Starting phenix.real_space_refine on Fri Mar 6 17:38:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rn3_4941/03_2026/6rn3_4941.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rn3_4941/03_2026/6rn3_4941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6rn3_4941/03_2026/6rn3_4941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rn3_4941/03_2026/6rn3_4941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rn3_4941/03_2026/6rn3_4941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rn3_4941/03_2026/6rn3_4941.map" } resolution = 4.0 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 31 5.49 5 S 127 5.16 5 C 20485 2.51 5 N 5933 2.21 5 O 6295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32871 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5430 Classifications: {'peptide': 689} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 664} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 659} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5406 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 659} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5340 Classifications: {'peptide': 675} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 651} Chain breaks: 5 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 24} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.78, per 1000 atoms: 0.24 Number of scatterers: 32871 At special positions: 0 Unit cell: (144.56, 182, 166.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 127 16.00 P 31 15.00 O 6295 8.00 N 5933 7.00 C 20485 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=19, symmetry=0 Number of additional bonds: simple=19, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7680 Finding SS restraints... Secondary structure from input PDB file: 188 helices and 29 sheets defined 63.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 195 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.639A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 247' Processing helix chain 'A' and resid 254 through 270 Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 295 through 305 Proline residue: A 301 - end of helix removed outlier: 3.727A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.877A pdb=" N PHE A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 358 Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.509A pdb=" N ILE A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 removed outlier: 4.222A pdb=" N ASP A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 443 through 493 Processing helix chain 'A' and resid 494 through 524 removed outlier: 3.849A pdb=" N MET A 498 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 499 " --> pdb=" O LEU A 495 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 532 through 544 removed outlier: 3.604A pdb=" N ILE A 536 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 561 Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.570A pdb=" N ALA A 589 " --> pdb=" O ARG A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.559A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.522A pdb=" N ARG A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.869A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 729 Processing helix chain 'A' and resid 733 through 749 Processing helix chain 'A' and resid 750 through 756 Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 806 Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 253 through 267 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.785A pdb=" N MET B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 285 " --> pdb=" O HIS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.713A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 4.307A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 342 through 361 Processing helix chain 'B' and resid 366 through 381 removed outlier: 3.545A pdb=" N ILE B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 406 Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 443 through 493 Processing helix chain 'B' and resid 494 through 524 removed outlier: 3.958A pdb=" N MET B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 532 through 545 removed outlier: 3.670A pdb=" N GLY B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 570 Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.532A pdb=" N GLY B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 623 removed outlier: 3.590A pdb=" N CYS B 615 " --> pdb=" O LYS B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 648 Processing helix chain 'B' and resid 653 through 659 removed outlier: 3.692A pdb=" N TYR B 656 " --> pdb=" O TYR B 653 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU B 657 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 659 " --> pdb=" O TYR B 656 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 653 through 659' Processing helix chain 'B' and resid 661 through 669 Processing helix chain 'B' and resid 687 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 removed outlier: 3.687A pdb=" N MET B 737 " --> pdb=" O ASP B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 805 Processing helix chain 'B' and resid 814 through 835 Proline residue: B 828 - end of helix Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 183 through 195 removed outlier: 3.607A pdb=" N ILE C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 removed outlier: 3.648A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.602A pdb=" N LEU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 284 removed outlier: 3.869A pdb=" N MET C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 284' Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 322 Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.564A pdb=" N HIS C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 380 removed outlier: 3.564A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.752A pdb=" N ILE C 391 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 443 through 493 Processing helix chain 'C' and resid 494 through 524 removed outlier: 4.014A pdb=" N MET C 498 " --> pdb=" O ASP C 494 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 552 through 561 Processing helix chain 'C' and resid 561 through 567 Processing helix chain 'C' and resid 573 through 590 removed outlier: 3.765A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 640 through 647 Processing helix chain 'C' and resid 661 through 669 removed outlier: 4.250A pdb=" N ARG C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 removed outlier: 3.746A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 679 through 682' Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.833A pdb=" N PHE C 687 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 4.078A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 removed outlier: 3.515A pdb=" N MET C 737 " --> pdb=" O ASP C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 790 Processing helix chain 'C' and resid 796 through 806 Processing helix chain 'C' and resid 814 through 834 Proline residue: C 828 - end of helix removed outlier: 3.552A pdb=" N LEU C 834 " --> pdb=" O ALA C 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 removed outlier: 3.505A pdb=" N GLN D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 226 Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 241 through 248 removed outlier: 3.889A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.761A pdb=" N MET D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 305 removed outlier: 3.611A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.592A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 342 through 361 Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 removed outlier: 3.620A pdb=" N ILE D 391 " --> pdb=" O PRO D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 Processing helix chain 'D' and resid 443 through 493 Processing helix chain 'D' and resid 494 through 524 removed outlier: 3.950A pdb=" N MET D 498 " --> pdb=" O ASP D 494 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Proline residue: D 507 - end of helix Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.851A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 removed outlier: 3.528A pdb=" N ARG D 561 " --> pdb=" O GLU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 573 through 590 removed outlier: 3.618A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'D' and resid 639 through 643 Processing helix chain 'D' and resid 655 through 659 removed outlier: 4.129A pdb=" N GLY D 659 " --> pdb=" O TYR D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.636A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 697 removed outlier: 4.365A pdb=" N PHE D 687 " --> pdb=" O HIS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 733 through 749 Processing helix chain 'D' and resid 750 through 757 removed outlier: 3.515A pdb=" N ARG D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 757 " --> pdb=" O PHE D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 767 through 790 Processing helix chain 'D' and resid 796 through 807 Processing helix chain 'D' and resid 814 through 825 removed outlier: 3.875A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 834 Processing helix chain 'E' and resid 159 through 163 removed outlier: 3.544A pdb=" N LYS E 162 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 183 through 195 Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 242 through 247 removed outlier: 3.708A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 Processing helix chain 'E' and resid 279 through 285 removed outlier: 4.465A pdb=" N GLY E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.667A pdb=" N LEU E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 299 through 304' Processing helix chain 'E' and resid 316 through 323 Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.779A pdb=" N LEU E 329 