Starting phenix.real_space_refine on Fri Mar 6 10:20:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qs7_4626/03_2026/6qs7_4626.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs7_4626/03_2026/6qs7_4626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qs7_4626/03_2026/6qs7_4626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs7_4626/03_2026/6qs7_4626.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qs7_4626/03_2026/6qs7_4626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs7_4626/03_2026/6qs7_4626.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1218 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 108 5.16 5 C 18010 2.51 5 N 5230 2.21 5 O 5487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28875 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4472 Classifications: {'peptide': 568} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 546} 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: "B" Number of atoms: 4562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 582, 4562 Classifications: {'peptide': 582} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 559} Chain breaks: 1 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: 4976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 4976 Classifications: {'peptide': 630} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 606} 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: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} 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: "E" Number of atoms: 4952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 4952 Classifications: {'peptide': 625} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 601} 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: 4496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4496 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 551} 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: "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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" 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} Time building chain proxies: 6.46, per 1000 atoms: 0.22 Number of scatterers: 28875 At special positions: 0 Unit cell: (124.95, 144.9, 157.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 32 15.00 Mg 8 11.99 O 5487 8.00 N 5230 7.00 C 18010 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=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6724 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 29 sheets defined 59.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 168 through 174 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.963A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.050A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY A 285 " --> pdb=" O HIS A 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 285' Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.650A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 316 through 323 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.736A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 Processing helix chain 'A' and resid 387 through 406 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.787A pdb=" N ARG A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 567 Processing helix chain 'A' and resid 573 through 589 removed outlier: 3.643A pdb=" N VAL A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 623 Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.738A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.535A 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: 3.832A pdb=" N ILE A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 727 Processing helix chain 'A' and resid 733 through 749 removed outlier: 3.512A pdb=" N MET A 737 " --> pdb=" O ASP A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 removed outlier: 3.655A pdb=" N ASN A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 790 Processing helix chain 'A' and resid 796 through 805 Processing helix chain 'A' and resid 813 through 827 removed outlier: 4.325A pdb=" N LEU A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 195 removed outlier: 3.798A pdb=" N ILE B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 removed outlier: 4.094A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 279 through 285 removed outlier: 3.735A pdb=" N MET B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Proline residue: B 301 - end of helix removed outlier: 4.041A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 323 removed outlier: 4.046A pdb=" N ARG B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 342 through 362 removed outlier: 5.247A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 380 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 532 through 544 removed outlier: 3.771A pdb=" N ILE B 536 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 573 through 589 removed outlier: 3.861A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 623 Processing helix chain 'B' and resid 641 through 648 Processing helix chain 'B' and resid 660 through 668 Processing helix chain 'B' and resid 683 through 687 removed outlier: 3.929A pdb=" N PHE B 687 " --> pdb=" O PRO B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'B' and resid 721 through 729 Processing helix chain 'B' and resid 733 through 749 Processing helix chain 'B' and resid 750 through 755 Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.724A pdb=" N LEU B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 834 Proline residue: B 828 - end of helix removed outlier: 3.555A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.895A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 Processing helix chain 'C' and resid 254 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.677A pdb=" N ARG C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 4.300A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 removed outlier: 3.567A pdb=" N ILE C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 removed outlier: 3.731A pdb=" N SER C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 429 Processing helix chain 'C' and resid 444 through 465 Processing helix chain 'C' and resid 532 through 544 removed outlier: 3.638A pdb=" N ILE C 536 " --> pdb=" O THR C 532 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 610 through 623 Processing helix chain 'C' and resid 635 through 637 No H-bonds generated for 'chain 'C' and resid 635 through 637' Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 655 through 659 removed outlier: 3.710A pdb=" N GLU C 658 " --> pdb=" O GLY C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 669 removed outlier: 4.234A pdb=" N ARG C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 682 removed outlier: 4.050A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.762A pdb=" N PHE C 687 " --> pdb=" O PRO C 684 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'C' and resid 721 through 729 Processing helix chain 'C' and resid 733 through 749 Processing helix chain 'C' and resid 767 through 790 removed outlier: 3.726A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 789 " --> pdb=" O ARG C 785 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY C 790 " --> pdb=" O LEU C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 807 Processing helix chain 'C' and resid 814 through 825 removed outlier: 3.793A pdb=" N LYS C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 835 Processing helix chain 'D' and resid 160 through 164 Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.736A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 270 removed outlier: 3.562A pdb=" N GLN D 269 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.292A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 323 removed outlier: 4.002A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 342 through 362 removed outlier: 3.511A pdb=" N THR D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 380 Processing helix chain 'D' and resid 387 through 407 Processing helix chain 'D' and resid 409 through 429 Processing helix chain 'D' and resid 444 through 465 Processing helix chain 'D' and resid 532 through 544 removed outlier: 3.843A pdb=" N ILE D 536 " --> pdb=" O THR D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 561 Processing helix chain 'D' and resid 561 through 566 Processing helix chain 'D' and resid 573 through 590 removed outlier: 3.758A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'D' and resid 635 through 637 No H-bonds generated for 'chain 'D' and resid 635 through 