.096677 restraints weight = 34628.829| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.07 r_work: 0.3058 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23404 Z= 0.139 Angle : 0.649 13.482 31356 Z= 0.325 Chirality : 0.039 0.164 3360 Planarity : 0.005 0.049 3796 Dihedral : 27.140 178.872 4378 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.70 % Allowed : 8.58 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.77 (0.14), residues: 2620 helix: -1.49 (0.11), residues: 1516 sheet: -0.43 (0.60), residues: 84 loop : -2.34 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 723 TYR 0.015 0.001 TYR A 353 PHE 0.030 0.002 PHE A 431 TRP 0.020 0.002 TRP B 699 HIS 0.003 0.001 HIS C 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (23400) covalent geometry : angle 0.64948 / 0.32 (31356) hydrogen bonds : bond 0.04065 / 2.62 ( 1033) hydrogen bonds : angle 4.37576 / 3.04 ( 3039) Misc. bond : bond 0.00045 / 0.02 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8397 (m) cc_final: 0.8190 (t) REVERT: A 177 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 772 LYS cc_start: 0.8095 (tppp) cc_final: 0.7880 (tppt) REVERT: B 162 LYS cc_start: 0.8902 (tptm) cc_final: 0.8649 (tppp) REVERT: B 189 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7667 (mptt) REVERT: B 473 ASP cc_start: 0.8397 (t0) cc_final: 0.7663 (t0) REVERT: B 723 ARG cc_start: 0.5598 (tpt170) cc_final: 0.5341 (tpt90) REVERT: B 772 LYS cc_start: 0.8138 (tppp) cc_final: 0.7901 (tppt) REVERT: C 195 SER cc_start: 0.8138 (p) cc_final: 0.7853 (t) REVERT: C 434 ARG cc_start: 0.8156 (ptt180) cc_final: 0.7800 (ptm-80) REVERT: C 506 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7373 (tttm) REVERT: C 772 LYS cc_start: 0.8346 (tppp) cc_final: 0.8049 (tppt) REVERT: D 434 ARG cc_start: 0.7987 (tmt170) cc_final: 0.7730 (ttp80) REVERT: D 506 LYS cc_start: 0.8171 (mmtm) cc_final: 0.7414 (tttm) REVERT: D 619 ARG cc_start: 0.6156 (tpm-80) cc_final: 0.5913 (tpt170) REVERT: D 772 LYS cc_start: 0.8331 (tppp) cc_final: 0.8029 (tppt) outliers start: 63 outliers final: 50 residues processed: 364 average time/residue: 0.1487 time to fit residues: 84.9904 Evaluate side-chains 289 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 768 CYS Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [87, 239, 40, 245, 250, 158, 112, 0, 252, 129, 50] chunk 87 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 250 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 562 GLN C 562 GLN ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 ASN C 702 GLN D 129 GLN D 168 HIS D 360 GLN D 562 GLN D 702 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.093190 restraints weight = 35088.036| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.14 r_work: 0.3000 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23404 Z= 0.147 Angle : 0.604 11.997 31356 Z= 0.302 Chirality : 0.039 0.170 3360 Planarity : 0.004 0.041 3796 Dihedral : 24.984 179.356 4378 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.69 % Favored : 94.16 % Rotamer: Outliers : 3.39 % Allowed : 10.21 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.16), residues: 2620 helix: -0.03 (0.13), residues: 1532 sheet: -0.78 (0.54), residues: 84 loop : -2.01 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.013 0.001 TYR A 353 PHE 0.030 0.001 PHE A 431 TRP 0.016 0.001 TRP B 699 HIS 0.002 0.001 HIS C 366 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (23400) covalent geometry : angle 0.60444 / 0.30 (31356) hydrogen bonds : bond 0.03633 / 2.35 ( 1033) hydrogen bonds : angle 3.92192 / 2.72 ( 3039) Misc. bond : bond 0.00009 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 251 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8524 (m) cc_final: 0.8263 (t) REVERT: A 177 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7932 (tt) REVERT: A 434 ARG cc_start: 0.8310 (tmt170) cc_final: 0.8098 (ttp80) REVERT: A 772 LYS cc_start: 0.8354 (tppp) cc_final: 0.8026 (tppt) REVERT: B 162 LYS cc_start: 0.9013 (tptm) cc_final: 0.8783 (tppp) REVERT: B 189 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7644 (mptt) REVERT: B 222 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8701 (mp) REVERT: B 554 MET cc_start: 0.9091 (tpp) cc_final: 0.8813 (tpp) REVERT: B 772 LYS cc_start: 0.8306 (tppp) cc_final: 0.8007 (tppt) REVERT: C 189 