Starting phenix.real_space_refine on Fri Mar 6 09:37:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qs8_4627/03_2026/6qs8_4627.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs8_4627/03_2026/6qs8_4627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qs8_4627/03_2026/6qs8_4627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs8_4627/03_2026/6qs8_4627.map" model { file = "/net/cci-nas-00/data/ceres_data/6qs8_4627/03_2026/6qs8_4627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs8_4627/03_2026/6qs8_4627.cif" } resolution = 3.9 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= 0.004 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 20 residue(s): 0.03s 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: 3 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: 7.60, per 1000 atoms: 0.26 Number of scatterers: 28875 At special positions: 0 Unit cell: (119.7, 143.85, 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 1.3 seconds 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 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: 182 helices and 32 sheets defined 59.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 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 211 through 226 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.552A pdb=" N LEU A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 246' Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.679A pdb=" N ARG A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 295 through 305 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 315 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: 3.561A pdb=" N TYR A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 381 removed outlier: 3.559A pdb=" N ILE A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 408 removed outlier: 4.430A pdb=" N LYS A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.718A 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: 3.585A pdb=" N VAL A 577 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 623 removed outlier: 3.648A pdb=" N LEU A 614 " --> pdb=" O GLY A 610 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.703A pdb=" N VAL A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 669 removed outlier: 3.504A pdb=" N ALA A 665 " --> pdb=" O TYR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 Processing helix chain 'A' and resid 685 through 697 removed outlier: 4.124A 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 734 through 749 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: 4.455A 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 Processing helix chain 'B' and resid 212 through 226 removed outlier: 3.707A pdb=" N VAL B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) 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: 3.775A pdb=" N MET B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 Proline residue: B 301 - end of helix removed outlier: 3.761A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 Processing helix chain 'B' and resid 326 through 332 Processing helix chain 'B' and resid 342 through 353 Processing helix chain 'B' and resid 353 through 362 Processing helix chain 'B' and resid 366 through 381 Processing helix chain 'B' and resid 387 through 407 Processing helix chain 'B' and resid 532 through 545 Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.540A pdb=" N VAL B 577 " --> pdb=" O GLN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 624 Processing helix chain 'B' and resid 635 through 637 No H-bonds generated for 'chain 'B' and resid 635 through 637' Processing helix chain 'B' and resid 639 through 641 No H-bonds generated for 'chain 'B' and resid 639 through 641' Processing helix chain 'B' and resid 642 through 648 Processing helix chain 'B' and resid 655 through 659 removed outlier: 3.516A pdb=" N GLU B 658 " --> pdb=" O GLY B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 669 removed outlier: 3.607A pdb=" N GLU B 664 " --> pdb=" O GLY B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 687 removed outlier: 4.308A 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 752 through 757 removed outlier: 3.677A pdb=" N ILE B 757 " --> pdb=" O PHE B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 790 Processing helix chain 'B' and resid 796 through 807 removed outlier: 3.518A pdb=" N LEU B 800 " --> pdb=" O SER B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 834 Proline residue: B 828 - end of helix removed outlier: 3.774A pdb=" N LEU B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.565A pdb=" N TYR C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) No H-bonds generated for '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: 3.579A pdb=" N VAL C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 248 removed outlier: 3.747A pdb=" N LEU C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 317 through 323 Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.860A pdb=" N ARG C 331 " --> pdb=" O ALA C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 362 removed outlier: 3.872A pdb=" N GLY C 352 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLU C 355 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ARG C 356 " --> pdb=" O GLY C 352 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 Processing helix chain 'C' and resid 387 through 407 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: 3.686A 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 removed outlier: 3.529A pdb=" N VAL C 577 " --> pdb=" O GLN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 660 through 669 removed outlier: 3.529A pdb=" N ARG C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 682 removed outlier: 3.856A pdb=" N ALA C 682 " --> pdb=" O VAL C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 687 removed outlier: 3.809A 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 788 removed outlier: 3.504A pdb=" N GLU C 788 " --> pdb=" O LYS C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 807 Processing helix chain 'C' and resid 814 through 825 removed outlier: 3.593A pdb=" N LYS C 818 " --> pdb=" O ALA C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 834 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 212 through 226 removed outlier: 3.737A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 249 removed outlier: 3.703A pdb=" N LEU D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.412A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 326 through 332 Processing helix chain 'D' and resid 342 through 362 Processing helix chain 'D' and resid 366 through 381 removed outlier: 3.524A pdb=" N ILE D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 552 through 560 Processing helix chain 'D' and resid 561 through 567 Processing helix chain 'D' and resid 573 through 589 removed outlier: 3.565A pdb=" N VAL D 577 " --> pdb=" O GLN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 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 641 through 648 Processing helix chain 'D' and resid 653 through 657 removed outlier: 3.744A pdb=" N TYR D 656 " --> pdb=" O TYR D 653 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU D 657 " --> pdb=" O VAL D 654 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 653 through 657' Processing helix chain 'D' and resid 661 through 669 removed outlier: 3.532A pdb=" N ARG D 669 " --> pdb=" O ALA D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 678 through 682 Processing helix chain 'D' and resid 684 through 697 Processing helix chain 'D' and resid 721 through 729 Processing helix chain 'D' and resid 733 through 749 removed outlier: 3.621A 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 806 Processing helix chain 'D' and resid 809 through 813 removed outlier: 3.707A pdb=" N TYR D 812 " --> pdb=" O ASP D 809 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY D 813 " --> pdb=" O PRO D 810 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 809 through 813' Processing helix chain 'D' and resid 814 through 825 removed outlier: 3.835A pdb=" N LYS D 818 " --> pdb=" O ALA D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 835 Processing helix chain 'E' and resid 160 through 164 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 246 removed outlier: 3.662A pdb=" N LEU E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 241 through 246' 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: 3.819A pdb=" N ALA E 304 " --> pdb=" O LYS