637' Processing helix chain 'D' and resid 642 through 647 Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.878A pdb=" N ARG D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 removed outlier: 3.616A pdb=" N LYS D 681 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 682 " --> pdb=" O VAL D 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 678 through 682' Processing helix chain 'D' and resid 683 through 697 removed outlier: 4.095A 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 removed outlier: 3.734A pdb=" N MET D 737 " --> pdb=" O ASP D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 756 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 834 removed outlier: 3.697A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Proline residue: D 828 - end of helix 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 225 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 241 through 249 removed outlier: 3.915A pdb=" N LEU E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA E 247 " --> pdb=" O GLY E 243 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLY E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA E 249 " --> pdb=" O LEU E 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 249' Processing helix chain 'E' and resid 253 through 270 Processing helix chain 'E' and resid 279 through 285 Processing helix chain 'E' and resid 295 through 304 Proline residue: E 301 - end of helix removed outlier: 4.013A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.532A pdb=" N ILE E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.847A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG E 331 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 358 Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.795A pdb=" N ILE E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 407 Processing helix chain 'E' and resid 409 through 429 Processing helix chain 'E' and resid 444 through 466 Processing helix chain 'E' and resid 532 through 544 removed outlier: 3.590A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 570 removed outlier: 3.665A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.566A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 624 Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 661 through 669 removed outlier: 3.801A pdb=" N ARG E 669 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 682 Processing helix chain 'E' and resid 686 through 697 Processing helix chain 'E' and resid 721 through 729 Processing helix chain 'E' and resid 733 through 749 removed outlier: 3.513A pdb=" N MET E 737 " --> pdb=" O ASP E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 788 Processing helix chain 'E' and resid 796 through 807 Processing helix chain 'E' and resid 814 through 835 removed outlier: 3.527A pdb=" N LYS E 818 " --> pdb=" O ALA E 814 " (cutoff:3.500A) 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 removed outlier: 3.949A pdb=" N VAL F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 233 Processing helix chain 'F' and resid 241 through 246 removed outlier: 3.592A pdb=" N LEU F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 Processing helix chain 'F' and resid 279 through 285 Processing helix chain 'F' and resid 295 through 304 Proline residue: F 301 - end of helix removed outlier: 3.774A pdb=" N ALA F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'F' and resid 327 through 332 Processing helix chain 'F' and resid 342 through 362 removed outlier: 4.875A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR F 357 " --> pdb=" O LEU F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 366 through 381 Processing helix chain 'F' and resid 387 through 407 Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'F' and resid 554 through 570 removed outlier: 4.699A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 589 Processing helix chain 'F' and resid 610 through 623 Processing helix chain 'F' and resid 642 through 647 Processing helix chain 'F' and resid 654 through 658 removed outlier: 4.084A pdb=" N GLU F 657 " --> pdb=" O VAL F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 669 Processing helix chain 'F' and resid 678 through 682 Processing helix chain 'F' and resid 683 through 696 removed outlier: 3.757A pdb=" N PHE F 687 " --> pdb=" O HIS F 683 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 729 Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 753 through 757 removed outlier: 3.601A pdb=" N ARG F 756 " --> pdb=" O PHE F 753 " (cutoff:3.500A) 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 835 Proline residue: F 828 - end of helix removed outlier: 3.660A pdb=" N LEU F 834 " --> pdb=" O ALA F 830 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 167 removed outlier: 4.468A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL A 311 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 275 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 8.978A pdb=" N THR A 315 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY A 206 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365 removed outlier: 8.134A pdb=" N GLN A 364 " --> pdb=" O VAL A 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 633 removed outlier: 3.641A pdb=" N PHE A 601 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 602 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 698 through 700 Processing sheet with id=AA5, first strand: chain 'A' and resid 793 through 795 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 removed outlier: 5.365A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 311 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU B 275 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR B 315 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.637A 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: 7.239A 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 633 removed outlier: 6.664A pdb=" N VAL B 630 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASP B 677 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 632 " --> pdb=" O ASP B 677 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU B 759 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 602 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 700 removed outlier: 3.544A pdb=" N LEU B 699 " --> pdb=" O VAL B 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 793 through 795 Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.516A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP C 278 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU C 240 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL C 311 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU C 275 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ALA C 313 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE C 277 " --> pdb=" O ALA C 313 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR C 314 " --> pdb=" O PRO C 202 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU C 204 " --> pdb=" O THR C 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.261A pdb=" N ILE C 674 " --> pdb=" O ILE C 715 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 759 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB5, first strand: chain 'C' and resid 844 through 848 removed outlier: 3.821A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.057A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N VAL D 311 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU D 275 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ALA D 313 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE D 277 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N THR D 315 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 364 through 365 removed outlier: 7.047A 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 630 through 633 removed outlier: 6.194A pdb=" N ILE D 674 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER D 600 " --> pdb=" O GLU D 759 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL D 761 " --> pdb=" O SER D 600 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU D 602 " --> pdb=" O VAL D 761 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 698 through 700 Processing sheet with id=AC1, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.723A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 165 through 167 removed outlier: 6.202A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ASP E 278 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU E 240 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL E 311 