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7645 (mptt) REVERT: C 254 LEU cc_start: 0.8737 (tp) cc_final: 0.8527 (tp) REVERT: C 434 ARG cc_start: 0.8292 (ptt180) cc_final: 0.7901 (ptm-80) REVERT: C 772 LYS cc_start: 0.8349 (tppp) cc_final: 0.8030 (tppt) REVERT: D 218 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8717 (mp) REVERT: D 434 ARG cc_start: 0.8360 (tmt170) cc_final: 0.8076 (ttp80) REVERT: D 554 MET cc_start: 0.9012 (tpp) cc_final: 0.8801 (mtp) REVERT: D 619 ARG cc_start: 0.6046 (tpm-80) cc_final: 0.5813 (tpt170) REVERT: D 714 PHE cc_start: 0.6682 (m-80) cc_final: 0.5969 (p90) REVERT: D 718 MET cc_start: 0.6416 (mtt) cc_final: 0.5574 (mtt) REVERT: D 772 LYS cc_start: 0.8282 (tppp) cc_final: 0.7951 (tppt) outliers start: 79 outliers final: 52 residues processed: 312 average time/residue: 0.1496 time to fit residues: 73.1798 Evaluate side-chains 278 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [127, 206, 30, 39, 233, 110, 76, 259, 54, 105, 207] chunk 127 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 562 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS C 360 GLN C 412 HIS ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 412 HIS ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.088479 restraints weight = 35402.261| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.21 r_work: 0.2918 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23404 Z= 0.218 Angle : 0.626 12.247 31356 Z= 0.315 Chirality : 0.041 0.177 3360 Planarity : 0.004 0.045 3796 Dihedral : 23.594 178.204 4378 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.31 % Favored : 94.54 % Rotamer: Outliers : 3.82 % Allowed : 11.11 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.66 (0.16), residues: 2620 helix: 0.52 (0.13), residues: 1528 sheet: -1.10 (0.52), residues: 84 loop : -1.88 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 577 TYR 0.016 0.001 TYR A 353 PHE 0.031 0.002 PHE C 431 TRP 0.014 0.001 TRP A 699 HIS 0.003 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (23400) covalent geometry : angle 0.62632 / 0.31 (31356) hydrogen bonds : bond 0.03708 / 2.38 ( 1033) hydrogen bonds : angle 3.94249 / 2.73 ( 3039) Misc. bond : bond 0.00012 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 233 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8465 (m) cc_final: 0.8214 (t) REVERT: A 434 ARG cc_start: 0.8450 (tmt170) cc_final: 0.8249 (ttp80) REVERT: A 714 PHE cc_start: 0.7031 (m-80) cc_final: 0.6041 (p90) REVERT: A 772 LYS cc_start: 0.8467 (tppp) cc_final: 0.8232 (tppt) REVERT: B 189 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7515 (tppt) REVERT: B 222 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8774 (mp) REVERT: B 772 LYS cc_start: 0.8349 (tppp) cc_final: 0.7979 (tppt) REVERT: C 140 LYS cc_start: 0.8489 (mmtt) cc_final: 0.7996 (tmmt) REVERT: C 189 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7576 (mptt) REVERT: C 434 ARG cc_start: 0.8298 (ptt180) cc_final: 0.7982 (ptm-80) REVERT: C 547 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8957 (tp) REVERT: C 772 LYS cc_start: 0.8363 (tppp) cc_final: 0.8067 (tppt) REVERT: D 218 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8666 (mp) REVERT: D 547 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9001 (tp) REVERT: D 714 PHE cc_start: 0.6869 (m-80) cc_final: 0.5906 (p90) REVERT: D 772 LYS cc_start: 0.8353 (tppp) cc_final: 0.8023 (tppt) outliers start: 89 outliers final: 66 residues processed: 304 average time/residue: 0.1496 time to fit residues: 71.7466 Evaluate side-chains 286 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 216 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain C residue 723 ARG Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 779 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [94, 81, 20, 17, 203, 202, 97, 90, 128, 167, 199] chunk 94 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 202 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN B 360 GLN ** C 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.091494 restraints weight = 35280.286| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.13 r_work: 0.2957 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23404 Z= 0.149 Angle : 0.571 13.371 31356 Z= 0.287 Chirality : 0.039 0.160 3360 Planarity : 0.004 0.038 3796 Dihedral : 22.514 173.768 