E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 323 Processing helix chain 'E' and resid 329 through 331 No H-bonds generated for 'chain 'E' and resid 329 through 331' Processing helix chain 'E' and resid 342 through 362 removed outlier: 4.550A pdb=" N LEU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS E 360 " --> pdb=" O ARG E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 381 removed outlier: 3.702A 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 545 removed outlier: 3.579A pdb=" N ILE E 536 " --> pdb=" O THR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 567 removed outlier: 3.874A pdb=" N ARG E 556 " --> pdb=" O MET E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 589 removed outlier: 3.538A pdb=" N VAL E 577 " --> pdb=" O GLN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 624 Processing helix chain 'E' and resid 641 through 647 Processing helix chain 'E' and resid 661 through 669 removed outlier: 3.517A pdb=" N ARG E 669 " --> pdb=" O ALA E 665 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 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: 3.537A pdb=" N MET E 737 " --> pdb=" O ASP E 733 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 790 removed outlier: 3.552A pdb=" N GLU E 788 " --> pdb=" O LYS E 784 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG E 789 " --> pdb=" O ARG E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 807 Processing helix chain 'E' and resid 814 through 825 Processing helix chain 'E' and resid 825 through 835 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.777A pdb=" N TYR F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) No H-bonds generated for '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: 3.807A 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 Processing helix chain 'F' and resid 254 through 270 removed outlier: 3.858A pdb=" N GLU F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) 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: 3.693A 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 342 through 353 Processing helix chain 'F' and resid 353 through 362 removed outlier: 3.628A 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: 4.487A pdb=" N HIS F 567 " --> pdb=" O GLU F 563 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS F 568 " --> pdb=" O GLN F 564 " (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 662 through 669 Processing helix chain 'F' and resid 678 through 682 removed outlier: 3.703A pdb=" N LYS F 681 " --> pdb=" O ALA F 678 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 682 " --> pdb=" O VAL F 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 678 through 682' Processing helix chain 'F' and resid 683 through 696 removed outlier: 4.145A pdb=" N PHE F 687 " --> pdb=" O HIS F 683 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN F 688 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE F 689 " --> pdb=" O ASP F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 729 removed outlier: 3.737A pdb=" N ILE F 725 " --> pdb=" O GLY F 721 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE F 729 " --> pdb=" O ILE F 725 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 749 Processing helix chain 'F' and resid 768 through 790 Processing helix chain 'F' and resid 796 through 808 Processing helix chain 'F' and resid 814 through 834 Proline residue: F 828 - end of helix removed outlier: 3.569A 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: 4.610A pdb=" N ASP A 278 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL A 311 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU A 275 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA A 313 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 277 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR A 314 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU A 204 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 364 through 365 removed outlier: 7.822A 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: 6.506A pdb=" N VAL A 630 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASP A 677 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A 632 " --> pdb=" O ASP A 677 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 759 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 3.640A 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: 5.792A pdb=" N ARG B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N PHE B 276 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP B 278 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LEU B 240 " --> pdb=" O ASP B 278 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 311 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU B 275 " --> pdb=" O VAL B 311 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N ALA B 313 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE B 277 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N THR B 315 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR B 314 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 5.655A 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: 6.832A 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: 3.614A pdb=" N GLY B 599 " --> pdb=" O THR B 712 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N SER B 600 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL B 761 " --> pdb=" O SER B 600 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 602 " --> pdb=" O VAL B 761 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 698 through 700 Processing sheet with id=AB1, first strand: chain 'B' and resid 793 through 795 removed outlier: 3.628A pdb=" N ARG B 845 " --> pdb=" O VAL B 856 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.043A pdb=" N ARG C 236 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE C 276 " --> pdb=" O ARG C 236 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 238 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP C 278 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU C 240 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL C 311 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 275 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ALA C 313 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE C 277 " --> pdb=" O ALA C 313 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.106A pdb=" N VAL C 203 " --> pdb=" O VAL C 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 364 through 365 removed outlier: 6.922A pdb=" N GLN C 364 " --> pdb=" O VAL C 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 630 through 633 removed outlier: 6.210A pdb=" N GLY C 599 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET C 716 " --> pdb=" O GLY C 599 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE C 601 " --> pdb=" O MET C 716 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER C 600 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL C 761 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU C 602 " --> pdb=" O VAL C 761 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 698 through 700 Processing sheet with id=AB7, first strand: chain 'C' and resid 792 through 795 removed outlier: 6.643A pdb=" N GLU C 792 " --> pdb=" O ILE C 844 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU C 846 " --> pdb=" O GLU C 792 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N HIS C 794 " --> pdb=" O LEU C 846 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL C 848 " --> pdb=" O HIS C 794 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 845 " --> pdb=" O VAL C 856 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.005A pdb=" N ARG D 236 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE D 276 " --> pdb=" O ARG D 236 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU D 238 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP D 278 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LEU D 240 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL D 311 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 275 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ALA D 313 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE D 277 " --> pdb=" O ALA D 313 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N THR D 315 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR D 314 " --> pdb=" O PRO D 202 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU D 204 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL D 203 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 364 