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 353 through 358 Processing helix chain 'E' and resid 366 through 381 Processing helix chain 'E' and resid 387 through 406 removed outlier: 3.627A pdb=" N ILE E 391 " --> pdb=" O PRO E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 430 Processing helix chain 'E' and resid 443 through 493 Processing helix chain 'E' and resid 495 through 524 removed outlier: 3.691A pdb=" N SER E 499 " --> pdb=" O LEU E 495 " (cutoff:3.500A) Proline residue: E 507 - end of helix Processing helix chain 'E' and resid 532 through 542 removed outlier: 3.615A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 561 removed outlier: 3.890A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG E 561 " --> pdb=" O GLU E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 568 Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.763A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 623 Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 653 through 657 removed outlier: 3.939A pdb=" N TYR E 656 " --> pdb=" O TYR E 653 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU E 657 " --> pdb=" O VAL E 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 653 through 657' Processing helix chain 'E' and resid 661 through 666 removed outlier: 3.532A pdb=" N ALA E 665 " --> pdb=" O TYR E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 682 removed outlier: 3.546A pdb=" N LYS E 681 " --> pdb=" O ALA E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 684 through 696 Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 734 through 749 Processing helix chain 'E' and resid 750 through 755 Processing helix chain 'E' and resid 767 through 790 Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'E' and resid 814 through 835 Proline residue: E 828 - end of helix Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 211 through 225 Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 253 through 269 Processing helix chain 'F' and resid 279 through 285 removed outlier: 3.910A pdb=" N MET F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 323 Processing helix chain 'F' and resid 342 through 354 removed outlier: 3.926A pdb=" N GLY F 352 " --> pdb=" O ALA F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 4.241A pdb=" N LEU F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS F 360 " --> pdb=" O ARG F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 360' Processing helix chain 'F' and resid 366 through 380 Processing helix chain 'F' and resid 387 through 407 Processing helix chain 'F' and resid 410 through 430 Processing helix chain 'F' and resid 443 through 493 Processing helix chain 'F' and resid 494 through 524 removed outlier: 3.794A pdb=" N MET F 498 " --> pdb=" O ASP F 494 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N SER F 499 " --> pdb=" O LEU F 495 " (cutoff:3.500A) Proline residue: F 507 - end of helix Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 554 through 569 Processing helix chain 'F' and resid 573 through 588 Processing helix chain 'F' and resid 610 through 623 Processing helix chain 'F' and resid 662 through 669 removed outlier: 3.726A pdb=" N VAL F 666 " --> pdb=" O LEU F 662 " (cutoff:3.500A) Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.664A pdb=" N LYS F 681 " --> pdb=" O ALA F 678 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 696 Processing helix chain 'F' and resid 720 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 768 through 790 Processing helix chain 'F' and resid 796 through 808 Processing helix chain 'F' and resid 814 through 834 Proline residue: F 828 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 167 removed outlier: 6.472A pdb=" N ARG A 236 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N PHE A 276 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU A 238 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 314 removed outlier: 8.303A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 365 removed outlier: 7.595A pdb=" N GLN A 364 " --> pdb=" O VAL A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 629 through 633 removed outlier: 6.167A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 674 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR A 717 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 676 " --> pdb=" O THR A 717 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER A 600 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 792 through 795 removed outlier: 6.851A pdb=" N GLU A 792 " --> pdb=" O ILE A 844 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU A 846 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N HIS A 794 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N VAL A 848 " --> pdb=" O HIS A 794 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.951A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 204 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.160A pdb=" N GLN B 364 " --> pdb=" O VAL B 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 630 through 631 removed outlier: 6.349A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL B 714 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER B 600 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL B 761 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU B 602 " --> pdb=" O VAL B 761 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB1, first strand: chain 'B' and resid 792 through 795 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.590A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.697A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.514A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ILE C 632 " --> pdb=" O ASP C 677 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLY C 599 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N MET C 716 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE C 601 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 761 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C 602 " --> pdb=" O VAL C 761 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 793 through 795 Processing sheet with id=AB6, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.167A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL D 203 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 364 through 365 removed outlier: 7.068A pdb=" N GLN D 364 " --> pdb=" O VAL D 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 602 through 603 removed outlier: 6.625A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.599A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.843A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 845 " --> pdb=" O VAL D 856 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 165 through 167 removed outlier: 5.775A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP E 278 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU E 240 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL E 311 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU E 275 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ALA E 313 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE E 277 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N THR E 315 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY E 206 " --> pdb=" O THR E 314 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 201 through 202 removed outlier: 7.583A pdb=" N ASN E 201 " --> pdb=" O GLN E 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.508A pdb=" N GLN E 364 " --> pdb=" O VAL E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 601 through 603 Processing sheet with id=AC5, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.619A pdb=" N VAL E 707 " --> pdb=" O LEU E 699 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 793 through 795 removed outlier: 7.418A pdb=" N HIS E 794 " --> pdb=" O LEU E 846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.951A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 312 through 314 Processing sheet with id=AC9, first strand: chain 'F' and resid 629 through 633 removed outlier: 3.702A pdb=" N THR F 717 " --> pdb=" O LEU F 676 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N SER F 600 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL F 761 " --> pdb=" O SER F 600 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU F 602 " --> pdb=" O VAL F 761 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 699 through 700 Processing sheet with id=AD2, first strand: chain 'F' and resid 792 through 795 removed outlier: 6.929A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG F 845 " --> pdb=" O VAL F 856 " (cutoff:3.500A) 1827 hydrogen bonds defined for protein. 