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU E 275 " --> pdb=" O VAL E 311 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA E 313 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 277 " --> pdb=" O ALA E 313 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N THR E 314 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN E 334 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL E 203 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 364 through 365 removed outlier: 7.244A 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 630 through 633 removed outlier: 6.432A pdb=" N SER E 600 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL E 761 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU E 602 " --> pdb=" O VAL E 761 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 698 through 700 removed outlier: 3.525A pdb=" N LEU E 699 " --> pdb=" O VAL E 707 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 846 through 848 Processing sheet with id=AC7, first strand: chain 'F' and resid 165 through 167 removed outlier: 5.822A pdb=" N ASP F 278 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N VAL F 311 " --> pdb=" O VAL F 273 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU F 275 " --> pdb=" O VAL F 311 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA F 313 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE F 277 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR F 315 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR F 314 " --> pdb=" O PRO F 202 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU F 204 " --> pdb=" O THR F 314 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.047A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 630 through 633 removed outlier: 6.465A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE F 601 " --> pdb=" O MET F 716 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER F 718 " --> pdb=" O PHE F 601 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 603 " --> pdb=" O SER F 718 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU F 602 " --> pdb=" O GLU F 759 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL F 761 " --> pdb=" O LEU F 602 " (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: 6.936A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) 1463 hydrogen bonds defined for protein. 4299 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: 5.46 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 10032 1.34 - 1.50: 7639 1.50 - 1.65: 11433 1.65 - 1.80: 160 1.80 - 1.95: 34 Bond restraints: 29298 Sorted by residual: bond pdb=" CA MET C 634 " pdb=" C MET C 634 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.72e-02 3.38e+03 2.56e+01 bond pdb=" C GLY A 253 " pdb=" N GLU A 254 " ideal model delta sigma weight residual 1.332 1.264 0.068 1.40e-02 5.10e+03 2.36e+01 bond pdb=" C ALA D 682 " pdb=" N HIS D 683 " ideal model delta sigma weight residual 1.333 1.224 0.108 2.74e-02 1.33e+03 1.56e+01 bond pdb=" C PHE C 749 " pdb=" N ARG C 750 " ideal model delta sigma weight residual 1.333 1.246 0.086 2.74e-02 1.33e+03 9.90e+00 bond pdb=" CB GLN D 692 " pdb=" CG GLN D 692 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.85e+00 ... (remaining 29293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 38556 2.81 - 5.62: 918 5.62 - 8.42: 105 8.42 - 11.23: 15 11.23 - 14.04: 4 Bond angle restraints: 39598 Sorted by residual: angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.48 9.10 1.95e+00 2.63e-01 2.18e+01 angle pdb=" C GLY F 730 " pdb=" N GLU F 731 " pdb=" CA GLU F 731 " ideal model delta sigma weight residual 122.08 128.02 -5.94 1.47e+00 4.63e-01 1.63e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 122.46 111.80 10.66 2.70e+00 1.37e-01 1.56e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 113.18 104.14 9.04 2.37e+00 1.78e-01 1.46e+01 angle pdb=" CA LEU E 646 " pdb=" CB LEU E 646 " pdb=" CG LEU E 646 " ideal model delta sigma weight residual 116.30 129.49 -13.19 3.50e+00 8.16e-02 1.42e+01 ... (remaining 39593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.96: 17560 23.96 - 47.93: 423 47.93 - 71.89: 73 71.89 - 95.85: 8 95.85 - 119.82: 2 Dihedral angle restraints: 18066 sinusoidal: 7643 harmonic: 10423 Sorted by residual: dihedral pdb=" CA MET C 293 " pdb=" C MET C 293 " pdb=" N ASP C 294 " pdb=" CA ASP C 294 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" C5' ADP F1001 " pdb=" O5' ADP F1001 " pdb=" PA ADP F1001 " pdb=" O2A ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -179.81 119.82 1 2.00e+01 2.50e-03 3.59e+01 dihedral pdb=" O1B ADP F1001 " pdb=" O3A ADP F1001 " pdb=" PB ADP F1001 " pdb=" PA ADP F1001 " ideal model delta sinusoidal sigma weight residual -60.00 -176.25 116.25 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 18063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3091 0.057 - 0.113: 1107 0.113 - 0.170: 252 0.170 - 0.226: 24 0.226 - 0.283: 5 Chirality restraints: 4479 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 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CG LEU B 694 " pdb=" CB LEU B 694 " pdb=" CD1 LEU B 694 " pdb=" CD2 LEU B 694 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB VAL D 679 " pdb=" CA VAL D 679 " pdb=" CG1 VAL D 679 " pdb=" CG2 VAL D 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4476 not shown) Planarity restraints: 5170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 300 " 0.049 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO B 301 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.013 2.00e-02 2.50e+03 2.18e-02 8.30e+00 pdb=" CG PHE C 763 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 823 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C GLN C 823 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN C 823 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN C 824 " 0.016 2.00e-02 2.50e+03 ... (remaining 5167 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 352 2.61 - 3.18: 24414 3.18 - 3.76: 44349 3.76 - 4.33: 61439 4.33 - 4.90: 101355 Nonbonded interactions: 231909 Sorted by model distance: nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.041 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.046 2.170 nonbonded pdb=" OG1 THR C 612 " pdb="MG MG C1004 " model vdw 2.062 2.170 nonbonded pdb=" OG1 THR D 612 " pdb="MG MG D1004 " model vdw 2.067 2.170 nonbonded pdb=" O1B AGS D1001 " pdb="MG MG D1003 " model vdw 2.067 2.170 ... (remaining 231904 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 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 408 or resid 527 thro \ ugh 543 or resid 553 through 858)) selection = (chain 'D' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'E' and (resid 159 through 408 or resid 527 through 543 or resid 553 thro \ ugh 858)) selection = (chain 'F' and (resid 159 through 287 or resid 293 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.754 29307 Z= 0.620 Angle : 1.053 14.039 39598 Z= 0.564 Chirality : 0.059 0.283 4479 Planarity : 0.008 0.074 5170 Dihedral : 11.169 119.815 11342 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.20 % Allowed : 0.76 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.83 (0.11), residues: 3563 helix: -2.30 (0.09), residues: 1903 sheet: -2.75 (0.25), residues: 339 loop : -2.58 (0.15), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 332 TYR 0.037 0.003 TYR D 653 PHE 0.043 0.004 PHE C 763 TRP 0.037 0.005 TRP B 543 HIS 0.013 0.002 HIS F 747 Details of bonding type rmsd covalent geometry : bond 0.01052 (29298) covalent geometry : angle 1.05254 (39598) hydrogen bonds : bond 0.16776 ( 1463) hydrogen bonds : angle 7.71386 ( 4299) Misc. bond : bond 0.25136 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 930 time to evaluate : 1.068 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 251 TYR cc_start: 0.8656 (m-10) cc_final: 0.7590 (m-10) REVERT: A 326 ASP cc_start: 0.8334 (t70) cc_final: 0.8079 (t0) REVERT: A 564 GLN cc_start: 0.8854 (tt0) cc_final: 0.8317 (tp-100) REVERT: A 642 SER cc_start: 0.7711 (m) cc_final: 0.7277 (p) REVERT: A 671 TYR cc_start: 0.8824 (m-80) cc_final: 0.8620 (m-80) REVERT: A 738 LYS cc_start: 0.7540 (ttmt) cc_final: 0.7288 (pttm) REVERT: A 794 HIS cc_start: 0.7673 (m170) cc_final: 0.7074 (t70) REVERT: A 842 LYS cc_start: 0.4084 (mttt) cc_final: 0.3826 (mmtm) REVERT: B 354 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8171 (tttm) REVERT: B 533 ASP cc_start: 0.7983 (p0) cc_final: 0.7663 (p0) REVERT: B 562 MET cc_start: 0.8927 (tpt) cc_final: 0.8701 (tpt) REVERT: B 634 MET cc_start: 0.9387 (mmm) cc_final: 0.9181 (mmm) REVERT: B 