through 365 removed outlier: 6.787A pdb=" N GLN D 364 " --> pdb=" O VAL D 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 630 through 633 removed outlier: 3.740A pdb=" N GLY D 599 " --> pdb=" O THR D 712 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 759 " --> pdb=" O SER D 600 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 698 through 700 Processing sheet with id=AC3, first strand: chain 'D' and resid 792 through 795 removed outlier: 6.881A pdb=" N GLU D 792 " --> pdb=" O ILE D 844 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU D 846 " --> pdb=" O GLU D 792 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N HIS D 794 " --> pdb=" O LEU D 846 " (cutoff:3.500A) removed outlier: 9.102A pdb=" N VAL D 848 " --> pdb=" O HIS D 794 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 165 through 167 removed outlier: 6.076A pdb=" N ARG E 236 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE E 276 " --> pdb=" O ARG E 236 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU E 238 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP E 278 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N LEU E 240 " --> pdb=" O ASP E 278 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA E 313 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR E 314 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LEU E 204 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN E 334 " --> pdb=" O ASN E 201 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL E 203 " --> pdb=" O GLN E 334 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 364 through 365 removed outlier: 6.922A pdb=" N GLN E 364 " --> pdb=" O VAL E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 630 through 633 removed outlier: 6.718A pdb=" N SER E 600 " --> pdb=" O GLU E 759 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL E 761 " --> pdb=" O SER E 600 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU E 602 " --> pdb=" O VAL E 761 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 698 through 700 Processing sheet with id=AC8, first strand: chain 'E' and resid 792 through 793 removed outlier: 6.570A pdb=" N GLU E 792 " --> pdb=" O ILE E 844 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 847 through 848 Processing sheet with id=AD1, first strand: chain 'F' and resid 165 through 167 removed outlier: 6.429A pdb=" N ARG F 236 " --> pdb=" O ILE F 274 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N PHE F 276 " --> pdb=" O ARG F 236 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU F 238 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP F 278 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU F 240 " --> pdb=" O ASP F 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 364 through 365 removed outlier: 7.139A pdb=" N GLN F 364 " --> pdb=" O VAL F 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 599 through 604 removed outlier: 3.727A pdb=" N GLY F 599 " --> pdb=" O THR F 712 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE F 601 " --> pdb=" O VAL F 714 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL F 630 " --> pdb=" O LEU F 675 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 677 " --> pdb=" O VAL F 630 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE F 632 " --> pdb=" O ASP F 677 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 699 through 700 Processing sheet with id=AD5, first strand: chain 'F' and resid 792 through 795 removed outlier: 6.903A pdb=" N GLU F 792 " --> pdb=" O ILE F 844 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU F 846 " --> pdb=" O GLU F 792 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS F 794 " --> pdb=" O LEU F 846 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N VAL F 848 " --> pdb=" O HIS F 794 " (cutoff:3.500A) 1470 hydrogen bonds defined for protein. 4326 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: 5.73 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10263 1.36 - 1.51: 8656 1.51 - 1.65: 10184 1.65 - 1.80: 174 1.80 - 1.95: 20 Bond restraints: 29297 Sorted by residual: bond pdb=" CG1 ILE B 584 " pdb=" CD1 ILE B 584 " ideal model delta sigma weight residual 1.513 1.380 0.133 3.90e-02 6.57e+02 1.16e+01 bond pdb=" CG1 ILE D 584 " pdb=" CD1 ILE D 584 " ideal model delta sigma weight residual 1.513 1.381 0.132 3.90e-02 6.57e+02 1.15e+01 bond pdb=" CG1 ILE C 584 " pdb=" CD1 ILE C 584 " ideal model delta sigma weight residual 1.513 1.391 0.122 3.90e-02 6.57e+02 9.77e+00 bond pdb=" CB GLU B 752 " pdb=" CG GLU B 752 " ideal model delta sigma weight residual 1.520 1.430 0.090 3.00e-02 1.11e+03 8.97e+00 bond pdb=" CB PRO B 650 " pdb=" CG PRO B 650 " ideal model delta sigma weight residual 1.492 1.352 0.140 5.00e-02 4.00e+02 7.81e+00 ... (remaining 29292 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 38721 2.99 - 5.98: 781 5.98 - 8.97: 78 8.97 - 11.96: 9 11.96 - 14.95: 5 Bond angle restraints: 39594 Sorted by residual: angle pdb=" C LEU A 299 " pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 120.09 126.79 -6.70 1.25e+00 6.40e-01 2.87e+01 angle pdb=" C SER C 644 " pdb=" N ARG C 645 " pdb=" CA ARG C 645 " ideal model delta sigma weight residual 121.58 112.42 9.16 1.95e+00 2.63e-01 2.21e+01 angle pdb=" CB LYS B 199 " pdb=" CG LYS B 199 " pdb=" CD LYS B 199 " ideal model delta sigma weight residual 111.30 100.76 10.54 2.30e+00 1.89e-01 2.10e+01 angle pdb=" C ALA C 247 " pdb=" N GLY C 248 " pdb=" CA GLY C 248 " ideal model delta sigma weight residual 121.82 111.65 10.17 2.30e+00 1.89e-01 1.95e+01 angle pdb=" CA LEU D 646 " pdb=" CB LEU D 646 " pdb=" CG LEU D 646 " ideal model delta sigma weight residual 116.30 131.25 -14.95 3.50e+00 8.16e-02 1.82e+01 ... (remaining 39589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.36: 17624 26.36 - 52.72: 383 52.72 - 79.09: 52 79.09 - 105.45: 4 105.45 - 131.81: 2 Dihedral angle restraints: 18065 sinusoidal: 7643 harmonic: 10422 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 180.00 141.73 38.27 0 5.00e+00 4.00e-02 5.86e+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 300.00 168.19 131.81 1 2.00e+01 2.50e-03 4.00e+01 dihedral pdb=" CA ASP A 624 " pdb=" C ASP A 624 " pdb=" N SER A 625 " pdb=" CA SER A 625 " ideal model delta harmonic sigma weight residual -180.00 -148.79 -31.21 0 5.00e+00 4.00e-02 3.90e+01 ... (remaining 18062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3441 0.070 - 0.141: 928 0.141 - 0.211: 103 0.211 - 0.281: 4 0.281 - 0.351: 3 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 -2.28 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB VAL C 679 " pdb=" CA VAL C 679 " pdb=" CG1 VAL C 679 " pdb=" CG2 VAL C 679 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.71e+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 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4476 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 763 " 0.020 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 763 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE D 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE D 763 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 763 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 763 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE D 763 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 763 " 0.019 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE B 763 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE B 763 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 763 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 763 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 763 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE B 763 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 763 " 0.018 2.00e-02 2.50e+03 2.38e-02 9.88e+00 pdb=" CG PHE C 763 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 763 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE C 763 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 763 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE C 763 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE C 763 " 0.005 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 263 2.59 - 3.17: 23283 3.17 - 3.75: 44160 3.75 - 4.32: 62571 4.32 - 4.90: 103283 Nonbonded interactions: 233560 Sorted by model distance: nonbonded pdb=" O1B AGS D 902 " pdb="MG MG D 904 " model vdw 2.018 2.170 nonbonded pdb=" O2G AGS E1002 " pdb="MG MG E1003 " model vdw 2.024 2.170 nonbonded pdb=" OG1 THR E 612 " pdb="MG MG E1003 " model vdw 2.045 