5391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.85 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11712 1.36 - 1.51: 9837 1.51 - 1.66: 11539 1.66 - 1.80: 211 1.80 - 1.95: 22 Bond restraints: 33321 Sorted by residual: bond pdb=" CA SER C 600 " pdb=" CB SER C 600 " ideal model delta sigma weight residual 1.528 1.427 0.101 2.61e-02 1.47e+03 1.51e+01 bond pdb=" C ALA E 814 " pdb=" N ARG E 815 " ideal model delta sigma weight residual 1.332 1.298 0.034 1.09e-02 8.42e+03 9.48e+00 bond pdb=" CG ARG E 815 " pdb=" CD ARG E 815 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.81e+00 bond pdb=" CA SER D 600 " pdb=" CB SER D 600 " ideal model delta sigma weight residual 1.522 1.486 0.036 1.27e-02 6.20e+03 7.84e+00 bond pdb=" CA ALA B 628 " pdb=" CB ALA B 628 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.51e-02 4.39e+03 7.23e+00 ... (remaining 33316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 44478 4.20 - 8.41: 452 8.41 - 12.61: 33 12.61 - 16.82: 3 16.82 - 21.02: 4 Bond angle restraints: 44970 Sorted by residual: angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CA PRO B 409 " ideal model delta sigma weight residual 127.00 148.02 -21.02 2.40e+00 1.74e-01 7.67e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CA PRO E 409 " ideal model delta sigma weight residual 127.00 147.50 -20.50 2.40e+00 1.74e-01 7.30e+01 angle pdb=" C SER B 407 " pdb=" N PRO B 409 " pdb=" CD PRO B 409 " ideal model delta sigma weight residual 120.60 103.18 17.42 2.20e+00 2.07e-01 6.27e+01 angle pdb=" C SER E 407 " pdb=" N PRO E 409 " pdb=" CD PRO E 409 " ideal model delta sigma weight residual 120.60 103.33 17.27 2.20e+00 2.07e-01 6.16e+01 angle pdb=" N LEU E 444 " pdb=" CA LEU E 444 " pdb=" C LEU E 444 " ideal model delta sigma weight residual 113.50 106.47 7.03 1.23e+00 6.61e-01 3.26e+01 ... (remaining 44965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.42: 20149 26.42 - 52.85: 453 52.85 - 79.27: 50 79.27 - 105.70: 5 105.70 - 132.12: 2 Dihedral angle restraints: 20659 sinusoidal: 8775 harmonic: 11884 Sorted by residual: dihedral pdb=" CA GLU C 207 " pdb=" C GLU C 207 " pdb=" N PRO C 208 " pdb=" CA PRO C 208 " ideal model delta harmonic sigma weight residual 180.00 -146.01 -33.99 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA HIS E 568 " pdb=" C HIS E 568 " pdb=" N ARG E 569 " pdb=" CA ARG E 569 " ideal model delta harmonic sigma weight residual 180.00 146.55 33.45 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA LEU F 245 " pdb=" C LEU F 245 " pdb=" N VAL F 246 " pdb=" CA VAL F 246 " ideal model delta harmonic sigma weight residual -180.00 -147.73 -32.27 0 5.00e+00 4.00e-02 4.17e+01 ... (remaining 20656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3464 0.057 - 0.114: 1286 0.114 - 0.172: 294 0.172 - 0.229: 41 0.229 - 0.286: 8 Chirality restraints: 5093 Sorted by residual: chirality pdb=" CB VAL B 679 " pdb=" CA VAL B 679 " pdb=" CG1 VAL B 679 " pdb=" CG2 VAL B 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" PA AGS D1002 " pdb=" O2A AGS D1002 " pdb=" O3A AGS D1002 " pdb=" O5' AGS D1002 " both_signs ideal model delta sigma weight residual True 3.18 -2.91 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ARG D 815 " pdb=" N ARG D 815 " pdb=" C ARG D 815 " pdb=" CB ARG D 815 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5090 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1002 " 0.019 2.00e-02 2.50e+03 2.14e-02 1.26e+01 pdb=" C2 ADP A1002 " 0.009 2.00e-02 2.50e+03 pdb=" C4 ADP A1002 " -0.056 2.00e-02 2.50e+03 pdb=" C5 ADP A1002 " -0.000 2.00e-02 2.50e+03 pdb=" C6 ADP A1002 " -0.001 2.00e-02 2.50e+03 pdb=" C8 ADP A1002 " 0.003 2.00e-02 2.50e+03 pdb=" N1 ADP A1002 " -0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1002 " 0.026 2.00e-02 2.50e+03 pdb=" N6 ADP A1002 " 0.001 2.00e-02 2.50e+03 pdb=" N7 ADP A1002 " 0.020 2.00e-02 2.50e+03 pdb=" N9 ADP A1002 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO B 301 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 683 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.77e+00 pdb=" N PRO A 684 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 684 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 684 " 0.043 5.00e-02 4.00e+02 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3689 2.74 - 3.28: 31586 3.28 - 3.82: 53987 3.82 - 4.36: 63138 4.36 - 4.90: 107130 Nonbonded interactions: 259530 Sorted by model distance: nonbonded pdb=" O1B AGS B1001 " pdb=" O2G AGS B1001 " model vdw 2.198 3.040 nonbonded pdb=" O1B AGS E1002 " pdb=" O2A AGS E1002 " model vdw 2.199 3.040 nonbonded pdb=" O1B AGS C1001 " pdb=" O2G AGS C1001 " model vdw 2.220 3.040 nonbonded pdb=" O1B AGS C1002 " pdb=" O2G AGS C1002 " model vdw 2.232 3.040 nonbonded pdb=" O1B AGS B1002 " pdb=" O2G AGS B1002 " model vdw 2.235 3.040 ... (remaining 259525 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 159 through 543 or resid 553 through 858)) selection = (chain 'B' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'C' and (resid 159 through 287 or resid 293 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'D' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'E' and (resid 159 through 543 or resid 553 through 858)) selection = (chain 'F' and resid 159 through 858) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.060 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 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 : 0.010 0.109 33340 Z= 0.453 Angle : 1.151 21.024 44970 Z= 0.615 Chirality : 0.061 0.286 5093 Planarity : 0.008 0.086 5872 Dihedral : 11.261 132.121 12979 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.97 % Favored : 91.98 % Rotamer: Outliers : 0.35 % Allowed : 0.90 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.08 % 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: -3.79 (0.11), residues: 4053 helix: -2.10 (0.08), residues: 2310 sheet: -3.11 (0.23), residues: 374 loop : -2.76 (0.15), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 815 TYR 0.028 0.003 TYR F 671 PHE 0.046 0.004 PHE C 763 TRP 0.037 0.005 TRP D 543 HIS 0.018 0.003 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.01050 (33321) covalent geometry : angle 1.15069 (44970) hydrogen bonds : bond 0.14656 ( 1827) hydrogen bonds : angle 7.22084 ( 5391) Misc. bond : bond 0.00612 ( 19) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1138 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7701 (mtpp) REVERT: A 180 VAL cc_start: 0.6759 (t) cc_final: 0.6313 (m) REVERT: A 181 ILE cc_start: 0.8080 (mt) cc_final: 0.7876 (mp) REVERT: A 241 ASP cc_start: 0.7032 (t0) cc_final: 0.6748 (t0) REVERT: A 322 TYR cc_start: 0.8094 (m-80) cc_final: 0.7884 (m-80) REVERT: A 363 VAL cc_start: 0.6968 (m) cc_final: 0.6191 (m) REVERT: A 430 MET cc_start: -0.1309 (mmm) cc_final: -0.1609 (mtm) REVERT: A 616 LYS cc_start: 0.7333 (mttt) cc_final: 0.7001 (mttt) REVERT: A 740 LEU cc_start: 0.7619 (tp) cc_final: 0.7307 (pp) REVERT: A 804 SER cc_start: 0.5371 (t) cc_final: 0.5079 (p) REVERT: B 194 LEU cc_start: 0.8817 (mt) cc_final: 0.8567 (mp) REVERT: B 457 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8460 (tm-30) REVERT: B 524 MET cc_start: 0.1090 (mmm) cc_final: -0.0488 (ptt) REVERT: B 533 ASP cc_start: 0.8393 (p0) cc_final: 0.8108 (p0) REVERT: B 562 MET cc_start: 0.6919 (tmt) cc_final: 0.5970 (ttp) REVERT: B 633 ASP cc_start: 0.8186 (m-30) cc_final: 0.7353 (m-30) REVERT: B 634 MET cc_start: 0.7932 (mmm) cc_final: 0.7460 (tpp) REVERT: B 685 ASP cc_start: 0.7333 (p0) cc_final: 0.6810 (p0) REVERT: B 693 VAL cc_start: 0.8838 (t) cc_final: 0.8613 (t) REVERT: B 736 HIS cc_start: 0.8142 (m170) cc_final: 0.7702 (m90) REVERT: B 747 HIS cc_start: 0.7110 (m-70) cc_final: 0.6820 (m90) REVERT: B 802 LEU cc_start: 0.8343 (mp) cc_final: 0.8086 (pp) REVERT: C 178 ASP cc_start: 0.7721 (m-30) cc_final: 0.7419 (p0) REVERT: C 200 ASN cc_start: 0.8927 (m-40) cc_final: 0.7958 (p0) REVERT: C 217 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 259 LEU cc_start: 0.7925 (tp) cc_final: 0.6721 (tp) REVERT: C 314 THR cc_start: 0.8978 (t) cc_final: 0.8731 (p) REVERT: C 345 ASP cc_start: 0.8007 (m-30) cc_final: 0.7222 (t0) REVERT: C 410 GLU cc_start: 0.3172 (mp0) cc_final: 0.2575 (tt0) REVERT: C 656 TYR cc_start: 0.7566 (t80) cc_final: 0.7024 (t80) REVERT: C 696 ASP cc_start: 0.7786 (m-30) cc_final: 0.7473 (m-30) REVERT: C 747 HIS cc_start: 0.8027 (m-70) cc_final: 0.7811 (m-70) REVERT: C 791 TYR cc_start: 0.7319 (m-80) cc_final: 0.6325 (m-10) REVERT: D 187 ILE cc_start: 0.7700 (mt) cc_final: 0.7492 (mt) REVERT: D 293 MET cc_start: 0.3836 (tpt) cc_final: 0.3545 (tpp) REVERT: D 319 TYR cc_start: 0.8737 (t80) cc_final: 0.8159 (t80) REVERT: D 430 MET cc_start: 0.2930 (mmm) cc_final: 0.1866 (ppp) REVERT: D 562 MET cc_start: 0.8153 (tpt) cc_final: 0.7909 (tpt) REVERT: D 630 VAL cc_start: 0.8412 (t) cc_final: 0.8143 (t) REVERT: D 680 GLU cc_start: 0.8065 (pm20) cc_final: 0.7437 (pp20) REVERT: D 689 ILE cc_start: 0.8038 (mm) cc_final: 0.7291 (mm) REVERT: D 780 LYS cc_start: 0.8726 (mttt) cc_final: 0.8205 (tmmt) REVERT: D 808 TYR cc_start: 0.6799 (t80) cc_final: 0.6405 (t80) REVERT: D 827 ASN cc_start: 0.8791 (m-40) cc_final: 0.8484 (m110) REVERT: E 185 GLU cc_start: 0.8328 (tt0) cc_final: 0.7955 (tp30) REVERT: E 187 ILE cc_start: 0.7993 (mt) cc_final: 0.7789 (mt) REVERT: E 460 GLU cc_start: 0.8667 (tp30) cc_final: 0.8303 (mm-30) REVERT: E 551 MET cc_start: 0.6682 (mmp) cc_final: 0.6310 (mtm) REVERT: E 739 GLU cc_start: 0.8263 (tp30) cc_final: 0.7685 (pt0) REVERT: E 762 VAL cc_start: 0.7432 (t) cc_final: 0.7146 (p) REVERT: E 783 TYR cc_start: 0.7344 (m-10) cc_final: 0.6912 (m-10) REVERT: E 784 LYS cc_start: 0.9032 (tttt) cc_final: 0.8829 (ptpt) REVERT: F 245 LEU cc_start: 0.8758 (mt) cc_final: 0.8228 (mp) REVERT: F 582 ASN cc_start: 0.8539 (m-40) cc_final: 0.8225 (t0) REVERT: F 673 VAL cc_start: 0.7253 (t) cc_final: 0.6958 (m) REVERT: F 680 GLU cc_start: 0.6386 (pm20) cc_final: 0.6160 (pm20) REVERT: F 686 VAL cc_start: 0.7984 (t) cc_final: 0.7478 (t) REVERT: F 766 LEU cc_start: 0.7586 (pt) cc_final: 0.6738 (mp) REVERT: F 779 LEU cc_start: 0.7997 (mm) cc_final: 0.7553 (tp) REVERT: F 795 ILE cc_start: 0.7435 (tt) cc_final: 0.7152 (tt) REVERT: F 796 SER cc_start: 0.8671 (t) cc_final: 0.8328 (p) REVERT: F 817 LEU cc_start: 0.8942 (tp) cc_final: 0.8533 (tp) REVERT: F 821 ILE cc_start: 0.8586 (mt) cc_final: 0.8104 (mt) outliers start: 12 outliers final: 0 residues processed: 1149 average time/residue: 0.2369 time to fit residues: 417.0453 Evaluate side-chains 609 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 609 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.3980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 361 HIS A 726 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN A 849 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS B 281 HIS B 334 GLN B 362 HIS B 620 ASN B 641 HIS B 748 ASN B 794 HIS B 823 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN C 512 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN D 195 GLN D 281 HIS D 567 HIS D 595 ASN D 692 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN D 858 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS E 309 HIS E 427 GLN E 512 GLN E 567 HIS E 755 ASN E 806 ASN E 857 GLN F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN F 361 HIS F 512 GLN F 688 ASN F 747 HIS F 770 HIS F 831 GLN F 849 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.139807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108636 restraints weight = 68026.