677 ASP cc_start: 0.8035 (t0) cc_final: 0.7530 (t0) REVERT: B 700 THR cc_start: 0.8368 (m) cc_final: 0.7854 (p) REVERT: B 729 PHE cc_start: 0.7758 (t80) cc_final: 0.7128 (t80) REVERT: B 779 LEU cc_start: 0.9279 (mt) cc_final: 0.8961 (mp) REVERT: B 802 LEU cc_start: 0.8709 (mp) cc_final: 0.8219 (pp) REVERT: B 818 LYS cc_start: 0.9031 (mtpt) cc_final: 0.8818 (ttpp) REVERT: B 826 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8421 (mp0) REVERT: C 236 ARG cc_start: 0.8344 (mmt180) cc_final: 0.7967 (mmp80) REVERT: C 241 ASP cc_start: 0.7731 (t0) cc_final: 0.7312 (t0) REVERT: C 246 VAL cc_start: 0.9248 (t) cc_final: 0.8986 (p) REVERT: C 257 GLU cc_start: 0.8393 (tt0) cc_final: 0.8040 (tt0) REVERT: C 334 GLN cc_start: 0.8499 (mm110) cc_final: 0.7885 (mm-40) REVERT: C 388 ASP cc_start: 0.8750 (t70) cc_final: 0.8483 (t0) REVERT: C 423 LYS cc_start: 0.8683 (tptm) cc_final: 0.8383 (ttpt) REVERT: C 532 THR cc_start: 0.8264 (p) cc_final: 0.7997 (m) REVERT: C 692 GLN cc_start: 0.8103 (mt0) cc_final: 0.7650 (mt0) REVERT: C 705 ARG cc_start: 0.7652 (ptt-90) cc_final: 0.7202 (ptp90) REVERT: C 780 LYS cc_start: 0.9083 (mttt) cc_final: 0.8707 (tptt) REVERT: C 786 LEU cc_start: 0.9154 (mt) cc_final: 0.8923 (tp) REVERT: C 801 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8562 (ttpp) REVERT: C 826 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7515 (mt-10) REVERT: D 161 LEU cc_start: 0.8922 (mt) cc_final: 0.8555 (mt) REVERT: D 163 LYS cc_start: 0.8995 (mmtm) cc_final: 0.8557 (mptt) REVERT: D 265 ASP cc_start: 0.8066 (m-30) cc_final: 0.7721 (t0) REVERT: D 330 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7996 (tm-30) REVERT: D 345 ASP cc_start: 0.8374 (m-30) cc_final: 0.7777 (m-30) REVERT: D 552 MET cc_start: 0.7720 (ptm) cc_final: 0.6986 (ppp) REVERT: D 644 SER cc_start: 0.8837 (m) cc_final: 0.8534 (p) REVERT: D 696 ASP cc_start: 0.8757 (m-30) cc_final: 0.8544 (m-30) REVERT: D 780 LYS cc_start: 0.8736 (mttt) cc_final: 0.8221 (mtmm) REVERT: D 827 ASN cc_start: 0.8692 (m-40) cc_final: 0.8064 (m110) REVERT: E 162 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8322 (pttm) REVERT: E 191 ILE cc_start: 0.8699 (mt) cc_final: 0.8398 (mm) REVERT: E 205 ILE cc_start: 0.8775 (mt) cc_final: 0.8396 (pt) REVERT: E 257 GLU cc_start: 0.8923 (tt0) cc_final: 0.8510 (mm-30) REVERT: E 359 LEU cc_start: 0.8970 (mp) cc_final: 0.8690 (mp) REVERT: E 426 GLN cc_start: 0.8706 (tt0) cc_final: 0.8353 (mt0) REVERT: E 458 LEU cc_start: 0.7723 (mt) cc_final: 0.7452 (mt) REVERT: E 568 HIS cc_start: 0.7151 (m170) cc_final: 0.6924 (m-70) REVERT: E 633 ASP cc_start: 0.8844 (m-30) cc_final: 0.8528 (m-30) REVERT: E 634 MET cc_start: 0.9076 (mmm) cc_final: 0.8801 (tpp) REVERT: E 707 VAL cc_start: 0.9405 (t) cc_final: 0.9142 (m) REVERT: E 726 GLN cc_start: 0.7752 (mt0) cc_final: 0.7282 (pt0) REVERT: F 178 ASP cc_start: 0.8100 (m-30) cc_final: 0.7650 (p0) REVERT: F 217 GLU cc_start: 0.7958 (mt-10) cc_final: 0.6709 (mt-10) REVERT: F 330 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7274 (pt0) REVERT: F 335 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8333 (ttmm) REVERT: F 376 LEU cc_start: 0.7946 (mt) cc_final: 0.7688 (pp) REVERT: F 393 LEU cc_start: 0.7670 (mt) cc_final: 0.7196 (mp) REVERT: F 538 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7389 (tp30) REVERT: F 563 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6314 (pt0) REVERT: F 582 ASN cc_start: 0.8946 (m-40) cc_final: 0.8659 (m-40) REVERT: F 595 ASN cc_start: 0.8543 (m-40) cc_final: 0.7792 (t0) REVERT: F 626 ASP cc_start: 0.7472 (m-30) cc_final: 0.6969 (p0) REVERT: F 629 MET cc_start: 0.8167 (ptm) cc_final: 0.7787 (ptp) REVERT: F 630 VAL cc_start: 0.8421 (t) cc_final: 0.7928 (t) REVERT: F 631 ARG cc_start: 0.7982 (ttt180) cc_final: 0.7528 (ttt180) REVERT: F 638 MET cc_start: 0.7561 (mtm) cc_final: 0.7344 (mmm) REVERT: F 691 LEU cc_start: 0.9074 (mt) cc_final: 0.8840 (pp) REVERT: F 736 HIS cc_start: 0.8428 (m170) cc_final: 0.8039 (m-70) REVERT: F 821 ILE cc_start: 0.8900 (mt) cc_final: 0.8326 (mt) outliers start: 6 outliers final: 1 residues processed: 936 average time/residue: 0.2329 time to fit residues: 319.4388 Evaluate side-chains 482 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 201 ASN A 404 GLN A 692 GLN A 726 GLN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 827 ASN B 297 ASN B 620 ASN B 641 HIS B 692 GLN B 747 HIS B 748 ASN B 822 GLN C 692 GLN C 794 HIS ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 GLN D 201 ASN D 567 HIS D 641 HIS D 692 GLN D 726 GLN D 748 ASN D 822 GLN E 297 ASN E 309 HIS E 334 GLN E 641 HIS F 281 HIS F 309 HIS ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 770 HIS F 776 GLN F 849 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.125410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096718 restraints weight = 56842.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099208 restraints weight = 30993.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.100823 restraints weight = 20611.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101843 restraints weight = 15866.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102350 restraints weight = 13512.119| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29307 Z= 0.159 Angle : 0.724 14.668 39598 Z= 0.362 Chirality : 0.046 0.196 4479 Planarity : 0.006 0.061 5170 Dihedral : 9.758 91.776 4209 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.39 % Allowed : 8.94 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.13), residues: 3563 helix: -0.77 (0.11), residues: 1940 sheet: -2.49 (0.25), residues: 385 loop : -1.92 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 561 TYR 0.027 0.002 TYR E 380 PHE 0.016 0.002 PHE F 729 TRP 0.021 0.002 TRP D 543 HIS 0.013 0.001 HIS E 794 Details of bonding type rmsd covalent geometry : bond 0.00344 (29298) covalent geometry : angle 0.72443 (39598) hydrogen bonds : bond 0.05116 ( 1463) hydrogen bonds : angle 5.67013 ( 4299) Misc. bond : bond 0.00358 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 578 time to evaluate : 1.147 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 250 LYS cc_start: 0.7737 (ttpt) cc_final: 0.7134 (ttpt) REVERT: A 251 TYR cc_start: 0.8194 (m-10) cc_final: 0.7402 (m-10) REVERT: A 564 GLN cc_start: 0.8679 (tt0) cc_final: 0.8193 (tp-100) REVERT: A 642 SER cc_start: 0.7485 (m) cc_final: 0.7068 (p) REVERT: A 671 TYR cc_start: 0.8575 (m-80) cc_final: 0.8370 (m-80) REVERT: A 692 GLN cc_start: 0.8088 (mt0) cc_final: 0.7777 (mt0) REVERT: A 752 GLU cc_start: 0.7151 (tt0) cc_final: 0.6894 (mt-10) REVERT: A 794 HIS cc_start: 0.7785 (m170) cc_final: 0.7186 (t70) REVERT: A 842 LYS cc_start: 0.3894 (mttt) cc_final: 0.3538 (mmtm) REVERT: B 298 MET cc_start: 0.8679 (mtp) cc_final: 0.8415 (mtp) REVERT: B 692 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: B 700 THR cc_start: 0.8727 (m) cc_final: 0.8215 (p) REVERT: B 754 ILE cc_start: 0.9422 (pt) cc_final: 0.9181 (mt) REVERT: B 774 ILE cc_start: 0.9073 (mt) cc_final: 0.8812 (mt) REVERT: B 779 LEU cc_start: 0.9053 (mt) cc_final: 0.8834 (mt) REVERT: B 817 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8465 (tt) REVERT: C 192 GLN cc_start: 0.8614 (mt0) cc_final: 0.8401 (mt0) REVERT: C 388 ASP cc_start: 0.8641 (t70) cc_final: 0.8425 (t0) REVERT: C 758 ASP cc_start: 0.7897 (m-30) cc_final: 0.7636 (m-30) REVERT: D 161 LEU cc_start: 0.9033 (mt) cc_final: 0.8606 (mt) REVERT: D 163 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8361 (mptt) REVERT: D 345 ASP cc_start: 0.7982 (m-30) cc_final: 0.7624 (m-30) REVERT: D 827 ASN cc_start: 0.8529 (m-40) cc_final: 0.7902 (m110) REVERT: E 162 LYS cc_start: 0.8569 (mmmt) cc_final: 0.8323 (pttm) REVERT: E 185 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: E 707 VAL cc_start: 0.9496 (t) cc_final: 0.9207 (m) REVERT: F 217 GLU cc_start: 0.7874 (mt-10) cc_final: 0.6768 (mt-10) REVERT: F 330 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7119 (pt0) REVERT: F 538 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7606 (tp30) REVERT: F 540 LEU cc_start: 0.7842 (mm) cc_final: 0.7338 (mm) REVERT: F 582 ASN cc_start: 0.8715 (m-40) cc_final: 0.8401 (m-40) REVERT: F 595 ASN cc_start: 0.8219 (m-40) cc_final: 0.7615 (t0) REVERT: F 746 SER cc_start: 0.8667 (m) cc_final: 0.8382 (p) REVERT: F 821 ILE cc_start: 0.9095 (mt) cc_final: 0.8801 (mt) outliers start: 72 outliers final: 34 residues processed: 623 average time/residue: 0.1904 time to fit residues: 185.5937 Evaluate side-chains 473 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 436 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 235 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 ASN B 748 ASN C 201 ASN C 421 GLN C 794 HIS C 822 GLN D 620 ASN D 857 GLN E 309 HIS E 620 ASN ** F 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092529 restraints weight = 58336.