4378 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.27 % Rotamer: Outliers : 3.73 % Allowed : 12.35 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.17), residues: 2620 helix: 1.02 (0.13), residues: 1508 sheet: -1.14 (0.51), residues: 84 loop : -1.77 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 430 TYR 0.012 0.001 TYR A 353 PHE 0.031 0.001 PHE A 431 TRP 0.014 0.001 TRP A 699 HIS 0.003 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (23400) covalent geometry : angle 0.57082 / 0.29 (31356) hydrogen bonds : bond 0.03246 / 2.10 ( 1033) hydrogen bonds : angle 3.79854 / 2.64 ( 3039) Misc. bond : bond 0.00011 / 0.01 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 225 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.8412 (m) cc_final: 0.8199 (t) REVERT: A 434 ARG cc_start: 0.8411 (tmt170) cc_final: 0.8182 (ttp80) REVERT: A 714 PHE cc_start: 0.6873 (m-80) cc_final: 0.6155 (p90) REVERT: A 772 LYS cc_start: 0.8422 (tppp) cc_final: 0.8181 (tppt) REVERT: B 189 LYS cc_start: 0.8035 (mmmt) cc_final: 0.7573 (tppt) REVERT: B 467 LEU cc_start: 0.8599 (mp) cc_final: 0.8349 (mp) REVERT: B 772 LYS cc_start: 0.8376 (tppp) cc_final: 0.8020 (tppt) REVERT: C 189 LYS cc_start: 0.8141 (mmmt) cc_final: 0.7633 (mptt) REVERT: C 254 LEU cc_start: 0.8813 (tp) cc_final: 0.8570 (tp) REVERT: C 434 ARG cc_start: 0.8278 (ptt180) cc_final: 0.7981 (ptm-80) REVERT: C 547 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8927 (tp) REVERT: C 772 LYS cc_start: 0.8472 (tppp) cc_final: 0.8160 (tppt) REVERT: D 189 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7639 (mptt) REVERT: D 218 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8744 (mm) REVERT: D 547 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8998 (tp) REVERT: D 714 PHE cc_start: 0.6819 (m-80) cc_final: 0.6068 (p90) REVERT: D 772 LYS cc_start: 0.8479 (tppp) cc_final: 0.8142 (tppt) outliers start: 87 outliers final: 66 residues processed: 290 average time/residue: 0.1499 time to fit residues: 68.8812 Evaluate side-chains 276 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain B residue 722 PHE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 306 PHE Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Chi-restraints excluded: chain D residue 779 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [214, 125, 218, 71, 235, 146, 165, 219, 168, 130, 202] chunk 214 optimal weight: 0.0870 chunk 125 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 chunk 146 optimal weight: 0.0060 chunk 165 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 130 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 overall best weight: 0.4974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 ASN A 129 GLN C 630 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094746 restraints weight = 35028.129| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.07 r_work: 0.3020 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23404 Z= 0.102 Angle : 0.532 12.775 31356 Z= 0.268 Chirality : 0.037 0.175 3360 Planarity : 0.003 0.038 3796 Dihedral : 21.513 172.611 4378 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 2.92 % Allowed : 13.55 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.28 (0.17), residues: 2620 helix: 1.44 (0.14), residues: 1508 sheet: -0.90 (0.50), residues: 84 loop : -1.68 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 723 TYR 0.009 0.001 TYR A 353 PHE 0.030 0.001 PHE A 431 TRP 0.014 0.001 TRP C 699 HIS 0.002 0.000 HIS D 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (23400) covalent geometry : angle 0.53232 / 0.27 (31356) hydrogen bonds : bond 0.02866 / 1.87 ( 1033) hydrogen bonds : angle 3.67361 / 2.55 ( 3039) Misc. bond : bond 0.00008 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 226 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 772 LYS cc_start: 0.8416 (tppp) cc_final: 0.8060 (tppt) REVERT: B 162 LYS cc_start: 0.9171 (tptm) cc_final: 0.8945 (tppp) REVERT: B 189 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7646 (tppt) REVERT: B 772 LYS cc_start: 0.8392 (tppp) cc_final: 0.8068 (tppt) REVERT: C 140 LYS cc_start: 0.8381 (mmtt) cc_final: 0.7951 (tmmt) REVERT: C 189 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7633 (mptt) REVERT: C 434 ARG cc_start: 0.8209 (ptt180) cc_final: 0.7873 (ptm-80) REVERT: C 772 LYS cc_start: 