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109252 restraints weight = 44812.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.110048 restraints weight = 29023.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110731 restraints weight = 25637.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110790 restraints weight = 21777.358| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33340 Z= 0.167 Angle : 0.736 9.362 44970 Z= 0.377 Chirality : 0.045 0.267 5093 Planarity : 0.006 0.070 5872 Dihedral : 9.814 128.367 4741 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.74 % Allowed : 11.55 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.96 (0.12), residues: 4053 helix: -0.47 (0.10), residues: 2347 sheet: -2.74 (0.24), residues: 377 loop : -2.18 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 756 TYR 0.026 0.002 TYR F 671 PHE 0.018 0.002 PHE B 729 TRP 0.018 0.003 TRP D 462 HIS 0.021 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00358 (33321) covalent geometry : angle 0.73561 (44970) hydrogen bonds : bond 0.05168 ( 1827) hydrogen bonds : angle 5.45461 ( 5391) Misc. bond : bond 0.00604 ( 19) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 699 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 MET cc_start: 0.7692 (mmm) cc_final: 0.7427 (tpt) REVERT: A 322 TYR cc_start: 0.8111 (m-80) cc_final: 0.7902 (m-80) REVERT: A 481 GLN cc_start: 0.6566 (pt0) cc_final: 0.5954 (tt0) REVERT: A 519 LEU cc_start: 0.8142 (tp) cc_final: 0.7883 (mp) REVERT: A 623 PHE cc_start: 0.6974 (t80) cc_final: 0.6639 (t80) REVERT: B 335 LYS cc_start: 0.7388 (mtpt) cc_final: 0.7184 (tttt) REVERT: B 358 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6953 (pt0) REVERT: B 524 MET cc_start: 0.1366 (mmm) cc_final: -0.0277 (ptt) REVERT: B 533 ASP cc_start: 0.8014 (p0) cc_final: 0.7768 (p0) REVERT: B 584 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8974 (tp) REVERT: B 633 ASP cc_start: 0.7756 (m-30) cc_final: 0.6665 (m-30) REVERT: B 634 MET cc_start: 0.7713 (mmm) cc_final: 0.7342 (tpp) REVERT: B 685 ASP cc_start: 0.6999 (p0) cc_final: 0.6716 (p0) REVERT: B 758 ASP cc_start: 0.8147 (t0) cc_final: 0.7918 (t0) REVERT: C 200 ASN cc_start: 0.8340 (m-40) cc_final: 0.7937 (p0) REVERT: C 345 ASP cc_start: 0.7588 (m-30) cc_final: 0.7058 (t0) REVERT: C 524 MET cc_start: 0.5046 (tpp) cc_final: 0.4548 (tpt) REVERT: C 656 TYR cc_start: 0.7613 (t80) cc_final: 0.7304 (t80) REVERT: C 696 ASP cc_start: 0.8003 (m-30) cc_final: 0.7575 (m-30) REVERT: C 700 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7551 (p) REVERT: D 252 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6016 (ttt180) REVERT: D 317 ASP cc_start: 0.8429 (t0) cc_final: 0.8141 (t0) REVERT: D 319 TYR cc_start: 0.8398 (t80) cc_final: 0.8016 (t80) REVERT: D 430 MET cc_start: 0.3129 (mmm) cc_final: 0.2258 (ppp) REVERT: D 533 ASP cc_start: 0.7364 (p0) cc_final: 0.6887 (m-30) REVERT: D 552 MET cc_start: 0.7390 (ppp) cc_final: 0.6976 (ppp) REVERT: D 614 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9048 (tt) REVERT: D 642 SER cc_start: 0.8863 (m) cc_final: 0.8526 (t) REVERT: D 680 GLU cc_start: 0.7660 (pm20) cc_final: 0.7440 (pp20) REVERT: D 692 GLN cc_start: 0.7532 (tt0) cc_final: 0.7145 (tt0) REVERT: D 780 LYS cc_start: 0.8606 (mttt) cc_final: 0.8376 (tmmt) REVERT: D 797 ASP cc_start: 0.7772 (p0) cc_final: 0.7538 (p0) REVERT: D 827 ASN cc_start: 0.8556 (m-40) cc_final: 0.7279 (m110) REVERT: E 526 LEU cc_start: 0.6686 (mt) cc_final: 0.6358 (tt) REVERT: E 633 ASP cc_start: 0.5903 (t0) cc_final: 0.5658 (m-30) REVERT: E 683 HIS cc_start: 0.6927 (OUTLIER) cc_final: 0.6619 (m170) REVERT: E 737 MET cc_start: 0.7074 (tpp) cc_final: 0.6671 (tpp) REVERT: E 783 TYR cc_start: 0.7313 (m-10) cc_final: 0.7067 (m-10) REVERT: E 821 ILE cc_start: 0.8475 (mt) cc_final: 0.8213 (mp) REVERT: F 282 THR cc_start: 0.7732 (m) cc_final: 0.7043 (m) REVERT: F 336 VAL cc_start: 0.8728 (t) cc_final: 0.8515 (m) REVERT: F 582 ASN cc_start: 0.8464 (m-40) cc_final: 0.8086 (t0) REVERT: F 766 LEU cc_start: 0.7132 (pt) cc_final: 0.6595 (mp) REVERT: F 817 LEU cc_start: 0.9054 (tp) cc_final: 0.8581 (tp) REVERT: F 821 ILE cc_start: 0.8261 (mt) cc_final: 0.7832 (mt) REVERT: F 850 GLU cc_start: 0.5855 (pm20) cc_final: 0.5488 (tt0) outliers start: 94 outliers final: 44 residues processed: 760 average time/residue: 0.2017 time to fit residues: 248.8686 Evaluate side-chains 598 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 549 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 700 THR Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 199 LYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 264 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 323 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 354 optimal weight: 0.0050 chunk 393 optimal weight: 6.9990 chunk 243 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 281 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 154 optimal weight: 0.2980 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 512 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 ASN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN F 269 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.138175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.106039 restraints weight = 68355.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108154 restraints weight = 41203.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108973 restraints weight = 27443.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109470 restraints weight = 22935.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.109723 restraints weight = 21040.003| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33340 Z= 0.173 Angle : 0.711 15.082 44970 Z= 0.363 Chirality : 0.044 0.195 5093 Planarity : 0.005 0.062 5872 Dihedral : 9.359 160.173 4741 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.03 % Allowed : 13.82 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.29 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.18 (0.13), residues: 4053 helix: 0.27 (0.11), residues: 2338 sheet: -2.60 (0.25), residues: 392 loop : -1.99 (0.16), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 756 TYR 0.035 0.002 TYR B 783 PHE 0.022 0.002 PHE F 621 TRP 0.018 0.002 TRP D 462 HIS 0.009 0.001 HIS F 281 Details of bonding type rmsd covalent geometry : bond 0.00373 (33321) covalent geometry : angle 0.71106 (44970) hydrogen bonds : bond 0.04738 ( 1827) hydrogen bonds : angle 5.12124 ( 5391) Misc. bond : bond 0.00212 ( 19) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 575 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 GLN cc_start: 0.6672 (pt0) cc_final: 0.5951 (tt0) REVERT: A 519 LEU cc_start: 0.7993 (tp) cc_final: 0.7716 (mt) REVERT: A 562 MET cc_start: 0.8240 (mmm) cc_final: 0.7942 (mmm) REVERT: B 293 MET cc_start: 0.6756 (tpp) cc_final: 0.6460 (mtt) REVERT: B 358 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6969 (pt0) REVERT: B 524 MET cc_start: 0.1307 (mmm) cc_final: -0.0187 (ptt) REVERT: B 533 ASP cc_start: 0.8064 (p0) cc_final: 0.7767 (p0) REVERT: B 634 MET cc_start: 0.7892 (mmm) cc_final: 0.7624 (tpp) REVERT: B 685 ASP cc_start: 0.7078 (p0) cc_final: 0.6860 (p0) REVERT: B 783 TYR cc_start: 0.7793 (m-80) cc_final: 0.7428 (m-80) REVERT: C 242 MET cc_start: 0.7111 (mtm) cc_final: 0.6901 (mtt) REVERT: C 260 LYS cc_start: 0.8849 (tttt) cc_final: 0.8407 (tptt) REVERT: C 293 MET cc_start: 0.7777 (tpp) cc_final: 0.7105 (tmm) REVERT: C 345 ASP cc_start: 0.7412 (m-30) cc_final: 0.6912 (t0) REVERT: C 696 ASP cc_start: 0.8178 (m-30) cc_final: 0.7615 (m-30) REVERT: C 700 THR cc_start: 0.8001 (m) cc_final: 0.7563 (p) REVERT: D 252 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6180 (ttt180) REVERT: D 331 ARG cc_start: 0.7880 (ptm-80) cc_final: 0.7389 (ptm-80) REVERT: D 430 MET cc_start: 0.2688 (mmm) cc_final: 0.1815 (ppp) REVERT: D 533 ASP cc_start: 0.7355 (p0) cc_final: 0.6862 (m-30) REVERT: D 614 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9313 (tt) REVERT: D 636 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 642 SER cc_start: 0.8945 (m) cc_final: 0.8673 (t) REVERT: D 692 GLN cc_start: 0.7575 (tt0) cc_final: 0.7332 (tt0) REVERT: D 752 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7136 (mt-10) REVERT: D 780 LYS cc_start: 0.8649 (mttt) cc_final: 0.8441 (tmtt) REVERT: D 797 ASP cc_start: 0.7880 (p0) cc_final: 0.7595 (p0) REVERT: D 822 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7240 (tp40) REVERT: D 827 ASN cc_start: 0.8427 (m-40) cc_final: 0.8196 (m110) REVERT: E 460 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7916 (tp30) REVERT: E 633 ASP cc_start: 0.6772 (t0) cc_final: 0.6454 (m-30) REVERT: E 737 MET cc_start: 0.7219 (tpp) cc_final: 0.6930 (tpp) REVERT: E 783 TYR cc_start: 0.7487 (m-10) cc_final: 0.7214 (m-10) REVERT: F 336 VAL cc_start: 0.8740 (t) cc_final: 0.8404 (m) REVERT: F 403 MET cc_start: 0.8398 (mmp) cc_final: 0.7706 (mtm) REVERT: F 443 MET cc_start: 0.5788 (ppp) cc_final: 0.5573 (ppp) REVERT: F 695 ASP cc_start: 0.5764 (t0) cc_final: 0.4783 (m-30) REVERT: F 725 ILE cc_start: 0.6756 (mt) cc_final: 0.6555 (mt) REVERT: F 766 LEU cc_start: 0.7020 (pt) cc_final: 0.6466 (mp) REVERT: F 821 ILE cc_start: 0.8260 (mt) cc_final: 0.7953 (mt) REVERT: F 850 GLU cc_start: 0.5508 (pm20) cc_final: 0.5132 (tt0) outliers start: 104 outliers final: 62 residues processed: 630 average time/residue: 0.1909 time to fit residues: 201.8870 Evaluate side-chains 550 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 485 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 838 LEU Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 70 optimal weight: 0.0370 chunk 353 optimal weight: 6.9990 chunk 363 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 391 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 688 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 GLN C 692 GLN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS C 822 GLN D 641 HIS D 703 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN F 195 GLN F 269 GLN F 849 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.137548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.103835 restraints weight = 69002.