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.094072 restraints weight = 31583.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095492 restraints weight = 20209.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095738 restraints weight = 17649.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095685 restraints weight = 15413.527| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 29307 Z= 0.267 Angle : 0.755 14.300 39598 Z= 0.381 Chirality : 0.047 0.164 4479 Planarity : 0.005 0.058 5170 Dihedral : 9.416 87.341 4209 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.19 % Allowed : 11.77 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3563 helix: -0.22 (0.11), residues: 1968 sheet: -2.44 (0.24), residues: 393 loop : -1.73 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 631 TYR 0.024 0.002 TYR D 653 PHE 0.026 0.002 PHE C 729 TRP 0.015 0.002 TRP D 543 HIS 0.020 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00622 (29298) covalent geometry : angle 0.75539 (39598) hydrogen bonds : bond 0.05324 ( 1463) hydrogen bonds : angle 5.43220 ( 4299) Misc. bond : bond 0.00318 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 440 time to evaluate : 0.996 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 250 LYS cc_start: 0.7980 (ttpt) cc_final: 0.7283 (ttpt) REVERT: A 251 TYR cc_start: 0.8262 (m-10) cc_final: 0.7456 (m-10) REVERT: A 564 GLN cc_start: 0.8617 (tt0) cc_final: 0.8174 (tp-100) REVERT: A 641 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5820 (p-80) REVERT: A 642 SER cc_start: 0.7529 (m) cc_final: 0.7304 (p) REVERT: A 794 HIS cc_start: 0.7581 (m170) cc_final: 0.7278 (t70) REVERT: B 298 MET cc_start: 0.8719 (mtp) cc_final: 0.8416 (mtp) REVERT: B 581 SER cc_start: 0.9268 (m) cc_final: 0.8807 (p) REVERT: B 634 MET cc_start: 0.9227 (mmm) cc_final: 0.8963 (mpp) REVERT: B 808 TYR cc_start: 0.5584 (t80) cc_final: 0.4950 (t80) REVERT: C 241 ASP cc_start: 0.7626 (t0) cc_final: 0.7370 (t0) REVERT: C 293 MET cc_start: 0.7525 (tpt) cc_final: 0.7312 (mmm) REVERT: C 392 ASP cc_start: 0.8178 (m-30) cc_final: 0.7909 (m-30) REVERT: C 421 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8073 (tt0) REVERT: D 163 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8325 (mptt) REVERT: D 413 ASP cc_start: 0.7427 (t70) cc_final: 0.7154 (t0) REVERT: D 710 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8543 (mtp180) REVERT: D 827 ASN cc_start: 0.8539 (m-40) cc_final: 0.8010 (m110) REVERT: E 162 LYS cc_start: 0.8628 (mmmt) cc_final: 0.8379 (pttm) REVERT: E 454 GLN cc_start: 0.7482 (mm110) cc_final: 0.7214 (mm110) REVERT: E 528 ARG cc_start: 0.6290 (mmt180) cc_final: 0.5810 (mmp-170) REVERT: E 707 VAL cc_start: 0.9554 (t) cc_final: 0.9228 (m) REVERT: F 330 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7208 (pt0) REVERT: F 563 GLU cc_start: 0.7195 (tp30) cc_final: 0.6915 (tp30) REVERT: F 582 ASN cc_start: 0.8774 (m-40) cc_final: 0.8481 (m-40) REVERT: F 595 ASN cc_start: 0.8304 (m-40) cc_final: 0.7722 (t0) REVERT: F 629 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.6514 (mtm) REVERT: F 746 SER cc_start: 0.8793 (m) cc_final: 0.8519 (p) REVERT: F 821 ILE cc_start: 0.9104 (mt) cc_final: 0.8809 (mt) outliers start: 96 outliers final: 62 residues processed: 502 average time/residue: 0.1839 time to fit residues: 146.9286 Evaluate side-chains 454 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 388 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 748 ASN Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 281 HIS Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 716 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 297 ASN Chi-restraints excluded: chain F residue 310 CYS Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 762 VAL Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 8.9990 chunk 188 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 321 optimal weight: 8.9990 chunk 136 optimal weight: 2.9990 chunk 290 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN D 281 HIS D 421 GLN D 692 GLN E 309 HIS E 857 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091302 restraints weight = 58450.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.093696 restraints weight = 32100.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.095254 restraints weight = 21576.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.096236 restraints weight = 16769.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.096684 restraints weight = 14369.998| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29307 Z= 0.200 Angle : 0.681 15.670 39598 Z= 0.339 Chirality : 0.045 0.250 4479 Planarity : 0.005 0.057 5170 Dihedral : 9.097 85.234 4209 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.39 % Allowed : 12.57 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3563 helix: 0.15 (0.11), residues: 1981 sheet: -2.41 (0.25), residues: 376 loop : -1.54 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 258 TYR 0.025 0.002 TYR E 319 PHE 0.016 0.002 PHE E 621 TRP 0.013 0.002 TRP D 543 HIS 0.005 0.001 HIS D 764 Details of bonding type rmsd covalent geometry : bond 0.00462 (29298) covalent geometry : angle 0.68079 (39598) hydrogen bonds : bond 0.04846 ( 1463) hydrogen bonds : angle 5.22054 ( 4299) Misc. bond : bond 0.00253 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 437 time to evaluate : 1.289 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 250 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7198 (ttpt) REVERT: A 251 TYR cc_start: 0.8290 (m-10) cc_final: 0.7519 (m-10) REVERT: A 564 GLN cc_start: 0.8586 (tt0) cc_final: 0.8152 (tp-100) REVERT: A 641 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.5732 (p-80) REVERT: A 794 HIS cc_start: 0.7807 (m170) cc_final: 0.7251 (t70) REVERT: B 283 MET cc_start: 0.8902 (tmm) cc_final: 0.8702 (tmm) REVERT: B 298 MET cc_start: 0.8693 (mtp) cc_final: 0.8387 (mtp) REVERT: B 543 TRP cc_start: 0.7866 (m-10) cc_final: 0.7631 (m-10) REVERT: B 581 SER cc_start: 0.9236 (m) cc_final: 0.8776 (p) REVERT: B 708 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: B 808 TYR cc_start: 0.5504 (t80) cc_final: 0.4994 (t80) REVERT: C 241 ASP cc_start: 0.7687 (t0) cc_final: 0.7388 (t0) REVERT: D 163 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8344 (mptt) REVERT: D 827 ASN cc_start: 0.8546 (m-40) cc_final: 0.8046 (m110) REVERT: E 562 MET cc_start: 0.6408 (tmm) cc_final: 0.6007 (tmm) REVERT: E 685 ASP cc_start: 0.8612 (t0) cc_final: 0.8357 (t0) REVERT: E 707 VAL cc_start: 0.9577 (t) cc_final: 0.9257 (m) REVERT: E 737 MET cc_start: 0.8803 (tpt) cc_final: 0.8570 (tpp) REVERT: F 330 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7328 (pt0) REVERT: F 582 ASN cc_start: 0.8800 (m-40) cc_final: 0.8455 (m-40) REVERT: F 595 ASN cc_start: 0.8307 (m-40) cc_final: 0.7749 (t0) REVERT: F 661 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.5371 (t80) REVERT: F 676 LEU cc_start: 0.9407 (tt) cc_final: 0.9193 (tt) REVERT: F 742 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7731 (mm) REVERT: F 746 SER cc_start: 0.8765 (m) cc_final: 0.8494 (p) REVERT: F 821 ILE cc_start: 0.9094 (mt) cc_final: 0.8797 (mt) outliers start: 102 outliers final: 57 residues processed: 507 average time/residue: 0.1853 time to fit residues: 150.4443 Evaluate side-chains 440 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 379 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 716 MET Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain E residue 851 ASP Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 274 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 chunk 224 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 359 optimal weight: 9.9990 chunk 242 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 857 GLN E 309 HIS F 688 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091316 restraints weight = 57871.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.093776 restraints weight = 30973.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095369 restraints weight = 20397.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.096383 restraints weight = 15676.