0.8398 (tppp) cc_final: 0.8179 (tppt) REVERT: D 116 ARG cc_start: 0.8165 (tmm-80) cc_final: 0.7698 (ttm170) REVERT: D 189 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7642 (mptt) REVERT: D 218 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8809 (mp) REVERT: D 714 PHE cc_start: 0.6677 (m-80) cc_final: 0.6191 (p90) REVERT: D 718 MET cc_start: 0.6386 (mtt) cc_final: 0.6071 (mtt) REVERT: D 772 LYS cc_start: 0.8489 (tppp) cc_final: 0.8096 (tppt) outliers start: 68 outliers final: 53 residues processed: 277 average time/residue: 0.1548 time to fit residues: 66.8256 Evaluate side-chains 264 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [21, 209, 177, 236, 227, 8, 176, 45, 254, 65, 147] chunk 21 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 236 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 254 optimal weight: 4.9990 chunk 65 optimal weight: 0.0970 chunk 147 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 GLN B 412 HIS C 630 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095262 restraints weight = 35192.993| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.09 r_work: 0.3018 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23404 Z= 0.105 Angle : 0.527 13.712 31356 Z= 0.264 Chirality : 0.037 0.183 3360 Planarity : 0.003 0.037 3796 Dihedral : 20.794 171.529 4378 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.47 % Rotamer: Outliers : 2.96 % Allowed : 13.29 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.17), residues: 2620 helix: 1.68 (0.14), residues: 1508 sheet: -0.76 (0.51), residues: 84 loop : -1.57 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 719 TYR 0.009 0.001 TYR A 353 PHE 0.030 0.001 PHE A 431 TRP 0.013 0.001 TRP A 699 HIS 0.002 0.001 HIS B 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (23400) covalent geometry : angle 0.52726 / 0.26 (31356) hydrogen bonds : bond 0.02836 / 1.85 ( 1033) hydrogen bonds : angle 3.60307 / 2.50 ( 3039) Misc. bond : bond 0.00005 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 216 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.8031 (tmm-80) cc_final: 0.7594 (ttm170) REVERT: A 127 ASN cc_start: 0.6365 (p0) cc_final: 0.5997 (p0) REVERT: A 714 PHE cc_start: 0.6538 (m-80) cc_final: 0.6099 (p90) REVERT: A 772 LYS cc_start: 0.8417 (tppp) cc_final: 0.8068 (tppt) REVERT: B 189 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7684 (tppt) REVERT: B 772 LYS cc_start: 0.8553 (tppp) cc_final: 0.8206 (tppt) REVERT: C 189 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7693 (tppt) REVERT: C 434 ARG cc_start: 0.8224 (ptt180) cc_final: 0.7897 (ptm-80) REVERT: C 772 LYS cc_start: 0.8472 (tppp) cc_final: 0.8150 (tppt) REVERT: D 116 ARG cc_start: 0.8072 (tmm-80) cc_final: 0.7843 (ttm170) REVERT: D 189 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7691 (tppt) REVERT: D 547 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8872 (tp) REVERT: D 772 LYS cc_start: 0.8529 (tppp) cc_final: 0.8186 (tppt) outliers start: 69 outliers final: 60 residues processed: 268 average time/residue: 0.1411 time to fit residues: 60.1533 Evaluate side-chains 265 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 544 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [94, 254, 128, 24, 60, 93, 55, 15, 189, 61, 42] chunk 94 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 128 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 42 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 360 GLN B 412 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096212 restraints weight = 34765.756| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.07 r_work: 0.3045 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 23404 Z= 0.100 Angle : 0.525 13.356 31356 Z= 0.261 Chirality : 0.037 0.181 3360 Planarity : 0.003 0.038 3796 Dihedral : 20.219 170.297 4378 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Rotamer: Outliers : 2.87 % Allowed : 13.94 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.17), residues: 2620 helix: 1.80 (0.14), residues: 1508 sheet: -0.71 (0.50), residues: 84 loop : -1.51 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 719 TYR 0.008 0.001 TYR A 353 PHE 0.031 0.001 PHE A 431 TRP 0.012 0.001 TRP D 699 HIS 0.002 0.000 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (23400) covalent geometry : angle 0.52470 / 0.26 (31356) hydrogen bonds : bond 0.02741 / 1.78 ( 1033) hydrogen bonds : angle 3.59035 / 2.49 ( 3039) Misc. bond : bond 0.00006 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 214 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7947 (tmm-80) cc_final: 0.7593 (ttm170) REVERT: A 772 LYS cc_start: 0.8414 (tppp) cc_final: 0.8101 (tppt) REVERT: B 189 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7739 (tppt) REVERT: B 327 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8796 (mt) REVERT: B 772 LYS cc_start: 0.8559 (tppp) cc_final: 0.8212 (tppt) REVERT: C 140 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7781 (tmmt) REVERT: C 189 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7696 (mptt) REVERT: C 434 ARG cc_start: 0.8202 (ptt180) cc_final: 0.7876 (ptm-80) REVERT: C 772 LYS cc_start: 0.8478 (tppp) cc_final: 0.8172 (tppt) REVERT: D 116 ARG cc_start: 0.8041 (tmm-80) cc_final: 0.7680 (ttm170) REVERT: D 189 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7710 (mptt) REVERT: D 772 LYS cc_start: 0.8498 (tppp) cc_final: 0.8112 (tppt) outliers start: 67 outliers final: 57 residues processed: 265 average time/residue: 0.1520 time to fit residues: 63.4198 Evaluate side-chains 263 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 528 SER Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [83, 20, 166, 165, 37, 54, 41, 26, 256, 141, 25] chunk 83 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 165 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 256 optimal weight: 0.0060 chunk 141 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096260 restraints weight = 35065.392| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.08 r_work: 0.3046 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 23404 Z= 0.102 Angle : 0.530 13.325 31356 Z= 0.263 Chirality : 0.037 0.268 3360 Planarity : 0.003 0.039 3796 Dihedral : 19.719 167.641 4378 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 2.83 % Allowed : 14.19 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.17), residues: 2620 helix: 1.90 (0.14), residues: 1504 sheet: -0.67 (0.50), residues: 84 loop : -1.47 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 719 TYR 0.008 0.001 TYR A 353 PHE 0.031 0.001 PHE A 431 TRP 0.012 0.001 TRP D 699 HIS 0.002 0.000 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (23400) covalent geometry : angle 0.53011 / 0.26 (31356) hydrogen bonds : bond 0.02746 / 1.79 ( 1033) hydrogen bonds : angle 3.57455 / 2.49 ( 3039) Misc. bond : bond 0.00006 / 0.00 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7939 (tmm-80) cc_final: 0.7613 (ttm170) REVERT: A 189 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7712 (mptt) REVERT: A 772 LYS cc_start: 0.8425 (tppp) cc_final: 0.8128 (tppt) REVERT: B 189 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7739 (tppt) REVERT: B 327 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8803 (mt) REVERT: B 471 VAL cc_start: 0.8507 (m) cc_final: 0.8272 (p) REVERT: B 772 LYS cc_start: 0.8559 (tppp) cc_final: 0.8217 (tppt) REVERT: C 116 ARG cc_start: 0.8104 (tmm-80) cc_final: 0.7813 (ttm170) REVERT: C 140 LYS cc_start: 0.8449 (mmtt) cc_final: 0.7771 (tmmt) REVERT: C 189 LYS cc_start: 0.8199 (mmmt) cc_final: 0.7702 (mptt) REVERT: C 434 ARG cc_start: 0.8234 (ptt180) cc_final: 0.7843 (ptm-80) REVERT: C 772 LYS cc_start: 0.8544 (tppp) cc_final: 0.8185 (tppt) REVERT: D 116 ARG cc_start: 0.8059 (tmm-80) cc_final: 0.7724 (ttm170) REVERT: D 189 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7721 (mptt) REVERT: D 772 LYS cc_start: 0.8495 (tppp) cc_final: 0.8238 (tppt) outliers start: 66 outliers final: 59 residues processed: 258 average time/residue: 0.1498 time to fit residues: 60.4106 Evaluate side-chains 266 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 206 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 654 ASN Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [129, 133, 132, 84, 228, 216, 121, 142, 29, 168, 35] chunk 129 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 228 optimal weight: 0.9990 chunk 216 optimal weight: 0.3980 chunk 121 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS C 168 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.095834 restraints weight = 35113.524| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.10 r_work: 0.3027 