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106208 restraints weight = 40791.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107836 restraints weight = 28415.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.108873 restraints weight = 22483.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109405 restraints weight = 19437.575| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 33340 Z= 0.166 Angle : 0.674 11.132 44970 Z= 0.341 Chirality : 0.044 0.294 5093 Planarity : 0.005 0.056 5872 Dihedral : 9.097 164.534 4741 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.58 % Allowed : 14.35 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.73 (0.13), residues: 4053 helix: 0.63 (0.11), residues: 2353 sheet: -2.34 (0.25), residues: 396 loop : -1.85 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 528 TYR 0.026 0.002 TYR C 734 PHE 0.019 0.002 PHE A 749 TRP 0.022 0.002 TRP D 462 HIS 0.012 0.001 HIS E 736 Details of bonding type rmsd covalent geometry : bond 0.00367 (33321) covalent geometry : angle 0.67384 (44970) hydrogen bonds : bond 0.04480 ( 1827) hydrogen bonds : angle 4.92809 ( 5391) Misc. bond : bond 0.00305 ( 19) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 541 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7926 (t0) REVERT: A 481 GLN cc_start: 0.6455 (pt0) cc_final: 0.5741 (tt0) REVERT: A 519 LEU cc_start: 0.8031 (tp) cc_final: 0.7827 (mt) REVERT: A 528 ARG cc_start: 0.6868 (tpp-160) cc_final: 0.6198 (tpp-160) REVERT: A 686 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8926 (m) REVERT: A 716 MET cc_start: 0.8507 (mtp) cc_final: 0.8156 (ptp) REVERT: B 201 ASN cc_start: 0.9073 (m-40) cc_final: 0.8834 (m-40) REVERT: B 358 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7091 (pt0) REVERT: B 524 MET cc_start: 0.1360 (mmm) cc_final: -0.0160 (ptt) REVERT: B 533 ASP cc_start: 0.8018 (p0) cc_final: 0.7807 (p0) REVERT: B 562 MET cc_start: 0.6571 (tmt) cc_final: 0.5469 (tmm) REVERT: B 634 MET cc_start: 0.7808 (mmm) cc_final: 0.7522 (tpp) REVERT: B 685 ASP cc_start: 0.7285 (p0) cc_final: 0.7054 (p0) REVERT: B 700 THR cc_start: 0.8359 (m) cc_final: 0.7715 (p) REVERT: C 260 LYS cc_start: 0.8847 (tttt) cc_final: 0.8557 (tptt) REVERT: C 280 LEU cc_start: 0.9137 (tp) cc_final: 0.8840 (tp) REVERT: C 293 MET cc_start: 0.7906 (tpp) cc_final: 0.7244 (tmm) REVERT: C 323 ILE cc_start: 0.9052 (mm) cc_final: 0.8728 (mm) REVERT: C 345 ASP cc_start: 0.7458 (m-30) cc_final: 0.6971 (t0) REVERT: C 405 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8419 (mt) REVERT: C 524 MET cc_start: 0.3941 (tpt) cc_final: 0.3516 (tpt) REVERT: C 696 ASP cc_start: 0.8130 (m-30) cc_final: 0.7707 (m-30) REVERT: C 700 THR cc_start: 0.8188 (m) cc_final: 0.7718 (p) REVERT: C 705 ARG cc_start: 0.7565 (ptt90) cc_final: 0.7183 (ptt-90) REVERT: D 252 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6307 (ttt180) REVERT: D 331 ARG cc_start: 0.7934 (ptm-80) cc_final: 0.7496 (ttp-170) REVERT: D 377 SER cc_start: 0.8718 (m) cc_final: 0.8453 (p) REVERT: D 430 MET cc_start: 0.2700 (mmm) cc_final: 0.1986 (ppp) REVERT: D 533 ASP cc_start: 0.7499 (p0) cc_final: 0.7122 (m-30) REVERT: D 614 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9352 (tt) REVERT: D 634 MET cc_start: 0.7524 (mmt) cc_final: 0.7294 (mpp) REVERT: D 636 GLU cc_start: 0.7389 (mt-10) cc_final: 0.6999 (mt-10) REVERT: D 797 ASP cc_start: 0.7892 (p0) cc_final: 0.7575 (p0) REVERT: D 822 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7687 (tp-100) REVERT: E 319 TYR cc_start: 0.8397 (t80) cc_final: 0.8053 (t80) REVERT: E 330 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7181 (tp30) REVERT: E 430 MET cc_start: 0.2331 (ppp) cc_final: 0.1800 (mmp) REVERT: E 460 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7748 (mm-30) REVERT: E 562 MET cc_start: 0.8199 (tpp) cc_final: 0.7960 (tpt) REVERT: E 633 ASP cc_start: 0.7066 (t0) cc_final: 0.6840 (m-30) REVERT: E 737 MET cc_start: 0.7254 (tpp) cc_final: 0.6906 (tpp) REVERT: E 739 GLU cc_start: 0.7671 (pt0) cc_final: 0.7375 (tp30) REVERT: E 783 TYR cc_start: 0.7554 (m-10) cc_final: 0.7300 (m-10) REVERT: F 403 MET cc_start: 0.8370 (mmp) cc_final: 0.7816 (mtm) REVERT: F 604 LEU cc_start: 0.7641 (mt) cc_final: 0.7345 (mt) REVERT: F 725 ILE cc_start: 0.6735 (mt) cc_final: 0.6508 (mt) REVERT: F 801 LYS cc_start: 0.8941 (pttp) cc_final: 0.8219 (tppt) REVERT: F 821 ILE cc_start: 0.8282 (mt) cc_final: 0.7992 (mt) outliers start: 123 outliers final: 75 residues processed: 623 average time/residue: 0.1952 time to fit residues: 201.3807 Evaluate side-chains 552 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 471 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 647 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 703 GLN Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 856 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 359 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 9 optimal weight: 0.1980 chunk 170 optimal weight: 20.0000 chunk 190 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 chunk 280 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 396 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 711 ASN ** B 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS D 269 GLN D 502 GLN D 692 GLN D 822 GLN ** D 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN F 195 GLN ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 831 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.139025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.107778 restraints weight = 69436.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108187 restraints weight = 51124.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108780 restraints weight = 32720.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109300 restraints weight = 27824.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110362 restraints weight = 25422.358| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33340 Z= 0.132 Angle : 0.638 9.572 44970 Z= 0.320 Chirality : 0.043 0.235 5093 Planarity : 0.004 0.058 5872 Dihedral : 8.950 170.002 4741 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.61 % Allowed : 15.63 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.42 (0.13), residues: 4053 helix: 0.87 (0.11), residues: 2359 sheet: -2.15 (0.26), residues: 388 loop : -1.74 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 586 TYR 0.047 0.001 TYR B 783 PHE 0.017 0.002 PHE E 255 TRP 0.021 0.002 TRP D 462 HIS 0.014 0.001 HIS C 747 Details of bonding type rmsd covalent geometry : bond 0.00281 (33321) covalent geometry : angle 0.63816 (44970) hydrogen bonds : bond 0.04206 ( 1827) hydrogen bonds : angle 4.80222 ( 5391) Misc. bond : bond 0.00278 ( 19) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 517 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8041 (mp0) cc_final: 0.7321 (mp0) REVERT: A 242 MET cc_start: 0.8308 (mmt) cc_final: 0.7944 (mmt) REVERT: A 481 GLN cc_start: 0.6486 (pt0) cc_final: 0.5814 (tt0) REVERT: A 528 ARG cc_start: 0.6933 (tpp-160) cc_final: 0.5839 (tpp-160) REVERT: A 562 MET cc_start: 0.8333 (mmm) cc_final: 0.7971 (mmm) REVERT: B 293 MET cc_start: 0.6206 (tpp) cc_final: 0.5762 (mtt) REVERT: B 358 GLU cc_start: 0.7430 (mt-10) cc_final: 0.6978 (pt0) REVERT: B 524 MET cc_start: 0.1463 (mmm) cc_final: -0.0009 (ptt) REVERT: B 562 MET cc_start: 0.6280 (tmt) cc_final: 0.5279 (tmm) REVERT: B 700 THR cc_start: 0.8352 (m) cc_final: 0.7757 (p) REVERT: C 181 ILE cc_start: 0.9194 (mp) cc_final: 0.8906 (mt) REVERT: C 260 LYS cc_start: 0.8959 (tttt) cc_final: 0.8645 (tptt) REVERT: C 293 MET cc_start: 0.7963 (tpp) cc_final: 0.7209 (tmm) REVERT: C 323 ILE cc_start: 0.9061 (mm) cc_final: 0.8806 (mm) REVERT: C 345 ASP cc_start: 0.7372 (m-30) cc_final: 0.6894 (t0) REVERT: C 405 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8532 (mt) REVERT: C 524 MET cc_start: 0.4265 (tpt) cc_final: 0.3524 (tpp) REVERT: C 696 ASP cc_start: 0.8019 (m-30) cc_final: 0.7623 (m-30) REVERT: C 700 THR cc_start: 0.8259 (m) cc_final: 0.7885 (p) REVERT: D 252 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6237 (ttt180) REVERT: D 377 SER cc_start: 0.8754 (m) cc_final: 0.8533 (p) REVERT: D 638 MET cc_start: 0.6949 (ptp) cc_final: 0.6727 (mtm) REVERT: D 691 LEU cc_start: 0.8703 (mt) cc_final: 0.8430 (tp) REVERT: D 797 ASP cc_start: 0.7849 (p0) cc_final: 0.7566 (p0) REVERT: D 822 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7460 (tp40) REVERT: E 298 MET cc_start: 0.6396 (pmm) cc_final: 0.6150 (ptp) REVERT: E 330 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7262 (tp30) REVERT: E 336 VAL cc_start: 0.9130 (t) cc_final: 0.8894 (t) REVERT: E 430 MET cc_start: 0.2188 (ppp) cc_final: 0.1608 (mmp) REVERT: E 562 MET cc_start: 0.8251 (tpp) cc_final: 0.8009 (tpt) REVERT: E 633 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: E 681 LYS cc_start: 0.7129 (mptt) cc_final: 0.6853 (mptt) REVERT: E 683 HIS cc_start: 0.7451 (OUTLIER) cc_final: 0.7172 (m170) REVERT: E 737 MET cc_start: 0.7372 (tpp) cc_final: 0.7078 (tpp) REVERT: E 739 GLU cc_start: 0.7605 (pt0) cc_final: 0.7400 (tp30) REVERT: F 336 VAL cc_start: 0.8902 (t) cc_final: 0.8595 (m) REVERT: F 403 MET cc_start: 0.8235 (mmp) cc_final: 0.7837 (mtm) REVERT: F 604 LEU cc_start: 0.7429 (mt) cc_final: 0.7099 (mt) REVERT: F 725 ILE cc_start: 0.6878 (mt) cc_final: 0.6557 (mt) REVERT: F 821 ILE cc_start: 0.8189 (mt) cc_final: 0.7943 (mt) outliers start: 124 outliers final: 70 residues processed: 605 average time/residue: 0.1829 time to fit residues: 187.5062 Evaluate side-chains 536 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 461 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 703 GLN Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 792 GLU Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 548 VAL Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 773 SER Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 285 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 66 optimal weight: 30.0000 chunk 148 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 121 optimal weight: 7.9990 chunk 299 optimal weight: 20.0000 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 688 ASN A 823 GLN B 192 GLN B 195 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN D 488 GLN D 703 GLN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 567 HIS F 831 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.132061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.099167 restraints weight = 70381.