2.170 nonbonded pdb=" O1B AGS C1001 " pdb="MG MG C1003 " model vdw 2.062 2.170 nonbonded pdb=" O1B AGS D 901 " pdb="MG MG D 903 " model vdw 2.066 2.170 ... (remaining 233555 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.400 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 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 0.140 29305 Z= 0.454 Angle : 1.047 14.947 39594 Z= 0.565 Chirality : 0.061 0.351 4479 Planarity : 0.008 0.072 5168 Dihedral : 11.141 131.810 11341 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.17 % Allowed : 1.23 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.91 (0.11), residues: 3561 helix: -2.48 (0.08), residues: 1986 sheet: -2.65 (0.24), residues: 352 loop : -2.38 (0.16), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG C 351 TYR 0.039 0.003 TYR B 357 PHE 0.053 0.005 PHE D 763 TRP 0.038 0.006 TRP D 543 HIS 0.017 0.003 HIS F 747 Details of bonding type rmsd covalent geometry : bond 0.01126 (29297) covalent geometry : angle 1.04669 (39594) hydrogen bonds : bond 0.16835 ( 1470) hydrogen bonds : angle 8.11301 ( 4326) Misc. bond : bond 0.00795 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 912 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 LEU cc_start: 0.8601 (mt) cc_final: 0.8370 (tp) REVERT: A 700 THR cc_start: 0.8518 (m) cc_final: 0.8118 (p) REVERT: B 314 THR cc_start: 0.8952 (t) cc_final: 0.8618 (p) REVERT: B 399 SER cc_start: 0.8394 (m) cc_final: 0.8181 (p) REVERT: C 761 VAL cc_start: 0.9465 (m) cc_final: 0.8699 (p) REVERT: C 817 LEU cc_start: 0.8590 (tp) cc_final: 0.8140 (tp) REVERT: D 622 MET cc_start: 0.7406 (ttm) cc_final: 0.7139 (mtm) REVERT: D 677 ASP cc_start: 0.8076 (t0) cc_final: 0.7832 (t70) REVERT: E 277 ILE cc_start: 0.8599 (mt) cc_final: 0.8042 (pt) REVERT: E 293 MET cc_start: 0.3040 (tpt) cc_final: 0.2654 (tpt) REVERT: E 685 ASP cc_start: 0.7145 (p0) cc_final: 0.6281 (t0) REVERT: F 713 VAL cc_start: 0.5930 (t) cc_final: 0.5449 (t) outliers start: 5 outliers final: 0 residues processed: 916 average time/residue: 0.2287 time to fit residues: 307.6244 Evaluate side-chains 433 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN A 726 GLN A 770 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 195 GLN B 281 HIS B 297 ASN B 360 HIS B 692 GLN B 747 HIS ** B 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 849 ASN B 858 HIS C 195 GLN C 201 ASN C 297 ASN C 334 GLN C 421 GLN C 641 HIS C 688 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 GLN D 195 GLN D 641 HIS D 688 ASN D 692 GLN D 748 ASN D 806 ASN D 822 GLN E 192 GLN E 567 HIS E 641 HIS E 692 GLN E 703 GLN F 281 HIS ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS F 378 HIS F 573 GLN F 711 ASN F 726 GLN F 747 HIS F 794 HIS F 831 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084424 restraints weight = 73864.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.086803 restraints weight = 38565.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088369 restraints weight = 24672.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.089327 restraints weight = 18439.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089791 restraints weight = 15461.489| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29305 Z= 0.169 Angle : 0.731 14.048 39594 Z= 0.372 Chirality : 0.046 0.255 4479 Planarity : 0.006 0.061 5168 Dihedral : 9.621 100.839 4207 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.43 % Allowed : 10.97 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.97 (0.13), residues: 3561 helix: -0.69 (0.11), residues: 1995 sheet: -2.43 (0.24), residues: 368 loop : -1.73 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 645 TYR 0.023 0.002 TYR C 656 PHE 0.033 0.002 PHE D 729 TRP 0.009 0.002 TRP E 543 HIS 0.011 0.001 HIS F 378 Details of bonding type rmsd covalent geometry : bond 0.00367 (29297) covalent geometry : angle 0.73135 (39594) hydrogen bonds : bond 0.05111 ( 1470) hydrogen bonds : angle 5.92566 ( 4326) Misc. bond : bond 0.00193 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 491 time to evaluate : 0.984 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 562 MET cc_start: 0.4837 (tpp) cc_final: 0.3640 (tpp) REVERT: A 629 MET cc_start: 0.6386 (ptm) cc_final: 0.5802 (ppp) REVERT: A 700 THR cc_start: 0.9124 (m) cc_final: 0.8579 (p) REVERT: A 748 ASN cc_start: 0.8828 (m110) cc_final: 0.8507 (t0) REVERT: A 763 PHE cc_start: 0.3182 (OUTLIER) cc_final: 0.2968 (m-10) REVERT: B 326 ASP cc_start: 0.7910 (t0) cc_final: 0.7693 (t0) REVERT: B 562 MET cc_start: 0.8544 (tpt) cc_final: 0.7869 (ttt) REVERT: B 677 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: B 737 MET cc_start: 0.8857 (ttm) cc_final: 0.8579 (ttp) REVERT: B 784 LYS cc_start: 0.8838 (tmmt) cc_final: 0.8495 (tmmt) REVERT: B 826 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8286 (mp0) REVERT: C 186 GLU cc_start: 0.7749 (mp0) cc_final: 0.7466 (mp0) REVERT: C 413 ASP cc_start: 0.8261 (t0) cc_final: 0.7917 (t0) REVERT: C 453 ARG cc_start: 0.7733 (ttp80) cc_final: 0.7447 (ttp80) REVERT: C 644 SER cc_start: 0.9259 (m) cc_final: 0.9016 (p) REVERT: C 750 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6889 (mtm110) REVERT: D 424 LEU cc_start: 0.9131 (mt) cc_final: 0.8706 (tt) REVERT: D 562 MET cc_start: 0.8745 (tpt) cc_final: 0.8349 (tpt) REVERT: D 677 ASP cc_start: 0.8268 (t0) cc_final: 0.7962 (t70) REVERT: E 319 TYR cc_start: 0.7445 (t80) cc_final: 0.7138 (t80) REVERT: E 396 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7659 (mt-10) REVERT: E 644 SER cc_start: 0.8912 (m) cc_final: 0.8613 (p) REVERT: E 685 ASP cc_start: 0.8203 (p0) cc_final: 0.7678 (p0) REVERT: F 162 LYS cc_start: 0.7383 (mmmt) cc_final: 0.6894 (ptmm) REVERT: F 303 LEU cc_start: 0.8371 (pp) cc_final: 0.8101 (pp) REVERT: F 320 ARG cc_start: 0.8746 (ptm160) cc_final: 0.8250 (ptp-110) REVERT: F 575 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7905 (mt-10) REVERT: F 684 PRO cc_start: 0.7769 (Cg_exo) cc_final: 0.7532 (Cg_endo) outliers start: 73 outliers final: 43 residues processed: 537 average time/residue: 0.1898 time to fit residues: 160.4060 Evaluate side-chains 414 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 368 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 752 GLU Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 794 HIS Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 722 SER Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 752 GLU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 806 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 559 LEU Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain E residue 703 GLN Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 714 VAL Chi-restraints excluded: chain F residue 794 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 57 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 297 ASN A 567 HIS A 573 GLN A 719 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 GLN B 620 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 831 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 822 GLN D 748 ASN D 806 ASN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 574 ASN E 703 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 794 HIS F 858 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082947 restraints weight = 74585.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085115 restraints weight = 39701.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.086397 restraints weight = 23620.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086839 restraints weight = 18482.