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 23404 Z= 0.108 Angle : 0.541 13.268 31356 Z= 0.267 Chirality : 0.038 0.269 3360 Planarity : 0.003 0.039 3796 Dihedral : 19.332 165.186 4378 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 2.70 % Allowed : 14.24 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.17), residues: 2620 helix: 1.79 (0.14), residues: 1536 sheet: -0.69 (0.50), residues: 84 loop : -1.52 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 719 TYR 0.008 0.001 TYR A 353 PHE 0.030 0.001 PHE A 431 TRP 0.012 0.001 TRP A 699 HIS 0.002 0.001 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (23400) covalent geometry : angle 0.54150 / 0.27 (31356) hydrogen bonds : bond 0.02804 / 1.81 ( 1033) hydrogen bonds : angle 3.59376 / 2.50 ( 3039) Misc. bond : bond 0.00006 / 0.00 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 ARG cc_start: 0.7969 (tmm-80) cc_final: 0.7643 (ttm170) REVERT: A 189 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7681 (mptt) REVERT: A 390 ASP cc_start: 0.7924 (t0) cc_final: 0.7722 (t0) REVERT: A 772 LYS cc_start: 0.8434 (tppp) cc_final: 0.8129 (tppt) REVERT: B 189 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7711 (tppt) REVERT: B 772 LYS cc_start: 0.8366 (tppp) cc_final: 0.8092 (tppt) REVERT: C 116 ARG cc_start: 0.8050 (tmm-80) cc_final: 0.7749 (ttm170) REVERT: C 140 LYS cc_start: 0.8572 (mmtt) cc_final: 0.7875 (tmmt) REVERT: C 189 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7677 (mptt) REVERT: C 434 ARG cc_start: 0.8200 (ptt180) cc_final: 0.7810 (ptm-80) REVERT: C 772 LYS cc_start: 0.8541 (tppp) cc_final: 0.8179 (tppt) REVERT: D 116 ARG cc_start: 0.8041 (tmm-80) cc_final: 0.7702 (ttm170) REVERT: D 189 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7712 (mptt) REVERT: D 772 LYS cc_start: 0.8489 (tppp) cc_final: 0.8228 (tppt) outliers start: 63 outliers final: 57 residues processed: 262 average time/residue: 0.1551 time to fit residues: 63.9361 Evaluate side-chains 262 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 431 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 544 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 767 ASN Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 431 PHE Chi-restraints excluded: chain B residue 496 GLN Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 HIS Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 431 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 496 GLN Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 722 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 431 PHE Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 496 GLN Chi-restraints excluded: chain D residue 644 ILE Chi-restraints excluded: chain D residue 660 VAL Chi-restraints excluded: chain D residue 722 PHE Chi-restraints excluded: chain D residue 727 LEU Chi-restraints excluded: chain D residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: [152, 155, 156, 65, 256, 3, 102, 179, 47, 141, 56] chunk 152 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 256 optimal weight: 0.0060 chunk 3 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 ASN B 168 HIS B 412 HIS C 168 HIS C 360 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.126220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.095749 restraints weight = 35229.446| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.11 r_work: 0.3024 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23404 Z= 0.109 Angle : 0.549 13.387 31356 Z= 0.270 Chirality : 0.038 0.273 3360 Planarity : 0.003 0.051 3796 Dihedral : 19.106 163.312 4378 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 2.57 % Allowed : 14.67 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.17), residues: 2620 helix: 1.82 (0.14), residues: 1536 sheet: -0.69 (0.50), residues: 84 loop : -1.50 (0.20), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 723 TYR 0.008 0.001 TYR A 353 PHE 0.030 0.001 PHE A 431 TRP 0.011 0.001 TRP D 699 HIS 0.002 0.001 HIS D 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (23400) covalent geometry : angle 0.54874 / 0.27 (31356) hydrogen bonds : bond 0.02827 / 1.82 ( 1033) hydrogen bonds : angle 3.59733 / 2.51 ( 3039) Misc. bond : bond 0.00005 / 0.00 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5660.68 seconds wall clock time: 97 minutes 38.35 seconds (5858.35 seconds total)