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.100619 restraints weight = 44602.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101404 restraints weight = 30359.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101873 restraints weight = 26447.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.101971 restraints weight = 24070.603| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 33340 Z= 0.293 Angle : 0.824 9.385 44970 Z= 0.418 Chirality : 0.049 0.237 5093 Planarity : 0.006 0.074 5872 Dihedral : 9.147 166.913 4741 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.99 % Allowed : 16.50 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.81 (0.13), residues: 4053 helix: 0.54 (0.10), residues: 2376 sheet: -2.47 (0.25), residues: 409 loop : -1.79 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 756 TYR 0.024 0.002 TYR D 656 PHE 0.021 0.003 PHE B 337 TRP 0.025 0.002 TRP A 543 HIS 0.015 0.002 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00664 (33321) covalent geometry : angle 0.82384 (44970) hydrogen bonds : bond 0.05197 ( 1827) hydrogen bonds : angle 5.16037 ( 5391) Misc. bond : bond 0.00395 ( 19) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 470 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8442 (mmt) cc_final: 0.8129 (mmt) REVERT: A 265 ASP cc_start: 0.7182 (m-30) cc_final: 0.6814 (t70) REVERT: A 392 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.8140 (t0) REVERT: A 481 GLN cc_start: 0.6747 (pt0) cc_final: 0.6142 (tt0) REVERT: A 528 ARG cc_start: 0.7102 (tpp-160) cc_final: 0.6432 (tpp-160) REVERT: A 601 PHE cc_start: 0.8655 (m-80) cc_final: 0.8373 (m-80) REVERT: B 293 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6678 (mtt) REVERT: B 358 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6992 (pt0) REVERT: B 622 MET cc_start: 0.7457 (mmm) cc_final: 0.7030 (mtt) REVERT: B 700 THR cc_start: 0.8705 (m) cc_final: 0.8263 (p) REVERT: B 708 ASP cc_start: 0.7743 (t0) cc_final: 0.7337 (p0) REVERT: C 181 ILE cc_start: 0.9155 (mp) cc_final: 0.8852 (mt) REVERT: C 260 LYS cc_start: 0.9034 (tttt) cc_final: 0.8793 (tptt) REVERT: C 293 MET cc_start: 0.8102 (tpp) cc_final: 0.7272 (tmm) REVERT: C 323 ILE cc_start: 0.9251 (mm) cc_final: 0.9027 (mm) REVERT: C 405 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8383 (mt) REVERT: C 540 LEU cc_start: 0.9178 (tp) cc_final: 0.8937 (tp) REVERT: C 700 THR cc_start: 0.8567 (m) cc_final: 0.8195 (p) REVERT: C 758 ASP cc_start: 0.8494 (t0) cc_final: 0.8006 (t0) REVERT: D 184 ASP cc_start: 0.7120 (p0) cc_final: 0.6890 (p0) REVERT: D 187 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8107 (tp) REVERT: D 217 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8131 (mm-30) REVERT: D 252 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6202 (ttp-170) REVERT: D 627 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6517 (pp20) REVERT: D 634 MET cc_start: 0.7877 (tpp) cc_final: 0.7490 (mmt) REVERT: D 674 ILE cc_start: 0.9540 (mm) cc_final: 0.9265 (mt) REVERT: D 797 ASP cc_start: 0.8077 (p0) cc_final: 0.7838 (p0) REVERT: E 184 ASP cc_start: 0.7861 (t0) cc_final: 0.7561 (t0) REVERT: E 233 LYS cc_start: 0.8026 (mmtt) cc_final: 0.7658 (mmtt) REVERT: E 298 MET cc_start: 0.6886 (pmm) cc_final: 0.6463 (ptp) REVERT: E 330 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7350 (tp30) REVERT: E 396 GLU cc_start: 0.8652 (tt0) cc_final: 0.8137 (mt-10) REVERT: E 633 ASP cc_start: 0.7618 (OUTLIER) cc_final: 0.7293 (m-30) REVERT: E 681 LYS cc_start: 0.7566 (mptt) cc_final: 0.7278 (mptt) REVERT: E 695 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7211 (t0) REVERT: E 739 GLU cc_start: 0.7752 (pt0) cc_final: 0.7461 (tp30) REVERT: F 403 MET cc_start: 0.8426 (mmp) cc_final: 0.8042 (mtm) REVERT: F 604 LEU cc_start: 0.7715 (mt) cc_final: 0.7397 (mt) REVERT: F 661 TYR cc_start: 0.6408 (m-80) cc_final: 0.6125 (m-80) REVERT: F 725 ILE cc_start: 0.7004 (mt) cc_final: 0.6762 (mt) REVERT: F 821 ILE cc_start: 0.8608 (mt) cc_final: 0.8402 (mt) outliers start: 137 outliers final: 87 residues processed: 567 average time/residue: 0.1897 time to fit residues: 180.6272 Evaluate side-chains 499 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 405 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 823 GLN Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 723 ASP Chi-restraints excluded: chain D residue 187 ILE Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain E residue 223 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 354 LYS Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 741 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 821 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 723 ASP Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 192 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 237 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 chunk 226 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN C 573 GLN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 823 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.136142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.103683 restraints weight = 70139.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.104689 restraints weight = 45393.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105404 restraints weight = 31446.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105915 restraints weight = 27094.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.106062 restraints weight = 24427.968| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33340 Z= 0.142 Angle : 0.674 10.508 44970 Z= 0.339 Chirality : 0.044 0.266 5093 Planarity : 0.004 0.058 5872 Dihedral : 8.992 172.399 4741 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.85 % Allowed : 18.71 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.13), residues: 4053 helix: 0.82 (0.11), residues: 2394 sheet: -2.26 (0.26), residues: 391 loop : -1.63 (0.17), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 586 TYR 0.022 0.001 TYR D 656 PHE 0.051 0.002 PHE C 729 TRP 0.027 0.002 TRP E 543 HIS 0.016 0.001 HIS F 567 Details of bonding type rmsd covalent geometry : bond 0.00305 (33321) covalent geometry : angle 0.67435 (44970) hydrogen bonds : bond 0.04370 ( 1827) hydrogen bonds : angle 4.83942 ( 5391) Misc. bond : bond 0.00300 ( 19) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 461 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8372 (mmt) cc_final: 0.8040 (mmt) REVERT: A 399 SER cc_start: 0.9099 (m) cc_final: 0.8883 (p) REVERT: A 481 GLN cc_start: 0.6632 (pt0) cc_final: 0.6108 (tt0) REVERT: A 519 LEU cc_start: 0.7883 (tp) cc_final: 0.7605 (mt) REVERT: A 528 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6484 (tpp-160) REVERT: A 562 MET cc_start: 0.8188 (mmt) cc_final: 0.7872 (mmt) REVERT: A 601 PHE cc_start: 0.8568 (m-80) cc_final: 0.8299 (m-80) REVERT: B 358 GLU cc_start: 0.7491 (mt-10) cc_final: 0.6741 (pt0) REVERT: B 524 MET cc_start: 0.1671 (mmt) cc_final: -0.0502 (ptt) REVERT: B 622 MET cc_start: 0.7224 (mmm) cc_final: 0.6851 (mtt) REVERT: B 700 THR cc_start: 0.8474 (m) cc_final: 0.8038 (p) REVERT: B 708 ASP cc_start: 0.7731 (t0) cc_final: 0.7401 (p0) REVERT: C 181 ILE cc_start: 0.9144 (mp) cc_final: 0.8880 (mt) REVERT: C 254 GLU cc_start: 0.8497 (tp30) cc_final: 0.8279 (tp30) REVERT: C 260 LYS cc_start: 0.8971 (tttt) cc_final: 0.8722 (tptt) REVERT: C 293 MET cc_start: 0.7885 (tpp) cc_final: 0.7050 (tmm) REVERT: C 405 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8289 (mt) REVERT: C 524 MET cc_start: 0.3927 (tpt) cc_final: 0.3555 (tpt) REVERT: C 700 THR cc_start: 0.8616 (m) cc_final: 0.8238 (p) REVERT: D 184 ASP cc_start: 0.7113 (p0) cc_final: 0.6842 (p0) REVERT: D 252 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6106 (ttt180) REVERT: D 627 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6679 (pp20) REVERT: D 634 MET cc_start: 0.7637 (tpp) cc_final: 0.7392 (mmt) REVERT: D 640 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7938 (ttpp) REVERT: D 797 ASP cc_start: 0.8069 (p0) cc_final: 0.7829 (p0) REVERT: E 184 ASP cc_start: 0.7900 (t0) cc_final: 0.7628 (t0) REVERT: E 233 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7639 (mmtt) REVERT: E 283 MET cc_start: 0.7855 (tpp) cc_final: 0.7558 (tpp) REVERT: E 298 MET cc_start: 0.6703 (pmm) cc_final: 0.6447 (ptp) REVERT: E 330 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7366 (tp30) REVERT: E 396 GLU cc_start: 0.8298 (tt0) cc_final: 0.7390 (mt-10) REVERT: E 460 GLU cc_start: 0.8306 (tp30) cc_final: 0.7878 (mm-30) REVERT: E 543 TRP cc_start: 0.8541 (t-100) cc_final: 0.7547 (m-90) REVERT: E 633 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: E 722 SER cc_start: 0.8557 (m) cc_final: 0.8344 (p) REVERT: E 739 GLU cc_start: 0.7652 (pt0) cc_final: 0.7350 (tp30) REVERT: E 752 GLU cc_start: 0.6597 (pm20) cc_final: 0.6293 (pm20) REVERT: F 192 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: F 258 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7095 (mmm-85) REVERT: F 359 LEU cc_start: 0.8322 (pp) cc_final: 0.7489 (mm) REVERT: F 403 MET cc_start: 0.8310 (mmp) cc_final: 0.8004 (mtm) REVERT: F 524 MET cc_start: 0.5663 (mmm) cc_final: 0.5324 (mmm) REVERT: F 604 LEU cc_start: 0.7573 (mt) cc_final: 0.7272 (mt) REVERT: F 661 TYR cc_start: 0.6331 (m-80) cc_final: 0.5967 (m-80) REVERT: F 801 LYS cc_start: 0.8945 (pttp) cc_final: 0.8383 (mmtt) REVERT: F 821 ILE cc_start: 0.8493 (mt) cc_final: 0.8233 (mt) outliers start: 98 outliers final: 71 residues processed: 528 average time/residue: 0.1859 time to fit residues: 165.9305 Evaluate side-chains 489 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 414 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 633 ASP Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 358 GLU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 23 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 386 optimal weight: 0.3980 chunk 353 optimal weight: 0.0040 chunk 112 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 292 optimal weight: 1.9990 chunk 159 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 overall best weight: 2.