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.096904 restraints weight = 13335.662| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29307 Z= 0.188 Angle : 0.671 15.820 39598 Z= 0.333 Chirality : 0.045 0.275 4479 Planarity : 0.005 0.058 5170 Dihedral : 8.922 83.026 4209 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.36 % Allowed : 13.30 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3563 helix: 0.42 (0.12), residues: 1980 sheet: -2.43 (0.24), residues: 373 loop : -1.39 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 258 TYR 0.022 0.002 TYR E 319 PHE 0.027 0.002 PHE C 729 TRP 0.012 0.002 TRP D 543 HIS 0.005 0.001 HIS D 764 Details of bonding type rmsd covalent geometry : bond 0.00436 (29298) covalent geometry : angle 0.67118 (39598) hydrogen bonds : bond 0.04685 ( 1463) hydrogen bonds : angle 5.11343 ( 4299) Misc. bond : bond 0.00258 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 412 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7206 (ttpt) REVERT: A 251 TYR cc_start: 0.8289 (m-10) cc_final: 0.7443 (m-10) REVERT: A 564 GLN cc_start: 0.8511 (tt0) cc_final: 0.8151 (tp-100) REVERT: A 641 HIS cc_start: 0.6596 (OUTLIER) cc_final: 0.5779 (p-80) REVERT: A 738 LYS cc_start: 0.7668 (tttt) cc_final: 0.7205 (pttm) REVERT: A 794 HIS cc_start: 0.7767 (m170) cc_final: 0.7260 (t70) REVERT: B 283 MET cc_start: 0.8893 (tmm) cc_final: 0.8634 (tmm) REVERT: B 543 TRP cc_start: 0.7894 (m-10) cc_final: 0.7660 (m-10) REVERT: B 581 SER cc_start: 0.9258 (m) cc_final: 0.8998 (p) REVERT: B 708 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: B 808 TYR cc_start: 0.5585 (t80) cc_final: 0.5056 (t80) REVERT: C 241 ASP cc_start: 0.7647 (t0) cc_final: 0.7355 (t0) REVERT: D 551 MET cc_start: 0.7066 (mmm) cc_final: 0.6663 (mmm) REVERT: D 692 GLN cc_start: 0.7825 (pt0) cc_final: 0.7533 (pt0) REVERT: D 710 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8489 (mtp85) REVERT: D 827 ASN cc_start: 0.8550 (m-40) cc_final: 0.8088 (m110) REVERT: E 528 ARG cc_start: 0.6083 (mmt180) cc_final: 0.5673 (mmp80) REVERT: E 562 MET cc_start: 0.6360 (tmm) cc_final: 0.6122 (tmm) REVERT: E 567 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7749 (t-90) REVERT: E 646 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9032 (pt) REVERT: E 685 ASP cc_start: 0.8510 (t0) cc_final: 0.8306 (t0) REVERT: E 707 VAL cc_start: 0.9562 (t) cc_final: 0.9259 (m) REVERT: E 756 ARG cc_start: 0.8291 (mmt90) cc_final: 0.7963 (mtt-85) REVERT: F 217 GLU cc_start: 0.7936 (pt0) cc_final: 0.7443 (tm-30) REVERT: F 305 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7850 (mtm-85) REVERT: F 330 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7329 (pt0) REVERT: F 582 ASN cc_start: 0.8869 (m-40) cc_final: 0.8498 (m-40) REVERT: F 595 ASN cc_start: 0.8231 (m-40) cc_final: 0.7739 (t0) REVERT: F 661 TYR cc_start: 0.6065 (OUTLIER) cc_final: 0.5149 (t80) REVERT: F 676 LEU cc_start: 0.9378 (tt) cc_final: 0.9079 (tt) REVERT: F 746 SER cc_start: 0.8703 (m) cc_final: 0.8486 (p) REVERT: F 821 ILE cc_start: 0.9082 (mt) cc_final: 0.8797 (mt) REVERT: F 851 ASP cc_start: 0.8086 (t0) cc_final: 0.7691 (t0) outliers start: 101 outliers final: 67 residues processed: 477 average time/residue: 0.1799 time to fit residues: 138.2317 Evaluate side-chains 447 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 374 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 716 MET Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 717 THR Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 191 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN E 309 HIS F 620 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.120405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.092700 restraints weight = 58143.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.094968 restraints weight = 32860.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.095386 restraints weight = 22116.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096351 restraints weight = 19321.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096561 restraints weight = 15928.187| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29307 Z= 0.181 Angle : 0.660 16.475 39598 Z= 0.328 Chirality : 0.044 0.275 4479 Planarity : 0.005 0.060 5170 Dihedral : 8.728 81.248 4209 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.52 % Allowed : 14.39 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.14), residues: 3563 helix: 0.54 (0.12), residues: 1995 sheet: -2.38 (0.24), residues: 401 loop : -1.29 (0.19), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 258 TYR 0.023 0.002 TYR A 812 PHE 0.016 0.002 PHE D 729 TRP 0.011 0.002 TRP D 543 HIS 0.012 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00421 (29298) covalent geometry : angle 0.66013 (39598) hydrogen bonds : bond 0.04560 ( 1463) hydrogen bonds : angle 5.02502 ( 4299) Misc. bond : bond 0.00253 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 405 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7181 (ttpt) REVERT: A 251 TYR cc_start: 0.8299 (m-10) cc_final: 0.7399 (m-10) REVERT: A 564 GLN cc_start: 0.8605 (tt0) cc_final: 0.8191 (tp-100) REVERT: A 641 HIS cc_start: 0.6752 (OUTLIER) cc_final: 0.5781 (p-80) REVERT: A 738 LYS cc_start: 0.7636 (tttt) cc_final: 0.7163 (pttm) REVERT: B 298 MET cc_start: 0.8765 (ttm) cc_final: 0.8521 (mtp) REVERT: B 543 TRP cc_start: 0.7836 (m-10) cc_final: 0.7591 (m-10) REVERT: B 581 SER cc_start: 0.9217 (m) cc_final: 0.8787 (p) REVERT: B 708 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7878 (m-30) REVERT: B 771 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9079 (mt) REVERT: B 808 TYR cc_start: 0.5606 (t80) cc_final: 0.5254 (t80) REVERT: C 241 ASP cc_start: 0.7634 (t0) cc_final: 0.7358 (t0) REVERT: C 421 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: D 551 MET cc_start: 0.7119 (mmm) cc_final: 0.6653 (mmm) REVERT: D 827 ASN cc_start: 0.8521 (m-40) cc_final: 0.8045 (m110) REVERT: E 528 ARG cc_start: 0.6164 (mmt180) cc_final: 0.5678 (mmp80) REVERT: E 567 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7811 (t-90) REVERT: E 707 VAL cc_start: 0.9572 (t) cc_final: 0.9246 (m) REVERT: E 756 ARG cc_start: 0.8275 (mmt90) cc_final: 0.7976 (mtt-85) REVERT: F 217 GLU cc_start: 0.8124 (pt0) cc_final: 0.7474 (tm-30) REVERT: F 305 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7898 (mtm-85) REVERT: F 330 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7298 (pt0) REVERT: F 582 ASN cc_start: 0.8948 (m-40) cc_final: 0.8501 (m110) REVERT: F 595 ASN cc_start: 0.8289 (m-40) cc_final: 0.7795 (t0) REVERT: F 629 MET cc_start: 0.7194 (ptp) cc_final: 0.6599 (mtt) REVERT: F 661 TYR cc_start: 0.6124 (OUTLIER) cc_final: 0.5376 (t80) REVERT: F 676 LEU cc_start: 0.9447 (tt) cc_final: 0.9188 (tt) REVERT: F 821 ILE cc_start: 0.9067 (mt) cc_final: 0.8782 (mt) REVERT: F 851 ASP cc_start: 0.8219 (t0) cc_final: 0.7735 (t0) outliers start: 106 outliers final: 76 residues processed: 475 average time/residue: 0.1684 time to fit residues: 129.0631 Evaluate side-chains 443 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 361 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 771 ILE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 747 HIS Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 716 MET Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 293 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 352 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 161 optimal weight: 0.8980 chunk 187 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 806 ASN F 620 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.120234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.092674 restraints weight = 58493.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094730 restraints weight = 32658.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095236 restraints weight = 22582.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096220 restraints weight = 19808.