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.086735 restraints weight = 16699.849| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29305 Z= 0.161 Angle : 0.666 12.052 39594 Z= 0.336 Chirality : 0.044 0.211 4479 Planarity : 0.005 0.053 5168 Dihedral : 9.089 99.629 4207 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.79 % Allowed : 12.70 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.14), residues: 3561 helix: 0.06 (0.11), residues: 1998 sheet: -2.51 (0.22), residues: 415 loop : -1.50 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 645 TYR 0.022 0.001 TYR F 671 PHE 0.024 0.002 PHE D 729 TRP 0.013 0.001 TRP E 543 HIS 0.007 0.001 HIS F 794 Details of bonding type rmsd covalent geometry : bond 0.00359 (29297) covalent geometry : angle 0.66623 (39594) hydrogen bonds : bond 0.04679 ( 1470) hydrogen bonds : angle 5.56335 ( 4326) Misc. bond : bond 0.00263 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 380 time to evaluate : 0.998 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 293 MET cc_start: 0.6643 (mmm) cc_final: 0.6398 (mmm) REVERT: A 629 MET cc_start: 0.6529 (ptm) cc_final: 0.5748 (ppp) REVERT: A 700 THR cc_start: 0.9115 (m) cc_final: 0.8560 (p) REVERT: B 326 ASP cc_start: 0.7949 (t0) cc_final: 0.7703 (t0) REVERT: B 392 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7631 (t0) REVERT: B 562 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7959 (ttt) REVERT: B 700 THR cc_start: 0.8898 (m) cc_final: 0.8685 (m) REVERT: B 784 LYS cc_start: 0.8773 (tmmt) cc_final: 0.8412 (tmmt) REVERT: B 826 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8474 (mp0) REVERT: C 186 GLU cc_start: 0.7787 (mp0) cc_final: 0.7524 (mp0) REVERT: C 413 ASP cc_start: 0.8485 (t0) cc_final: 0.7984 (t0) REVERT: C 453 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7292 (ttp80) REVERT: C 562 MET cc_start: 0.8601 (ttt) cc_final: 0.7990 (ttt) REVERT: C 644 SER cc_start: 0.9300 (m) cc_final: 0.8982 (p) REVERT: C 700 THR cc_start: 0.9214 (m) cc_final: 0.8778 (p) REVERT: C 737 MET cc_start: 0.8208 (tpp) cc_final: 0.7947 (tpp) REVERT: C 750 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6908 (mtm110) REVERT: D 418 ARG cc_start: 0.8542 (mmm160) cc_final: 0.8295 (tpt90) REVERT: D 424 LEU cc_start: 0.9206 (mt) cc_final: 0.8766 (tt) REVERT: D 696 ASP cc_start: 0.7923 (t0) cc_final: 0.7721 (t70) REVERT: D 806 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7463 (t0) REVERT: E 318 GLU cc_start: 0.7415 (mp0) cc_final: 0.6630 (mp0) REVERT: E 396 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7704 (mt-10) REVERT: E 644 SER cc_start: 0.9035 (m) cc_final: 0.8793 (p) REVERT: E 656 TYR cc_start: 0.7514 (t80) cc_final: 0.7017 (t80) REVERT: E 685 ASP cc_start: 0.8266 (p0) cc_final: 0.7698 (p0) REVERT: F 217 GLU cc_start: 0.8279 (pt0) cc_final: 0.7823 (pt0) REVERT: F 240 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8351 (pp) REVERT: F 308 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8593 (tt) REVERT: F 320 ARG cc_start: 0.9016 (ptm160) cc_final: 0.8702 (ptm160) REVERT: F 575 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7918 (mt-10) REVERT: F 684 PRO cc_start: 0.7715 (Cg_exo) cc_final: 0.7500 (Cg_endo) outliers start: 84 outliers final: 45 residues processed: 432 average time/residue: 0.1823 time to fit residues: 125.6245 Evaluate side-chains 381 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 330 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 794 HIS Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 806 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 276 PHE Chi-restraints excluded: chain E residue 413 ASP Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 794 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 352 optimal weight: 0.0570 chunk 183 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN A 858 HIS B 159 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 421 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 748 ASN D 857 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN F 378 HIS F 794 HIS F 823 GLN F 858 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.080805 restraints weight = 74968.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083028 restraints weight = 40035.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084134 restraints weight = 23670.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084550 restraints weight = 18982.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084488 restraints weight = 17070.821| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29305 Z= 0.196 Angle : 0.660 11.514 39594 Z= 0.333 Chirality : 0.045 0.345 4479 Planarity : 0.005 0.062 5168 Dihedral : 8.817 100.358 4207 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.26 % Allowed : 13.53 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.84 (0.14), residues: 3561 helix: 0.38 (0.12), residues: 1998 sheet: -2.45 (0.22), residues: 424 loop : -1.28 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 645 TYR 0.020 0.002 TYR F 671 PHE 0.021 0.002 PHE D 729 TRP 0.013 0.001 TRP E 543 HIS 0.020 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00438 (29297) covalent geometry : angle 0.65963 (39594) hydrogen bonds : bond 0.04603 ( 1470) hydrogen bonds : angle 5.39176 ( 4326) Misc. bond : bond 0.00290 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 357 time to evaluate : 1.191 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 325 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8370 (mmtp) REVERT: A 329 LEU cc_start: 0.9309 (tp) cc_final: 0.9054 (tp) REVERT: A 629 MET cc_start: 0.6437 (ptm) cc_final: 0.5740 (ppp) REVERT: A 700 THR cc_start: 0.9145 (m) cc_final: 0.8557 (p) REVERT: B 325 LYS cc_start: 0.8798 (mptt) cc_final: 0.8497 (mmtm) REVERT: B 392 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7753 (t0) REVERT: B 562 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7947 (ttt) REVERT: B 784 LYS cc_start: 0.8833 (tmmt) cc_final: 0.8493 (tmmt) REVERT: C 186 GLU cc_start: 0.7833 (mp0) cc_final: 0.7518 (mp0) REVERT: C 379 ARG cc_start: 0.8569 (ttt180) cc_final: 0.8360 (mtp-110) REVERT: C 413 ASP cc_start: 0.8593 (t0) cc_final: 0.8080 (t0) REVERT: C 453 ARG cc_start: 0.7686 (ttp80) cc_final: 0.7323 (ttp80) REVERT: C 634 MET cc_start: 0.8171 (mmm) cc_final: 0.7709 (mmm) REVERT: C 644 SER cc_start: 0.9231 (m) cc_final: 0.9002 (p) REVERT: C 700 THR cc_start: 0.9203 (m) cc_final: 0.8758 (p) REVERT: C 750 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6995 (mtm110) REVERT: D 418 ARG cc_start: 0.8559 (mmm160) cc_final: 0.8310 (tpt90) REVERT: D 424 LEU cc_start: 0.9226 (mt) cc_final: 0.8781 (tt) REVERT: D 562 MET cc_start: 0.8861 (tpt) cc_final: 0.8506 (tpt) REVERT: D 696 ASP cc_start: 0.8019 (t0) cc_final: 0.7759 (t70) REVERT: E 396 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7840 (mt-10) REVERT: E 588 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6401 (ttm170) REVERT: E 685 ASP cc_start: 0.8293 (p0) cc_final: 0.7677 (p0) REVERT: F 178 ASP cc_start: 0.8194 (m-30) cc_final: 0.7969 (m-30) REVERT: F 217 GLU cc_start: 0.8225 (pt0) cc_final: 0.7864 (pt0) REVERT: F 320 ARG cc_start: 0.9098 (ptm160) cc_final: 0.8533 (ptp-110) REVERT: F 575 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7931 (mt-10) REVERT: F 717 THR cc_start: 0.9171 (m) cc_final: 0.8877 (p) outliers start: 98 outliers final: 60 residues processed: 425 average time/residue: 0.1782 time to fit residues: 122.5252 Evaluate side-chains 380 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 316 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 794 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 421 GLN Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 588 ARG Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 794 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 274 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 359 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 806 ASN C 195 GLN C 264 ASN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 426 GLN D 445 ASN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN E 361 HIS ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 641 HIS F 794 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075692 restraints weight = 76928.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.077358 restraints weight = 46719.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078534 restraints weight = 27500.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078651 restraints weight = 23955.