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 778 GLN B 192 GLN ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.104276 restraints weight = 70275.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104055 restraints weight = 53552.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.104861 restraints weight = 35366.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105206 restraints weight = 30101.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105426 restraints weight = 27636.070| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.6752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33340 Z= 0.158 Angle : 0.676 11.754 44970 Z= 0.338 Chirality : 0.044 0.264 5093 Planarity : 0.004 0.059 5872 Dihedral : 8.851 172.421 4741 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.03 % Allowed : 18.95 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.13), residues: 4053 helix: 0.92 (0.11), residues: 2400 sheet: -2.23 (0.26), residues: 391 loop : -1.55 (0.18), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 756 TYR 0.022 0.001 TYR D 656 PHE 0.034 0.002 PHE C 729 TRP 0.014 0.001 TRP E 543 HIS 0.013 0.001 HIS F 567 Details of bonding type rmsd covalent geometry : bond 0.00351 (33321) covalent geometry : angle 0.67579 (44970) hydrogen bonds : bond 0.04298 ( 1827) hydrogen bonds : angle 4.79188 ( 5391) Misc. bond : bond 0.00433 ( 19) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 452 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8367 (mmt) cc_final: 0.8066 (mmt) REVERT: A 265 ASP cc_start: 0.7061 (m-30) cc_final: 0.6704 (t70) REVERT: A 481 GLN cc_start: 0.6677 (pt0) cc_final: 0.6088 (tt0) REVERT: A 519 LEU cc_start: 0.7821 (tp) cc_final: 0.7600 (mt) REVERT: A 524 MET cc_start: 0.1399 (tpp) cc_final: 0.1070 (ttm) REVERT: A 528 ARG cc_start: 0.7157 (tpp-160) cc_final: 0.6503 (tpp-160) REVERT: A 601 PHE cc_start: 0.8655 (m-80) cc_final: 0.8392 (m-80) REVERT: B 240 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8659 (mt) REVERT: B 329 LEU cc_start: 0.9449 (tp) cc_final: 0.9209 (tp) REVERT: B 358 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6845 (pt0) REVERT: B 524 MET cc_start: 0.1724 (mmt) cc_final: -0.0427 (ptt) REVERT: B 562 MET cc_start: 0.6338 (tmt) cc_final: 0.4825 (tmm) REVERT: B 622 MET cc_start: 0.7376 (mmm) cc_final: 0.7045 (mtt) REVERT: B 700 THR cc_start: 0.8465 (m) cc_final: 0.8040 (p) REVERT: B 708 ASP cc_start: 0.7720 (t0) cc_final: 0.7440 (p0) REVERT: B 843 VAL cc_start: 0.7784 (t) cc_final: 0.7495 (p) REVERT: C 181 ILE cc_start: 0.9082 (mp) cc_final: 0.8778 (mt) REVERT: C 217 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7544 (mt-10) REVERT: C 254 GLU cc_start: 0.8501 (tp30) cc_final: 0.8289 (tp30) REVERT: C 260 LYS cc_start: 0.8978 (tttt) cc_final: 0.8703 (tptt) REVERT: C 405 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8377 (mt) REVERT: C 524 MET cc_start: 0.4107 (tpt) cc_final: 0.3708 (tpt) REVERT: C 540 LEU cc_start: 0.9032 (tp) cc_final: 0.8789 (tp) REVERT: C 700 THR cc_start: 0.8592 (m) cc_final: 0.8253 (p) REVERT: D 184 ASP cc_start: 0.7175 (p0) cc_final: 0.6894 (p0) REVERT: D 252 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6260 (ttp-170) REVERT: D 640 LYS cc_start: 0.8279 (ttpt) cc_final: 0.8007 (ttpp) REVERT: D 692 GLN cc_start: 0.7786 (tt0) cc_final: 0.7346 (tt0) REVERT: D 797 ASP cc_start: 0.8101 (p0) cc_final: 0.7889 (p0) REVERT: E 184 ASP cc_start: 0.7927 (t0) cc_final: 0.7624 (t0) REVERT: E 233 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7741 (mmtt) REVERT: E 298 MET cc_start: 0.6820 (pmm) cc_final: 0.6407 (ptp) REVERT: E 330 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7347 (tp30) REVERT: E 460 GLU cc_start: 0.8187 (tp30) cc_final: 0.7858 (mm-30) REVERT: E 543 TRP cc_start: 0.8581 (t-100) cc_final: 0.8341 (m-90) REVERT: E 551 MET cc_start: 0.5685 (ptp) cc_final: 0.5017 (tmm) REVERT: E 722 SER cc_start: 0.8529 (m) cc_final: 0.8252 (p) REVERT: F 192 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: F 283 MET cc_start: 0.8177 (tpp) cc_final: 0.7904 (tpp) REVERT: F 359 LEU cc_start: 0.8397 (pp) cc_final: 0.7631 (mm) REVERT: F 392 ASP cc_start: 0.7329 (t0) cc_final: 0.7078 (t0) REVERT: F 403 MET cc_start: 0.8228 (mmp) cc_final: 0.8008 (mtm) REVERT: F 443 MET cc_start: 0.6220 (ppp) cc_final: 0.5979 (ppp) REVERT: F 661 TYR cc_start: 0.6490 (m-80) cc_final: 0.6255 (m-80) REVERT: F 801 LYS cc_start: 0.8879 (pttp) cc_final: 0.8321 (mmtt) REVERT: F 821 ILE cc_start: 0.8532 (mt) cc_final: 0.8214 (mt) outliers start: 104 outliers final: 76 residues processed: 521 average time/residue: 0.1768 time to fit residues: 156.8587 Evaluate side-chains 493 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 413 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 297 ASN Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 116 optimal weight: 0.0970 chunk 208 optimal weight: 0.9990 chunk 152 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 254 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** 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 = 0.3882 r_free = 0.3882 target = 0.136183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.104409 restraints weight = 69677.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104884 restraints weight = 52615.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104982 restraints weight = 34459.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.105398 restraints weight = 32374.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105658 restraints weight = 28617.270| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33340 Z= 0.143 Angle : 0.668 10.765 44970 Z= 0.334 Chirality : 0.044 0.221 5093 Planarity : 0.004 0.059 5872 Dihedral : 8.761 172.026 4741 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.97 % Allowed : 19.09 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 4053 helix: 0.98 (0.11), residues: 2406 sheet: -2.17 (0.26), residues: 391 loop : -1.46 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 586 TYR 0.025 0.001 TYR D 656 PHE 0.036 0.002 PHE C 729 TRP 0.013 0.001 TRP E 543 HIS 0.012 0.001 HIS F 567 Details of bonding type rmsd covalent geometry : bond 0.00314 (33321) covalent geometry : angle 0.66838 (44970) hydrogen bonds : bond 0.04160 ( 1827) hydrogen bonds : angle 4.73205 ( 5391) Misc. bond : bond 0.00275 ( 19) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 436 time to evaluate : 1.296 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 186 GLU cc_start: 0.8288 (mp0) cc_final: 0.7521 (mp0) REVERT: A 392 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.8008 (t0) REVERT: A 481 GLN cc_start: 0.6641 (pt0) cc_final: 0.6081 (tt0) REVERT: A 519 LEU cc_start: 0.8031 (tp) cc_final: 0.7757 (mt) REVERT: A 524 MET cc_start: 0.1335 (tpp) cc_final: 0.1057 (ttm) REVERT: A 528 ARG cc_start: 0.7157 (tpp-160) cc_final: 0.4715 (ptm160) REVERT: A 546 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6637 (tp) REVERT: A 601 PHE cc_start: 0.8631 (m-80) cc_final: 0.8369 (m-80) REVERT: B 329 LEU cc_start: 0.9438 (tp) cc_final: 0.9149 (tp) REVERT: B 358 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6971 (pt0) REVERT: B 524 MET cc_start: 0.1749 (mmt) cc_final: -0.0288 (ptt) REVERT: B 562 MET cc_start: 0.6266 (tmt) cc_final: 0.4877 (tmm) REVERT: B 622 MET cc_start: 0.7508 (mmm) cc_final: 0.7025 (mtt) REVERT: B 700 THR cc_start: 0.8419 (m) cc_final: 0.7988 (p) REVERT: B 708 ASP cc_start: 0.7695 (t0) cc_final: 0.7397 (p0) REVERT: B 843 VAL cc_start: 0.7876 (t) cc_final: 0.7586 (p) REVERT: C 181 ILE cc_start: 0.9112 (mp) cc_final: 0.8803 (mt) REVERT: C 254 GLU cc_start: 0.8500 (tp30) cc_final: 0.8287 (tp30) REVERT: C 260 LYS cc_start: 0.8986 (tttt) cc_final: 0.8726 (tptt) REVERT: C 405 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8283 (mt) REVERT: C 524 MET cc_start: 0.4115 (tpt) cc_final: 0.3730 (tpt) REVERT: C 540 LEU cc_start: 0.9033 (tp) cc_final: 0.8801 (tp) REVERT: C 700 THR cc_start: 0.8650 (m) cc_final: 0.8273 (p) REVERT: D 184 ASP cc_start: 0.7128 (p0) cc_final: 0.6818 (p0) REVERT: D 252 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6191 (ttp-170) REVERT: D 627 GLU cc_start: 0.6758 (pp20) cc_final: 0.6198 (pp20) REVERT: D 640 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7947 (ttpp) REVERT: D 657 GLU cc_start: 0.7592 (pm20) cc_final: 0.7122 (pm20) REVERT: D 797 ASP cc_start: 0.8102 (p0) cc_final: 0.7898 (p0) REVERT: E 184 ASP cc_start: 0.7956 (t0) cc_final: 0.7603 (t0) REVERT: E 