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.096270 restraints weight = 15865.247| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29307 Z= 0.182 Angle : 0.667 16.840 39598 Z= 0.329 Chirality : 0.045 0.290 4479 Planarity : 0.004 0.059 5170 Dihedral : 8.612 80.168 4209 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.59 % Allowed : 15.43 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3563 helix: 0.64 (0.12), residues: 1995 sheet: -2.35 (0.24), residues: 400 loop : -1.27 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 258 TYR 0.020 0.001 TYR E 319 PHE 0.018 0.002 PHE D 729 TRP 0.012 0.002 TRP D 543 HIS 0.005 0.001 HIS D 764 Details of bonding type rmsd covalent geometry : bond 0.00427 (29298) covalent geometry : angle 0.66697 (39598) hydrogen bonds : bond 0.04521 ( 1463) hydrogen bonds : angle 5.00500 ( 4299) Misc. bond : bond 0.00249 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 386 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7096 (ttpt) REVERT: A 251 TYR cc_start: 0.8331 (m-10) cc_final: 0.7439 (m-10) REVERT: A 564 GLN cc_start: 0.8567 (tt0) cc_final: 0.8179 (tp-100) REVERT: A 641 HIS cc_start: 0.6744 (OUTLIER) cc_final: 0.5762 (p-80) REVERT: A 738 LYS cc_start: 0.7640 (tttt) cc_final: 0.7086 (pttm) REVERT: B 581 SER cc_start: 0.9225 (m) cc_final: 0.8791 (p) REVERT: B 708 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: C 241 ASP cc_start: 0.7662 (t0) cc_final: 0.7373 (t0) REVERT: C 411 GLU cc_start: 0.8482 (mp0) cc_final: 0.8192 (mp0) REVERT: D 293 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4756 (ttm) REVERT: D 551 MET cc_start: 0.7229 (mmm) cc_final: 0.6767 (mmm) REVERT: D 827 ASN cc_start: 0.8542 (m-40) cc_final: 0.8083 (m110) REVERT: E 427 GLN cc_start: 0.7418 (pp30) cc_final: 0.7200 (pp30) REVERT: E 454 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7198 (mm110) REVERT: E 528 ARG cc_start: 0.6165 (mmt180) cc_final: 0.5561 (mmp80) REVERT: E 567 HIS cc_start: 0.8319 (OUTLIER) cc_final: 0.7778 (t-90) REVERT: E 707 VAL cc_start: 0.9572 (t) cc_final: 0.9262 (m) REVERT: E 756 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7960 (mtt-85) REVERT: F 217 GLU cc_start: 0.8178 (pt0) cc_final: 0.7505 (tm-30) REVERT: F 305 ARG cc_start: 0.8204 (mtm110) cc_final: 0.7896 (mtm-85) REVERT: F 330 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7279 (pt0) REVERT: F 403 MET cc_start: 0.8849 (tpt) cc_final: 0.8612 (tpp) REVERT: F 582 ASN cc_start: 0.8937 (m-40) cc_final: 0.8467 (m110) REVERT: F 595 ASN cc_start: 0.8292 (m-40) cc_final: 0.7818 (t0) REVERT: F 661 TYR cc_start: 0.5880 (OUTLIER) cc_final: 0.5033 (t80) REVERT: F 662 LEU cc_start: 0.8696 (tp) cc_final: 0.8478 (mt) REVERT: F 676 LEU cc_start: 0.9433 (tt) cc_final: 0.9150 (tt) REVERT: F 821 ILE cc_start: 0.9063 (mt) cc_final: 0.8783 (mt) outliers start: 108 outliers final: 86 residues processed: 457 average time/residue: 0.1699 time to fit residues: 125.8127 Evaluate side-chains 448 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 357 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 747 HIS Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 394 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 567 HIS Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 647 VAL Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 716 MET Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 392 ASP Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 696 ASP Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 70 optimal weight: 0.3980 chunk 300 optimal weight: 8.9990 chunk 180 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 181 optimal weight: 0.7980 chunk 203 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 857 GLN B 201 ASN B 281 HIS B 641 HIS B 692 GLN C 195 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 620 ASN E 309 HIS ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.123822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.095975 restraints weight = 57852.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098436 restraints weight = 31333.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100030 restraints weight = 20820.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.100974 restraints weight = 16068.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101606 restraints weight = 13830.881| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29307 Z= 0.122 Angle : 0.636 18.853 39598 Z= 0.311 Chirality : 0.043 0.260 4479 Planarity : 0.004 0.059 5170 Dihedral : 8.275 81.978 4209 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.69 % Allowed : 16.09 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3563 helix: 0.87 (0.12), residues: 1982 sheet: -2.30 (0.24), residues: 397 loop : -1.11 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 258 TYR 0.022 0.001 TYR B 783 PHE 0.019 0.002 PHE B 729 TRP 0.013 0.001 TRP D 543 HIS 0.005 0.001 HIS B 764 Details of bonding type rmsd covalent geometry : bond 0.00266 (29298) covalent geometry : angle 0.63621 (39598) hydrogen bonds : bond 0.03988 ( 1463) hydrogen bonds : angle 4.81525 ( 4299) Misc. bond : bond 0.00193 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 427 time to evaluate : 1.025 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 250 LYS cc_start: 0.7642 (ttpt) cc_final: 0.7121 (ttpt) REVERT: A 251 TYR cc_start: 0.8187 (m-10) cc_final: 0.7454 (m-10) REVERT: A 564 GLN cc_start: 0.8532 (tt0) cc_final: 0.8119 (tp-100) REVERT: A 641 HIS cc_start: 0.6531 (OUTLIER) cc_final: 0.5627 (p-80) REVERT: A 738 LYS cc_start: 0.7773 (tttt) cc_final: 0.7102 (pttm) REVERT: B 581 SER cc_start: 0.9156 (m) cc_final: 0.8784 (p) REVERT: B 620 ASN cc_start: 0.8833 (t0) cc_final: 0.8453 (t0) REVERT: B 692 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7529 (pt0) REVERT: B 708 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: C 184 ASP cc_start: 0.7424 (t0) cc_final: 0.7199 (t0) REVERT: C 411 GLU cc_start: 0.8302 (mp0) cc_final: 0.8090 (mp0) REVERT: C 708 ASP cc_start: 0.7867 (t0) cc_final: 0.7638 (t0) REVERT: C 812 TYR cc_start: 0.8064 (m-10) cc_final: 0.7841 (m-10) REVERT: D 163 LYS cc_start: 0.7752 (mptt) cc_final: 0.7380 (mppt) REVERT: D 189 ARG cc_start: 0.8533 (ttt-90) cc_final: 0.8333 (ttt-90) REVERT: D 305 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7691 (ttp-110) REVERT: D 551 MET cc_start: 0.7009 (mmm) cc_final: 0.6678 (mmm) REVERT: D 710 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8322 (mtp85) REVERT: D 827 ASN cc_start: 0.8396 (m-40) cc_final: 0.7936 (m110) REVERT: E 528 ARG cc_start: 0.6028 (mmt180) cc_final: 0.5577 (mmp80) REVERT: E 581 SER cc_start: 0.9177 (m) cc_final: 0.8864 (p) REVERT: E 636 GLU cc_start: 0.7330 (mt-10) cc_final: 0.7050 (mp0) REVERT: E 707 VAL cc_start: 0.9558 (t) cc_final: 0.9210 (m) REVERT: E 756 ARG cc_start: 0.8123 (mmt90) cc_final: 0.7801 (mtt-85) REVERT: F 217 GLU cc_start: 0.8082 (pt0) cc_final: 0.7460 (tm-30) REVERT: F 305 ARG cc_start: 0.8040 (mtm110) cc_final: 0.7772 (mtm-85) REVERT: F 403 MET cc_start: 0.8682 (tpt) cc_final: 0.8451 (tpp) REVERT: F 582 ASN cc_start: 0.8856 (m-40) cc_final: 0.8387 (m110) REVERT: F 661 TYR cc_start: 0.5574 (OUTLIER) cc_final: 0.4751 (t80) REVERT: F 821 ILE cc_start: 0.9072 (mt) cc_final: 0.8805 (mt) outliers start: 81 outliers final: 53 residues processed: 476 average time/residue: 0.1736 time to fit residues: 132.3529 Evaluate side-chains 430 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 372 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 403 MET Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 710 ARG Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 231 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 291 optimal weight: 0.0970 chunk 62 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN E 309 HIS E 567 HIS ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.122341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095435 restraints weight = 58142.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097261 restraints weight = 32614.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.099045 restraints weight = 21057.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099163 restraints weight = 16668.