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.078790 restraints weight = 21541.000| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 29305 Z= 0.359 Angle : 0.833 11.795 39594 Z= 0.421 Chirality : 0.050 0.251 4479 Planarity : 0.006 0.068 5168 Dihedral : 9.062 107.898 4207 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.82 % Allowed : 14.06 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.10 (0.14), residues: 3561 helix: 0.14 (0.11), residues: 2011 sheet: -2.51 (0.22), residues: 439 loop : -1.34 (0.19), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 645 TYR 0.018 0.003 TYR C 319 PHE 0.024 0.003 PHE B 729 TRP 0.022 0.002 TRP E 543 HIS 0.020 0.002 HIS C 641 Details of bonding type rmsd covalent geometry : bond 0.00808 (29297) covalent geometry : angle 0.83251 (39594) hydrogen bonds : bond 0.05531 ( 1470) hydrogen bonds : angle 5.73699 ( 4326) Misc. bond : bond 0.00425 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 319 time to evaluate : 1.106 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 622 MET cc_start: 0.7083 (ppp) cc_final: 0.6831 (ppp) REVERT: A 629 MET cc_start: 0.6855 (ptm) cc_final: 0.6445 (ppp) REVERT: A 737 MET cc_start: 0.7186 (tpp) cc_final: 0.6864 (tpp) REVERT: B 392 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7906 (t0) REVERT: B 710 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: B 784 LYS cc_start: 0.8953 (tmmt) cc_final: 0.8752 (tmmt) REVERT: C 186 GLU cc_start: 0.7838 (mp0) cc_final: 0.7574 (mp0) REVERT: C 413 ASP cc_start: 0.8810 (t0) cc_final: 0.8198 (t0) REVERT: C 453 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7295 (ttp80) REVERT: C 562 MET cc_start: 0.8850 (ttt) cc_final: 0.8202 (ttt) REVERT: C 634 MET cc_start: 0.8311 (mmm) cc_final: 0.7736 (mmm) REVERT: C 644 SER cc_start: 0.9442 (m) cc_final: 0.9180 (p) REVERT: C 700 THR cc_start: 0.9184 (m) cc_final: 0.8502 (p) REVERT: C 750 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7229 (mtm110) REVERT: D 424 LEU cc_start: 0.9221 (mt) cc_final: 0.8823 (tt) REVERT: D 562 MET cc_start: 0.9004 (tpt) cc_final: 0.8702 (tpt) REVERT: E 552 MET cc_start: 0.6886 (pmm) cc_final: 0.6472 (pmm) REVERT: E 588 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6504 (ttm170) REVERT: E 685 ASP cc_start: 0.8243 (p0) cc_final: 0.7872 (p0) REVERT: E 783 TYR cc_start: 0.8293 (m-80) cc_final: 0.8028 (m-80) REVERT: F 178 ASP cc_start: 0.8311 (m-30) cc_final: 0.8012 (m-30) REVERT: F 217 GLU cc_start: 0.8415 (pt0) cc_final: 0.8146 (pt0) REVERT: F 257 GLU cc_start: 0.8778 (tt0) cc_final: 0.8365 (tm-30) REVERT: F 293 MET cc_start: 0.3709 (tmm) cc_final: 0.2975 (tmm) REVERT: F 575 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7897 (mm-30) REVERT: F 737 MET cc_start: 0.6450 (tpt) cc_final: 0.5580 (mmp) REVERT: F 844 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7295 (mp) outliers start: 115 outliers final: 71 residues processed: 409 average time/residue: 0.1708 time to fit residues: 113.5553 Evaluate side-chains 368 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 292 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 195 GLN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 HIS Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 717 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 588 ARG 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 693 VAL Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 378 HIS Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 749 PHE Chi-restraints excluded: chain F residue 844 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 307 optimal weight: 8.9990 chunk 351 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 322 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 262 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 747 HIS C 195 GLN C 264 ASN C 641 HIS C 692 GLN C 747 HIS D 426 GLN D 445 ASN D 806 ASN D 822 GLN ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.103767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.078044 restraints weight = 75262.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080202 restraints weight = 40092.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.081626 restraints weight = 26074.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082508 restraints weight = 19781.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.082966 restraints weight = 16662.345| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29305 Z= 0.168 Angle : 0.658 18.319 39594 Z= 0.329 Chirality : 0.044 0.241 4479 Planarity : 0.005 0.067 5168 Dihedral : 8.714 105.894 4207 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.06 % Allowed : 15.66 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.63 (0.14), residues: 3561 helix: 0.55 (0.12), residues: 1999 sheet: -2.43 (0.22), residues: 425 loop : -1.16 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 258 TYR 0.022 0.002 TYR C 734 PHE 0.023 0.002 PHE D 729 TRP 0.010 0.001 TRP E 543 HIS 0.022 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00377 (29297) covalent geometry : angle 0.65803 (39594) hydrogen bonds : bond 0.04654 ( 1470) hydrogen bonds : angle 5.34775 ( 4326) Misc. bond : bond 0.00286 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 336 time to evaluate : 0.826 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 622 MET cc_start: 0.7245 (ppp) cc_final: 0.6935 (ppp) REVERT: A 629 MET cc_start: 0.6698 (ptm) cc_final: 0.6416 (ppp) REVERT: B 392 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7756 (t0) REVERT: B 562 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7941 (ttt) REVERT: B 710 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8023 (mtt90) REVERT: B 784 LYS cc_start: 0.8939 (tmmt) cc_final: 0.8733 (tmmt) REVERT: C 413 ASP cc_start: 0.8605 (t0) cc_final: 0.8086 (t0) REVERT: C 453 ARG cc_start: 0.7702 (ttp80) cc_final: 0.7350 (ttp80) REVERT: C 618 LEU cc_start: 0.9763 (OUTLIER) cc_final: 0.9159 (tt) REVERT: C 644 SER cc_start: 0.9249 (m) cc_final: 0.9030 (p) REVERT: C 645 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8655 (ptm160) REVERT: C 750 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7059 (mtm110) REVERT: D 424 LEU cc_start: 0.9116 (mt) cc_final: 0.8692 (tt) REVERT: D 562 MET cc_start: 0.8886 (tpt) cc_final: 0.8673 (tpt) REVERT: E 320 ARG cc_start: 0.8705 (ptm-80) cc_final: 0.8476 (ptm-80) REVERT: E 588 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6372 (ttm170) REVERT: E 685 ASP cc_start: 0.8285 (p0) cc_final: 0.7910 (p0) REVERT: E 783 TYR cc_start: 0.8172 (m-80) cc_final: 0.7905 (m-80) REVERT: E 822 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8410 (mm-40) REVERT: F 178 ASP cc_start: 0.8132 (m-30) cc_final: 0.7773 (m-30) REVERT: F 257 GLU cc_start: 0.8679 (tt0) cc_final: 0.8280 (tm-30) REVERT: F 575 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7844 (mm-30) REVERT: F 629 MET cc_start: 0.4709 (mtm) cc_final: 0.4450 (mtm) REVERT: F 737 MET cc_start: 0.6479 (tpt) cc_final: 0.5657 (mmp) REVERT: F 784 LYS cc_start: 0.8499 (pttm) cc_final: 0.8056 (ptmt) REVERT: F 844 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7012 (mp) outliers start: 92 outliers final: 65 residues processed: 403 average time/residue: 0.1764 time to fit residues: 115.3583 Evaluate side-chains 375 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 301 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 747 HIS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 588 ARG 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 692 GLN Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 844 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 293 optimal weight: 4.9990 chunk 108 optimal weight: 0.0270 chunk 7 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 259 optimal weight: 9.9990 chunk 350 optimal weight: 0.8980 chunk 352 optimal weight: 7.9990 chunk 298 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 692 GLN B 747 HIS C 264 ASN C 421 GLN C 747 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 822 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.104334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079392 restraints weight = 75452.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.080899 restraints weight = 47370.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082451 restraints weight = 27717.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.082617 restraints weight = 20641.