233 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7792 (mmtt) REVERT: E 298 MET cc_start: 0.6802 (pmm) cc_final: 0.6599 (ptp) REVERT: E 330 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7382 (tp30) REVERT: E 396 GLU cc_start: 0.8331 (tp30) cc_final: 0.7717 (tp30) REVERT: E 460 GLU cc_start: 0.8255 (tp30) cc_final: 0.7915 (mm-30) REVERT: E 543 TRP cc_start: 0.8697 (t-100) cc_final: 0.8339 (t-100) REVERT: E 551 MET cc_start: 0.5652 (ptp) cc_final: 0.5074 (tmm) REVERT: E 722 SER cc_start: 0.8517 (m) cc_final: 0.8207 (p) REVERT: F 192 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: F 359 LEU cc_start: 0.8330 (pp) cc_final: 0.7594 (mm) REVERT: F 392 ASP cc_start: 0.7401 (t0) cc_final: 0.7186 (t70) REVERT: F 403 MET cc_start: 0.8269 (mmp) cc_final: 0.8034 (mtm) REVERT: F 661 TYR cc_start: 0.6543 (m-80) cc_final: 0.6235 (m-80) REVERT: F 801 LYS cc_start: 0.8898 (pttp) cc_final: 0.8327 (mmtt) REVERT: F 821 ILE cc_start: 0.8476 (mt) cc_final: 0.8260 (mt) outliers start: 102 outliers final: 79 residues processed: 503 average time/residue: 0.1816 time to fit residues: 156.3841 Evaluate side-chains 494 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 410 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 568 HIS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 251 TYR Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 550 ARG Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 771 ILE Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 562 MET Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 403 optimal weight: 0.9980 chunk 343 optimal weight: 0.5980 chunk 303 optimal weight: 6.9990 chunk 314 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 257 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 ASN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** C 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN F 755 ASN F 831 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105421 restraints weight = 69573.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105236 restraints weight = 51550.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.105899 restraints weight = 39209.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.106850 restraints weight = 32077.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.106903 restraints weight = 27728.667| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.7126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33340 Z= 0.141 Angle : 0.678 12.998 44970 Z= 0.338 Chirality : 0.044 0.238 5093 Planarity : 0.004 0.059 5872 Dihedral : 8.708 172.899 4741 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.59 % Allowed : 19.62 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -0.05 (0.14), residues: 4053 helix: 1.05 (0.11), residues: 2393 sheet: -2.11 (0.26), residues: 393 loop : -1.35 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 586 TYR 0.028 0.001 TYR D 656 PHE 0.034 0.002 PHE C 729 TRP 0.013 0.001 TRP D 462 HIS 0.012 0.001 HIS F 567 Details of bonding type rmsd covalent geometry : bond 0.00310 (33321) covalent geometry : angle 0.67794 (44970) hydrogen bonds : bond 0.04100 ( 1827) hydrogen bonds : angle 4.66839 ( 5391) Misc. bond : bond 0.00268 ( 19) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8106 Ramachandran restraints generated. 4053 Oldfield, 0 Emsley, 4053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 435 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8269 (mp0) cc_final: 0.7524 (mp0) REVERT: A 481 GLN cc_start: 0.6739 (pt0) cc_final: 0.6181 (tt0) REVERT: A 519 LEU cc_start: 0.7946 (tp) cc_final: 0.7675 (mt) REVERT: A 524 MET cc_start: 0.1444 (tpp) cc_final: 0.1156 (ttm) REVERT: A 528 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6664 (tpp-160) REVERT: A 546 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6669 (tp) REVERT: A 601 PHE cc_start: 0.8624 (m-80) cc_final: 0.8388 (m-80) REVERT: B 241 ASP cc_start: 0.8102 (t70) cc_final: 0.7355 (t0) REVERT: B 329 LEU cc_start: 0.9412 (tp) cc_final: 0.9136 (tp) REVERT: B 358 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6979 (pt0) REVERT: B 524 MET cc_start: 0.1909 (mmt) cc_final: -0.0066 (ptt) REVERT: B 622 MET cc_start: 0.7334 (mmm) cc_final: 0.6816 (mtt) REVERT: B 700 THR cc_start: 0.8385 (m) cc_final: 0.8037 (p) REVERT: B 843 VAL cc_start: 0.7847 (t) cc_final: 0.7547 (p) REVERT: C 181 ILE cc_start: 0.8939 (mp) cc_final: 0.8654 (mt) REVERT: C 217 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7390 (mt-10) REVERT: C 254 GLU cc_start: 0.8492 (tp30) cc_final: 0.8287 (tp30) REVERT: C 260 LYS cc_start: 0.8971 (tttt) cc_final: 0.8715 (tptt) REVERT: C 293 MET cc_start: 0.7898 (mmm) cc_final: 0.7327 (tmm) REVERT: C 350 LEU cc_start: 0.9335 (mt) cc_final: 0.9001 (mt) REVERT: C 405 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8415 (mt) REVERT: C 540 LEU cc_start: 0.9070 (tp) cc_final: 0.8857 (tp) REVERT: C 700 THR cc_start: 0.8646 (m) cc_final: 0.8246 (p) REVERT: D 184 ASP cc_start: 0.7109 (p0) cc_final: 0.6815 (p0) REVERT: D 252 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6050 (ttp-170) REVERT: D 627 GLU cc_start: 0.6631 (pp20) cc_final: 0.6242 (pp20) REVERT: D 640 LYS cc_start: 0.8278 (ttpt) cc_final: 0.7986 (ttpp) REVERT: D 657 GLU cc_start: 0.7515 (pm20) cc_final: 0.7067 (pm20) REVERT: E 184 ASP cc_start: 0.7990 (t0) cc_final: 0.7601 (t0) REVERT: E 233 LYS cc_start: 0.8163 (mmtt) cc_final: 0.7792 (mmtt) REVERT: E 298 MET cc_start: 0.6801 (pmm) cc_final: 0.6552 (ptp) REVERT: E 330 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7381 (tp30) REVERT: E 460 GLU cc_start: 0.8231 (tp30) cc_final: 0.7944 (mm-30) REVERT: E 543 TRP cc_start: 0.8718 (t-100) cc_final: 0.8400 (t-100) REVERT: E 551 MET cc_start: 0.5654 (ptp) cc_final: 0.5451 (tmm) REVERT: E 722 SER cc_start: 0.8476 (m) cc_final: 0.8189 (p) REVERT: F 192 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: F 358 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5799 (mm-30) REVERT: F 392 ASP cc_start: 0.7373 (t0) cc_final: 0.7137 (t0) REVERT: F 629 MET cc_start: 0.8068 (ppp) cc_final: 0.7732 (ppp) REVERT: F 756 ARG cc_start: 0.6081 (ttp-170) cc_final: 0.5407 (ptp-170) REVERT: F 801 LYS cc_start: 0.8887 (pttp) cc_final: 0.8292 (mmtm) REVERT: F 821 ILE cc_start: 0.8553 (mt) cc_final: 0.8309 (mt) outliers start: 89 outliers final: 70 residues processed: 497 average time/residue: 0.1841 time to fit residues: 155.7240 Evaluate side-chains 479 residues out of total 3452 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 405 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 262 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 354 LYS Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 760 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 370 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 712 THR Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 252 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 543 TRP Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain D residue 683 HIS Chi-restraints excluded: chain D residue 708 ASP Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 822 GLN Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 388 ASP Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 683 HIS Chi-restraints excluded: chain E residue 693 VAL Chi-restraints excluded: chain E residue 712 THR Chi-restraints excluded: chain E residue 713 VAL Chi-restraints excluded: chain E residue 747 HIS Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 829 LEU Chi-restraints excluded: chain F residue 192 GLN Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 568 HIS Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 724 LEU Chi-restraints excluded: chain F residue 795 ILE Chi-restraints excluded: chain F residue 812 TYR Chi-restraints excluded: chain F residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 303 optimal weight: 6.9990 chunk 339 optimal weight: 0.0970 chunk 266 optimal weight: 7.9990 chunk 261 optimal weight: 0.0570 chunk 192 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 382 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 347 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 overall best weight: 1.0300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 362 HIS ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 770 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN ** B 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN C 719 ASN C 806 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN D 688 ASN ** D 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107110 restraints weight = 69224.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107440 restraints weight = 52153.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107309 restraints weight = 36609.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.107721 restraints weight = 33913.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108274 restraints weight = 30972.498| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33340 Z= 0.134 Angle : 0.678 12.439 44970 Z= 0.337 Chirality : 0.044 0.238 5093 Planarity : 0.004 0.060 5872 Dihedral : 8.654 173.840 4741 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.24 % Allowed : 20.37 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: 0.05 (0.14), residues: 4053 helix: 1.13 (0.11), residues: 2385 sheet: -2.08 (0.26), residues: 391 loop : -1.27 (0.18), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 586 TYR 0.029 0.001 TYR D 656 PHE 0.033 0.002 PHE C 729 TRP 0.013 0.001 TRP D 462 HIS 0.011 0.001 HIS F 567 Details of bonding type rmsd covalent geometry : bond 0.00290 (33321) covalent geometry : angle 0.67788 (44970) hydrogen bonds : bond 0.03992 ( 1827) hydrogen bonds : angle 4.61561 ( 5391) Misc. bond : bond 0.00253 ( 19) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5481.59 seconds wall clock time: 95 minutes 15.55 seconds (5715.55 seconds total)