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099176 restraints weight = 14919.199| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29307 Z= 0.152 Angle : 0.658 16.629 39598 Z= 0.323 Chirality : 0.044 0.239 4479 Planarity : 0.004 0.061 5170 Dihedral : 8.196 88.735 4209 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.53 % Allowed : 16.76 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3563 helix: 0.89 (0.12), residues: 1997 sheet: -2.28 (0.23), residues: 405 loop : -1.06 (0.19), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 258 TYR 0.020 0.001 TYR E 319 PHE 0.019 0.002 PHE B 729 TRP 0.012 0.001 TRP D 543 HIS 0.004 0.001 HIS D 764 Details of bonding type rmsd covalent geometry : bond 0.00352 (29298) covalent geometry : angle 0.65835 (39598) hydrogen bonds : bond 0.04165 ( 1463) hydrogen bonds : angle 4.82941 ( 4299) Misc. bond : bond 0.00225 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 387 time to evaluate : 0.797 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 250 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7168 (ttpt) REVERT: A 251 TYR cc_start: 0.8214 (m-10) cc_final: 0.7373 (m-10) REVERT: A 564 GLN cc_start: 0.8612 (tt0) cc_final: 0.8158 (tp-100) REVERT: A 641 HIS cc_start: 0.6585 (OUTLIER) cc_final: 0.5544 (p-80) REVERT: A 738 LYS cc_start: 0.7691 (tttt) cc_final: 0.7013 (pttm) REVERT: A 823 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7459 (mm-40) REVERT: B 581 SER cc_start: 0.9189 (m) cc_final: 0.8758 (p) REVERT: B 620 ASN cc_start: 0.8844 (t0) cc_final: 0.8479 (t0) REVERT: B 634 MET cc_start: 0.8738 (mmt) cc_final: 0.8488 (tpp) REVERT: B 708 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: C 411 GLU cc_start: 0.8320 (mp0) cc_final: 0.8047 (mp0) REVERT: C 812 TYR cc_start: 0.8120 (m-10) cc_final: 0.7900 (m-10) REVERT: D 305 ARG cc_start: 0.7996 (ttp-110) cc_final: 0.7782 (ttp-110) REVERT: D 794 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7478 (m-70) REVERT: D 827 ASN cc_start: 0.8484 (m-40) cc_final: 0.7918 (m110) REVERT: E 427 GLN cc_start: 0.7406 (pp30) cc_final: 0.7162 (pp30) REVERT: E 528 ARG cc_start: 0.6198 (mmt180) cc_final: 0.5698 (mmp80) REVERT: E 581 SER cc_start: 0.9156 (m) cc_final: 0.8887 (p) REVERT: E 707 VAL cc_start: 0.9536 (t) cc_final: 0.9187 (m) REVERT: E 756 ARG cc_start: 0.8132 (mmt90) cc_final: 0.7816 (mtt-85) REVERT: F 217 GLU cc_start: 0.8175 (pt0) cc_final: 0.7509 (tm-30) REVERT: F 403 MET cc_start: 0.8852 (tpt) cc_final: 0.8573 (tpp) REVERT: F 582 ASN cc_start: 0.8954 (m-40) cc_final: 0.8459 (m110) REVERT: F 629 MET cc_start: 0.6679 (ptp) cc_final: 0.6313 (mtt) REVERT: F 661 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.4938 (t80) REVERT: F 821 ILE cc_start: 0.9097 (mt) cc_final: 0.8826 (mt) outliers start: 76 outliers final: 60 residues processed: 433 average time/residue: 0.1738 time to fit residues: 120.9646 Evaluate side-chains 427 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 363 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 794 HIS Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 752 GLU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 353 optimal weight: 0.0270 chunk 29 optimal weight: 7.9990 chunk 320 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 296 optimal weight: 5.9990 chunk 150 optimal weight: 0.5980 chunk 231 optimal weight: 1.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 567 HIS ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.123393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096210 restraints weight = 57786.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098842 restraints weight = 31272.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099808 restraints weight = 20545.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101092 restraints weight = 15583.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100932 restraints weight = 13422.785| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29307 Z= 0.138 Angle : 0.655 16.395 39598 Z= 0.320 Chirality : 0.044 0.239 4479 Planarity : 0.004 0.059 5170 Dihedral : 8.089 92.685 4209 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.23 % Allowed : 17.05 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3563 helix: 0.95 (0.12), residues: 1999 sheet: -2.23 (0.24), residues: 380 loop : -0.98 (0.19), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 852 TYR 0.021 0.001 TYR E 319 PHE 0.042 0.002 PHE C 729 TRP 0.012 0.001 TRP D 543 HIS 0.006 0.001 HIS C 736 Details of bonding type rmsd covalent geometry : bond 0.00317 (29298) covalent geometry : angle 0.65501 (39598) hydrogen bonds : bond 0.04054 ( 1463) hydrogen bonds : angle 4.79484 ( 4299) Misc. bond : bond 0.00215 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7126 Ramachandran restraints generated. 3563 Oldfield, 0 Emsley, 3563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 383 time to evaluate : 1.107 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 250 LYS cc_start: 0.7628 (ttpt) cc_final: 0.7124 (ttpt) REVERT: A 251 TYR cc_start: 0.8175 (m-10) cc_final: 0.7339 (m-10) REVERT: A 564 GLN cc_start: 0.8565 (tt0) cc_final: 0.8132 (tp-100) REVERT: A 641 HIS cc_start: 0.6445 (OUTLIER) cc_final: 0.5459 (p-80) REVERT: A 738 LYS cc_start: 0.7638 (tttt) cc_final: 0.6926 (pttm) REVERT: A 818 LYS cc_start: 0.1820 (pttt) cc_final: 0.1431 (pttt) REVERT: A 823 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7420 (mm-40) REVERT: B 562 MET cc_start: 0.8334 (mmm) cc_final: 0.7665 (tpt) REVERT: B 581 SER cc_start: 0.9190 (m) cc_final: 0.8704 (p) REVERT: B 620 ASN cc_start: 0.8844 (t0) cc_final: 0.8489 (t0) REVERT: B 708 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: B 779 LEU cc_start: 0.8737 (mp) cc_final: 0.8037 (tt) REVERT: C 411 GLU cc_start: 0.8291 (mp0) cc_final: 0.8070 (mp0) REVERT: D 189 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8352 (ttt-90) REVERT: D 794 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.7417 (m-70) REVERT: D 827 ASN cc_start: 0.8474 (m-40) cc_final: 0.7887 (m110) REVERT: E 427 GLN cc_start: 0.7338 (pp30) cc_final: 0.7102 (pp30) REVERT: E 528 ARG cc_start: 0.6179 (mmt180) cc_final: 0.5714 (mmp80) REVERT: E 581 SER cc_start: 0.9176 (m) cc_final: 0.8912 (p) REVERT: E 636 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7203 (mp0) REVERT: E 707 VAL cc_start: 0.9563 (t) cc_final: 0.9220 (m) REVERT: E 756 ARG cc_start: 0.8148 (mmt90) cc_final: 0.7791 (mtt-85) REVERT: F 217 GLU cc_start: 0.8162 (pt0) cc_final: 0.7487 (tm-30) REVERT: F 403 MET cc_start: 0.8770 (tpt) cc_final: 0.8544 (tpp) REVERT: F 629 MET cc_start: 0.6596 (ptp) cc_final: 0.6294 (mtt) REVERT: F 737 MET cc_start: 0.8679 (mmm) cc_final: 0.7814 (mtt) REVERT: F 821 ILE cc_start: 0.9084 (mt) cc_final: 0.8824 (mt) outliers start: 67 outliers final: 59 residues processed: 425 average time/residue: 0.1688 time to fit residues: 116.0998 Evaluate side-chains 423 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 604 LEU Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 760 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 708 ASP Chi-restraints excluded: chain B residue 754 ILE Chi-restraints excluded: chain B residue 792 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 600 SER Chi-restraints excluded: chain C residue 634 MET Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 310 CYS Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 741 VAL Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 794 HIS Chi-restraints excluded: chain D residue 826 GLU Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 425 GLU Chi-restraints excluded: chain E residue 551 MET Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 575 GLU Chi-restraints excluded: chain E residue 600 SER Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 752 GLU Chi-restraints excluded: chain E residue 761 VAL Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 661 TYR Chi-restraints excluded: chain F residue 671 TYR Chi-restraints excluded: chain F residue 747 HIS Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 798 GLU Chi-restraints excluded: chain F residue 817 LEU Chi-restraints excluded: chain F residue 826 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 211 optimal weight: 8.9990 chunk 288 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN B 692 GLN C 748 ASN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS E 567 HIS ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094137 restraints weight = 58679.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095968 restraints weight = 32692.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097647 restraints weight = 21634.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097851 restraints weight = 16692.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097841 restraints weight = 14906.946| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29307 Z= 0.175 Angle : 0.683 19.917 39598 Z= 0.335 Chirality : 0.045 0.234 4479 Planarity : 0.004 0.061 5170 Dihedral : 8.076 96.406 4209 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.49 % Allowed : 16.99 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3563 helix: 0.93 (0.12), residues: 1996 sheet: -2.20 (0.24), residues: 389 loop : -0.98 (0.19), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 258 TYR 0.022 0.001 TYR F 656 PHE 0.024 0.002 PHE B 729 TRP 0.013 0.002 TRP D 543 HIS 0.005 0.001 HIS D 764 Details of bonding type rmsd covalent geometry : bond 0.00411 (29298) covalent geometry : angle 0.68347 (39598) hydrogen bonds : bond 0.04248 ( 1463) hydrogen bonds : angle 4.86602 ( 4299) Misc. bond : bond 0.00251 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4726.38 seconds wall clock time: 82 minutes 14.75 seconds (4934.75 seconds total)