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.082745 restraints weight = 19445.971| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29305 Z= 0.146 Angle : 0.644 18.426 39594 Z= 0.318 Chirality : 0.044 0.280 4479 Planarity : 0.005 0.066 5168 Dihedral : 8.493 103.699 4207 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.19 % Allowed : 16.19 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.37 (0.14), residues: 3561 helix: 0.75 (0.12), residues: 2000 sheet: -2.34 (0.22), residues: 434 loop : -1.00 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 710 TYR 0.019 0.001 TYR F 671 PHE 0.021 0.001 PHE D 729 TRP 0.007 0.001 TRP E 543 HIS 0.023 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00326 (29297) covalent geometry : angle 0.64436 (39594) hydrogen bonds : bond 0.04381 ( 1470) hydrogen bonds : angle 5.20917 ( 4326) Misc. bond : bond 0.00256 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 325 time to evaluate : 1.171 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 629 MET cc_start: 0.6671 (ptm) cc_final: 0.6427 (ppp) REVERT: A 737 MET cc_start: 0.7182 (tpp) cc_final: 0.6831 (tpt) REVERT: B 392 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7682 (t0) REVERT: B 562 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7967 (ttt) REVERT: B 641 HIS cc_start: 0.8979 (OUTLIER) cc_final: 0.8726 (p-80) REVERT: B 710 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8015 (mtt90) REVERT: B 784 LYS cc_start: 0.8929 (tmmt) cc_final: 0.8684 (tmmt) REVERT: C 413 ASP cc_start: 0.8714 (t0) cc_final: 0.8326 (t0) REVERT: C 453 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7358 (ttp80) REVERT: C 562 MET cc_start: 0.8875 (ttt) cc_final: 0.8390 (ttt) REVERT: C 644 SER cc_start: 0.9299 (m) cc_final: 0.9062 (p) REVERT: C 645 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8789 (ptm160) REVERT: C 750 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7025 (mtm110) REVERT: C 819 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.9116 (ptp90) REVERT: D 418 ARG cc_start: 0.8503 (mmm160) cc_final: 0.8224 (tpt90) REVERT: D 424 LEU cc_start: 0.9172 (mt) cc_final: 0.8755 (tt) REVERT: D 696 ASP cc_start: 0.7963 (t0) cc_final: 0.7647 (t70) REVERT: E 320 ARG cc_start: 0.8702 (ptm-80) cc_final: 0.8494 (ptm-80) REVERT: E 685 ASP cc_start: 0.8245 (p0) cc_final: 0.7864 (p0) REVERT: E 822 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8224 (mm-40) REVERT: F 178 ASP cc_start: 0.8158 (m-30) cc_final: 0.7899 (m-30) REVERT: F 257 GLU cc_start: 0.8700 (tt0) cc_final: 0.8296 (tm-30) REVERT: F 320 ARG cc_start: 0.9119 (ptm160) cc_final: 0.8523 (ptp-110) REVERT: F 575 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7682 (mm-30) REVERT: F 737 MET cc_start: 0.6542 (tpt) cc_final: 0.5653 (mmp) REVERT: F 784 LYS cc_start: 0.8559 (pttm) cc_final: 0.8109 (ptmt) REVERT: F 844 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7216 (mp) outliers start: 96 outliers final: 65 residues processed: 396 average time/residue: 0.1704 time to fit residues: 111.0167 Evaluate side-chains 371 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 297 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 692 GLN Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 819 ARG Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 633 ASP Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 844 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 70 optimal weight: 4.9990 chunk 300 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN A 692 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS B 747 HIS C 264 ASN C 692 GLN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 822 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.103387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078509 restraints weight = 76133.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.080955 restraints weight = 41073.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.081633 restraints weight = 23986.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.082079 restraints weight = 20579.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.082312 restraints weight = 18262.476| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29305 Z= 0.220 Angle : 0.701 17.592 39594 Z= 0.346 Chirality : 0.046 0.301 4479 Planarity : 0.005 0.067 5168 Dihedral : 8.522 104.558 4207 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.32 % Allowed : 16.66 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3561 helix: 0.69 (0.12), residues: 2007 sheet: -2.29 (0.23), residues: 429 loop : -1.09 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 756 TYR 0.018 0.002 TYR F 671 PHE 0.018 0.002 PHE C 729 TRP 0.013 0.001 TRP E 462 HIS 0.022 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00498 (29297) covalent geometry : angle 0.70119 (39594) hydrogen bonds : bond 0.04580 ( 1470) hydrogen bonds : angle 5.28153 ( 4326) Misc. bond : bond 0.00304 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 308 time to evaluate : 1.127 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: A 622 MET cc_start: 0.7128 (ppp) cc_final: 0.6493 (ppp) REVERT: A 629 MET cc_start: 0.6829 (ptm) cc_final: 0.6619 (ppp) REVERT: A 737 MET cc_start: 0.7196 (tpp) cc_final: 0.6984 (tpp) REVERT: A 757 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7951 (mm) REVERT: B 325 LYS cc_start: 0.8829 (mptt) cc_final: 0.8624 (mptt) REVERT: B 392 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7836 (t0) REVERT: B 562 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7949 (ttt) REVERT: B 641 HIS cc_start: 0.9008 (OUTLIER) cc_final: 0.8771 (p-80) REVERT: B 710 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: B 784 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8716 (tmmt) REVERT: C 186 GLU cc_start: 0.7987 (mp0) cc_final: 0.7640 (mp0) REVERT: C 413 ASP cc_start: 0.8695 (t0) cc_final: 0.8322 (t0) REVERT: C 453 ARG cc_start: 0.7771 (ttp80) cc_final: 0.7399 (ttp80) REVERT: C 562 MET cc_start: 0.8850 (ttt) cc_final: 0.8231 (ttt) REVERT: C 644 SER cc_start: 0.9261 (m) cc_final: 0.8998 (p) REVERT: C 645 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8681 (ptm160) REVERT: C 750 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7078 (mtm110) REVERT: D 418 ARG cc_start: 0.8533 (mmm160) cc_final: 0.8246 (tpt90) REVERT: D 424 LEU cc_start: 0.9144 (mt) cc_final: 0.8734 (tt) REVERT: E 320 ARG cc_start: 0.8729 (ptm-80) cc_final: 0.8493 (ptm-80) REVERT: E 685 ASP cc_start: 0.8246 (p0) cc_final: 0.7767 (p0) REVERT: E 822 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: F 257 GLU cc_start: 0.8791 (tt0) cc_final: 0.8368 (tm-30) REVERT: F 320 ARG cc_start: 0.9059 (ptm160) cc_final: 0.8496 (ptp-110) REVERT: F 575 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7767 (mm-30) REVERT: F 737 MET cc_start: 0.6558 (tpt) cc_final: 0.5876 (mmp) REVERT: F 784 LYS cc_start: 0.8592 (pttm) cc_final: 0.8155 (ptmt) REVERT: F 844 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7146 (mp) outliers start: 100 outliers final: 72 residues processed: 381 average time/residue: 0.1767 time to fit residues: 109.1027 Evaluate side-chains 370 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 289 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 710 ARG Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 795 ILE Chi-restraints excluded: chain D residue 806 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 760 VAL Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 844 ILE 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: 4.9990 chunk 6 optimal weight: 0.7980 chunk 294 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 291 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 344 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN C 360 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 822 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.104655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078926 restraints weight = 75253.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081099 restraints weight = 40066.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082359 restraints weight = 26094.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083366 restraints weight = 19947.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083823 restraints weight = 16765.372| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29305 Z= 0.139 Angle : 0.663 18.259 39594 Z= 0.323 Chirality : 0.044 0.307 4479 Planarity : 0.005 0.066 5168 Dihedral : 8.303 101.482 4207 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.66 % Allowed : 17.45 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 3561 helix: 0.87 (0.12), residues: 2006 sheet: -2.26 (0.23), residues: 437 loop : -0.97 (0.19), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 710 TYR 0.019 0.001 TYR F 671 PHE 0.021 0.001 PHE A 623 TRP 0.012 0.001 TRP E 462 HIS 0.023 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00312 (29297) covalent geometry : angle 0.66316 (39594) hydrogen bonds : bond 0.04233 ( 1470) hydrogen bonds : angle 5.10981 ( 4326) Misc. bond : bond 0.00250 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 329 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7232 (tpp) cc_final: 0.7011 (tpp) REVERT: A 757 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7827 (mm) REVERT: B 298 MET cc_start: 0.8615 (ttm) cc_final: 0.8412 (mtt) REVERT: B 392 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7689 (t0) REVERT: B 562 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7933 (ttt) REVERT: B 641 HIS cc_start: 0.8965 (OUTLIER) cc_final: 0.8729 (p-80) REVERT: B 784 LYS cc_start: 0.8857 (tmmt) cc_final: 0.8612 (tmmt) REVERT: C 186 GLU cc_start: 0.7866 (mp0) cc_final: 0.7602 (mp0) REVERT: C 264 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8462 (t0) REVERT: C 413 ASP cc_start: 0.8636 (t0) cc_final: 0.8204 (t0) REVERT: C 453 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7413 (ttp80) REVERT: C 562 MET cc_start: 0.8894 (ttt) cc_final: 0.8360 (ttt) REVERT: C 618 LEU cc_start: 0.9751 (OUTLIER) cc_final: 0.9504 (tt) REVERT: C 644 SER cc_start: 0.9159 (m) cc_final: 0.8957 (p) REVERT: C 645 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8806 (ptm160) REVERT: C 750 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.6872 (mtm110) REVERT: D 418 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8205 (tpt90) REVERT: D 424 LEU cc_start: 0.9111 (mt) cc_final: 0.8690 (tt) REVERT: D 696 ASP cc_start: 0.7931 (t0) cc_final: 0.7606 (t70) REVERT: E 685 ASP cc_start: 0.8269 (p0) cc_final: 0.7833 (p0) REVERT: E 822 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: F 257 GLU cc_start: 0.8733 (tt0) cc_final: 0.8309 (tm-30) REVERT: F 320 ARG cc_start: 0.8948 (ptm160) cc_final: 0.8632 (ptp-110) REVERT: F 562 MET cc_start: 0.7186 (ppp) cc_final: 0.6718 (ppp) REVERT: F 575 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7784 (mm-30) REVERT: F 634 MET cc_start: 0.2005 (tpp) cc_final: 0.1371 (tmm) REVERT: F 737 MET cc_start: 0.6506 (tpt) cc_final: 0.5803 (mmp) REVERT: F 784 LYS cc_start: 0.8594 (pttm) cc_final: 0.8179 (ptmt) REVERT: F 827 ASN cc_start: 0.8574 (m-40) cc_final: 0.8245 (m110) REVERT: F 844 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7146 (mp) outliers start: 80 outliers final: 57 residues processed: 387 average time/residue: 0.1750 time to fit residues: 110.8141 Evaluate side-chains 366 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 299 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 844 ILE 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: 0.8980 chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 353 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 320 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 ASN ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN D 822 GLN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 857 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.079459 restraints weight = 74826.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.081612 restraints weight = 39762.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083023 restraints weight = 25841.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.083788 restraints weight = 19497.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084442 restraints weight = 16609.790| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29305 Z= 0.139 Angle : 0.682 16.969 39594 Z= 0.330 Chirality : 0.044 0.321 4479 Planarity : 0.005 0.066 5168 Dihedral : 8.222 98.440 4207 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.46 % Allowed : 18.02 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 3561 helix: 0.99 (0.12), residues: 1999 sheet: -2.27 (0.23), residues: 421 loop : -0.96 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 710 TYR 0.052 0.001 TYR E 783 PHE 0.019 0.001 PHE D 729 TRP 0.011 0.001 TRP E 462 HIS 0.024 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00311 (29297) covalent geometry : angle 0.68175 (39594) hydrogen bonds : bond 0.04124 ( 1470) hydrogen bonds : angle 5.04120 ( 4326) Misc. bond : bond 0.00254 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7122 Ramachandran restraints generated. 3561 Oldfield, 0 Emsley, 3561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 324 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.7265 (tpp) cc_final: 0.7030 (tpp) REVERT: A 757 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7787 (mm) REVERT: B 552 MET cc_start: 0.7360 (tmm) cc_final: 0.7093 (tmm) REVERT: B 562 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7944 (ttt) REVERT: B 635 SER cc_start: 0.9096 (p) cc_final: 0.8791 (t) REVERT: B 641 HIS cc_start: 0.8948 (OUTLIER) cc_final: 0.8688 (p-80) REVERT: C 186 GLU cc_start: 0.7883 (mp0) cc_final: 0.7665 (mp0) REVERT: C 413 ASP cc_start: 0.8604 (t0) cc_final: 0.8198 (t0) REVERT: C 453 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7422 (ttp80) REVERT: C 562 MET cc_start: 0.8899 (ttt) cc_final: 0.8361 (ttt) REVERT: C 618 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9494 (tt) REVERT: C 645 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8725 (ptm160) REVERT: C 657 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7183 (tp30) REVERT: C 750 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.7009 (mtm110) REVERT: D 418 ARG cc_start: 0.8459 (mmm160) cc_final: 0.8175 (tpt90) REVERT: D 424 LEU cc_start: 0.9041 (mt) cc_final: 0.8620 (tt) REVERT: D 696 ASP cc_start: 0.7893 (t0) cc_final: 0.7571 (t70) REVERT: E 410 GLU cc_start: 0.8221 (pm20) cc_final: 0.8018 (pm20) REVERT: E 645 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.7936 (ttm-80) REVERT: E 685 ASP cc_start: 0.8286 (p0) cc_final: 0.7826 (p0) REVERT: E 737 MET cc_start: 0.7821 (tpp) cc_final: 0.7613 (tpp) REVERT: E 822 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8127 (mm-40) REVERT: F 257 GLU cc_start: 0.8702 (tt0) cc_final: 0.8265 (tm-30) REVERT: F 283 MET cc_start: 0.8148 (tpt) cc_final: 0.7676 (tpt) REVERT: F 562 MET cc_start: 0.7223 (ppp) cc_final: 0.6715 (ppp) REVERT: F 575 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7780 (mm-30) REVERT: F 634 MET cc_start: 0.2070 (tpp) cc_final: 0.1546 (tmm) REVERT: F 737 MET cc_start: 0.6372 (tpt) cc_final: 0.5673 (mmp) REVERT: F 784 LYS cc_start: 0.8594 (pttm) cc_final: 0.8180 (ptmt) REVERT: F 827 ASN cc_start: 0.8586 (m-40) cc_final: 0.8296 (m110) REVERT: F 844 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7042 (mp) outliers start: 74 outliers final: 60 residues processed: 378 average time/residue: 0.1741 time to fit residues: 107.3474 Evaluate side-chains 374 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 217 GLU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 618 LEU Chi-restraints excluded: chain C residue 633 ASP Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 715 ILE Chi-restraints excluded: chain D residue 760 VAL Chi-restraints excluded: chain D residue 761 VAL Chi-restraints excluded: chain D residue 806 ASN Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 403 MET Chi-restraints excluded: chain E residue 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 803 LEU Chi-restraints excluded: chain E residue 822 GLN Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 241 ASP Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 834 LEU Chi-restraints excluded: chain F residue 844 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 334 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 339 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 288 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 806 ASN ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.104740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.078986 restraints weight = 75846.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081173 restraints weight = 40475.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.082604 restraints weight = 26298.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.083406 restraints weight = 19899.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084050 restraints weight = 16888.180| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 29305 Z= 0.204 Angle : 0.827 59.191 39594 Z= 0.443 Chirality : 0.045 0.433 4479 Planarity : 0.005 0.149 5168 Dihedral : 8.215 98.189 4207 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.52 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3561 helix: 0.97 (0.12), residues: 2001 sheet: -2.26 (0.23), residues: 421 loop : -0.97 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG D 588 TYR 0.023 0.001 TYR E 783 PHE 0.019 0.001 PHE D 729 TRP 0.009 0.001 TRP E 462 HIS 0.023 0.001 HIS A 747 Details of bonding type rmsd covalent geometry : bond 0.00428 (29297) covalent geometry : angle 0.82694 (39594) hydrogen bonds : bond 0.04140 ( 1470) hydrogen bonds : angle 5.04424 ( 4326) Misc. bond : bond 0.00261 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4572.55 seconds wall clock time: 79 minutes 51.92 seconds (4791.92 seconds total)