Starting phenix.real_space_refine on Mon Sep 14 10:43:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qs8_4627/09_2026/6qs8_4627.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qs8_4627/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6qs8_4627/09_2026/6qs8_4627.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qs8_4627/09_2026/6qs8_4627.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qs8_4627/09_2026/6qs8_4627.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qs8_4627/09_2026/6qs8_4627.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qs8_4627/09_2026/6qs8_4627.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qs8_4627/09_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-2.2.1-6174/lib/python3.11/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: 6.49, per 1000 atoms: 0.22 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 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: 0.97 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: 6.03 Time building geometry restraints manager: 3.12 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: 17590 26.36 - 52.72: 333 52.72 - 79.09: 26 79.09 - 105.45: 4 105.45 - 131.81: 2 Dihedral angle restraints: 17955 sinusoidal: 7533 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 17952 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 26.890 Find NCS groups from input model: 0.970 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 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 : 10.417 131.810 11231 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/Z covalent geometry : bond 0.01126 / 0.45 (29297) covalent geometry : angle 1.04669 / 0.57 (39594) hydrogen bonds : bond 0.16835 / 11.25 ( 1470) hydrogen bonds : angle 8.11301 / 5.69 ( 4326) Misc. bond : bond 0.00795 / 0.36 ( 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 : 1.121 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: 0.2383 time to fit residues: 322.4735 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 : 1.053 ------------------------------------------------------------------------------- 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... A 281 HIS A 573 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN A 726 GLN A 764 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 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 726 GLN F 747 HIS F 794 HIS F 831 GLN F 849 ASN F 858 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.084485 restraints weight = 73935.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.086882 restraints weight = 38596.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088420 restraints weight = 24692.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089433 restraints weight = 18497.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.089917 restraints weight = 15438.352| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 29305 Z= 0.162 Angle : 0.733 14.244 39594 Z= 0.370 Chirality : 0.046 0.206 4479 Planarity : 0.006 0.061 5168 Dihedral : 7.583 102.755 4097 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.46 % Allowed : 10.64 % Favored : 86.90 % 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: -1.94 (0.13), residues: 3561 helix: -0.68 (0.11), residues: 1997 sheet: -2.46 (0.24), residues: 356 loop : -1.70 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 351 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/Z covalent geometry : bond 0.00357 / 0.16 (29297) covalent geometry : angle 0.73345 / 0.37 (39594) hydrogen bonds : bond 0.04998 / 3.41 ( 1470) hydrogen bonds : angle 5.90379 / 4.13 ( 4326) Misc. bond : bond 0.00180 / 0.08 ( 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 569 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 495 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 MET cc_start: 0.4832 (tpp) cc_final: 0.3644 (tpp) REVERT: A 629 MET cc_start: 0.6371 (ptm) cc_final: 0.5804 (ppp) REVERT: A 700 THR cc_start: 0.9124 (m) cc_final: 0.8580 (p) REVERT: A 748 ASN cc_start: 0.8817 (m110) cc_final: 0.8474 (t0) REVERT: A 763 PHE cc_start: 0.3272 (OUTLIER) cc_final: 0.3063 (m-10) REVERT: B 326 ASP cc_start: 0.7913 (t0) cc_final: 0.7689 (t0) REVERT: B 562 MET cc_start: 0.8534 (tpt) cc_final: 0.7854 (ttt) REVERT: B 677 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8527 (m-30) REVERT: B 737 MET cc_start: 0.8845 (ttm) cc_final: 0.8579 (ttp) REVERT: B 784 LYS cc_start: 0.8834 (tmmt) cc_final: 0.8633 (tmmt) REVERT: B 826 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8285 (mp0) REVERT: C 186 GLU cc_start: 0.7747 (mp0) cc_final: 0.7494 (mp0) REVERT: C 413 ASP cc_start: 0.8250 (t0) cc_final: 0.7910 (t0) REVERT: C 453 ARG cc_start: 0.7742 (ttp80) cc_final: 0.7438 (ttp80) REVERT: C 644 SER cc_start: 0.9242 (m) cc_final: 0.9021 (p) REVERT: C 750 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.6926 (mtm110) REVERT: D 424 LEU cc_start: 0.9125 (mt) cc_final: 0.8703 (tt) REVERT: D 562 MET cc_start: 0.8790 (tpt) cc_final: 0.8398 (tpt) REVERT: D 677 ASP cc_start: 0.8271 (t0) cc_final: 0.7942 (t70) REVERT: E 319 TYR cc_start: 0.7440 (t80) cc_final: 0.7154 (t80) REVERT: E 396 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7643 (mt-10) REVERT: E 644 SER cc_start: 0.8900 (m) cc_final: 0.8619 (p) REVERT: E 685 ASP cc_start: 0.8199 (p0) cc_final: 0.7691 (p0) REVERT: F 162 LYS cc_start: 0.7375 (mmmt) cc_final: 0.7007 (ptpt) REVERT: F 303 LEU cc_start: 0.8370 (pp) cc_final: 0.8103 (pp) REVERT: F 320 ARG cc_start: 0.8739 (ptm160) cc_final: 0.8218 (ptp-110) REVERT: F 575 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7874 (mt-10) REVERT: F 629 MET cc_start: 0.5592 (pmm) cc_final: 0.4663 (mtm) REVERT: F 684 PRO cc_start: 0.7760 (Cg_exo) cc_final: 0.7529 (Cg_endo) outliers start: 74 outliers final: 40 residues processed: 540 average time/residue: 0.1998 time to fit residues: 169.8093 Evaluate side-chains 417 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 374 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 MET 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 151 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 126 optimal weight: 0.0770 chunk 235 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 201 ASN A 297 ASN A 334 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 849 ASN B 159 GLN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS B 831 GLN C 195 GLN 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 574 ASN E 703 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 ASN F 858 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.110241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084445 restraints weight = 74343.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.086806 restraints weight = 37822.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087810 restraints weight = 22617.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088203 restraints weight = 18782.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088265 restraints weight = 16650.556| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29305 Z= 0.139 Angle : 0.652 12.577 39594 Z= 0.327 Chirality : 0.044 0.207 4479 Planarity : 0.005 0.053 5168 Dihedral : 7.163 101.027 4097 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.93 % Allowed : 12.43 % Favored : 84.64 % 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: -1.22 (0.14), residues: 3561 helix: 0.06 (0.11), residues: 1998 sheet: -2.57 (0.22), residues: 404 loop : -1.48 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 705 TYR 0.022 0.001 TYR F 671 PHE 0.023 0.002 PHE D 729 TRP 0.012 0.002 TRP E 543 HIS 0.005 0.001 HIS C 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (29297) covalent geometry : angle 0.65165 / 0.33 (39594) hydrogen bonds : bond 0.04555 / 3.11 ( 1470) hydrogen bonds : angle 5.51476 / 3.87 ( 4326) Misc. bond : bond 0.00247 / 0.12 ( 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 485 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 397 time to evaluate : 1.154 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 293 MET cc_start: 0.6562 (mmm) cc_final: 0.6329 (mmm) REVERT: A 629 MET cc_start: 0.6433 (ptm) cc_final: 0.5617 (ppp) REVERT: A 700 THR cc_start: 0.9128 (m) cc_final: 0.8514 (p) REVERT: B 325 LYS cc_start: 0.8789 (mptt) cc_final: 0.8494 (mmtm) REVERT: B 326 ASP cc_start: 0.7905 (t0) cc_final: 0.7662 (t0) REVERT: B 392 ASP cc_start: 0.8054 (OUTLIER) cc_final: 0.7585 (t0) REVERT: B 562 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7924 (ttt) REVERT: B 700 THR cc_start: 0.8881 (m) cc_final: 0.8669 (m) REVERT: B 737 MET cc_start: 0.8916 (ttm) cc_final: 0.8685 (ttp) REVERT: B 784 LYS cc_start: 0.8836 (tmmt) cc_final: 0.8393 (tmmt) REVERT: B 826 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8423 (mp0) REVERT: C 186 GLU cc_start: 0.7763 (mp0) cc_final: 0.7505 (mp0) REVERT: C 379 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8337 (mtp-110) REVERT: C 413 ASP cc_start: 0.8447 (t0) cc_final: 0.7954 (t0) REVERT: C 453 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7485 (ttp80) REVERT: C 562 MET cc_start: 0.8617 (ttt) cc_final: 0.7914 (ttt) REVERT: C 644 SER cc_start: 0.9238 (m) cc_final: 0.8948 (p) REVERT: C 700 THR cc_start: 0.9224 (m) cc_final: 0.8787 (p) REVERT: C 737 MET cc_start: 0.8180 (tpp) cc_final: 0.7912 (tpp) REVERT: C 750 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6850 (mtm110) REVERT: D 392 ASP cc_start: 0.7957 (m-30) cc_final: 0.7678 (t0) REVERT: D 418 ARG cc_start: 0.8512 (mmm160) cc_final: 0.8264 (tpt90) REVERT: D 424 LEU cc_start: 0.9170 (mt) cc_final: 0.8766 (tt) REVERT: D 696 ASP cc_start: 0.7898 (t0) cc_final: 0.7689 (t70) REVERT: D 806 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7419 (t0) REVERT: E 318 GLU cc_start: 0.7601 (mp0) cc_final: 0.6913 (mp0) REVERT: E 396 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7663 (mt-10) REVERT: E 644 SER cc_start: 0.8984 (m) cc_final: 0.8741 (p) REVERT: E 656 TYR cc_start: 0.7480 (t80) cc_final: 0.7113 (t80) REVERT: E 685 ASP cc_start: 0.8251 (p0) cc_final: 0.7733 (p0) REVERT: F 162 LYS cc_start: 0.7613 (mmmt) cc_final: 0.7115 (ptpt) REVERT: F 217 GLU cc_start: 0.8282 (pt0) cc_final: 0.7822 (pt0) REVERT: F 308 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8571 (tt) REVERT: F 575 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7934 (mt-10) REVERT: F 629 MET cc_start: 0.6256 (OUTLIER) cc_final: 0.5598 (mtm) REVERT: F 684 PRO cc_start: 0.7719 (Cg_exo) cc_final: 0.7516 (Cg_endo) outliers start: 88 outliers final: 44 residues processed: 450 average time/residue: 0.1868 time to fit residues: 135.1511 Evaluate side-chains 392 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 342 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 C residue 752 GLU 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 318 GLU 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 D residue 851 ASP 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 280 LEU 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 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 308 LEU Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 629 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 142 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 352 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 321 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 290 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 309 HIS A 360 HIS A 567 HIS ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 770 HIS ** A 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 HIS B 159 GLN B 620 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS C 321 GLN C 641 HIS ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 857 GLN ** E 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 378 HIS F 823 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079179 restraints weight = 75538.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.081374 restraints weight = 40062.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082761 restraints weight = 26053.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083686 restraints weight = 19688.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084193 restraints weight = 16614.453| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29305 Z= 0.234 Angle : 0.699 11.047 39594 Z= 0.352 Chirality : 0.046 0.369 4479 Planarity : 0.005 0.060 5168 Dihedral : 7.127 104.121 4097 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.49 % Allowed : 13.53 % Favored : 82.98 % 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: -0.86 (0.14), residues: 3561 helix: 0.35 (0.11), residues: 2000 sheet: -2.44 (0.22), residues: 423 loop : -1.27 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 756 TYR 0.019 0.002 TYR F 671 PHE 0.021 0.002 PHE D 729 TRP 0.015 0.001 TRP E 543 HIS 0.016 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (29297) covalent geometry : angle 0.69919 / 0.35 (39594) hydrogen bonds : bond 0.04784 / 3.29 ( 1470) hydrogen bonds : angle 5.43611 / 3.80 ( 4326) Misc. bond : bond 0.00333 / 0.15 ( 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 452 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 347 time to evaluate : 1.113 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 325 LYS cc_start: 0.8581 (mmtm) cc_final: 0.8374 (mmtp) REVERT: A 329 LEU cc_start: 0.9365 (tp) cc_final: 0.9104 (tp) REVERT: A 629 MET cc_start: 0.6463 (ptm) cc_final: 0.5907 (ppp) REVERT: A 700 THR cc_start: 0.9146 (m) cc_final: 0.8557 (p) REVERT: B 325 LYS cc_start: 0.8758 (mptt) cc_final: 0.8468 (mmtm) REVERT: B 392 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7790 (t0) REVERT: B 562 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7875 (ttt) REVERT: B 737 MET cc_start: 0.8956 (ttm) cc_final: 0.8726 (ttp) REVERT: B 784 LYS cc_start: 0.8891 (tmmt) cc_final: 0.8554 (tmmt) REVERT: C 186 GLU cc_start: 0.7840 (mp0) cc_final: 0.7540 (mp0) REVERT: C 379 ARG cc_start: 0.8593 (ttt180) cc_final: 0.8333 (mtp-110) REVERT: C 413 ASP cc_start: 0.8551 (t0) cc_final: 0.8025 (t0) REVERT: C 453 ARG cc_start: 0.7687 (ttp80) cc_final: 0.7300 (ttp80) REVERT: C 634 MET cc_start: 0.8270 (mmm) cc_final: 0.7829 (mmm) REVERT: C 644 SER cc_start: 0.9371 (m) cc_final: 0.9080 (p) REVERT: C 700 THR cc_start: 0.9223 (m) cc_final: 0.8757 (p) REVERT: C 750 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7011 (mtm110) REVERT: D 418 ARG cc_start: 0.8549 (mmm160) cc_final: 0.8275 (tpt90) REVERT: D 424 LEU cc_start: 0.9129 (mt) cc_final: 0.8678 (tt) REVERT: D 562 MET cc_start: 0.8893 (tpt) cc_final: 0.8543 (tpt) REVERT: D 696 ASP cc_start: 0.8096 (t0) cc_final: 0.7826 (t70) REVERT: E 329 LEU cc_start: 0.8944 (tp) cc_final: 0.8729 (tp) REVERT: E 396 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7919 (mt-10) REVERT: E 588 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6477 (ttm170) REVERT: E 685 ASP cc_start: 0.8241 (p0) cc_final: 0.7736 (p0) REVERT: F 217 GLU cc_start: 0.8095 (pt0) cc_final: 0.7754 (pt0) REVERT: F 293 MET cc_start: 0.2784 (OUTLIER) cc_final: 0.2260 (tmm) REVERT: F 575 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7894 (mm-30) REVERT: F 629 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5968 (mtm) REVERT: F 737 MET cc_start: 0.6083 (tpt) cc_final: 0.5108 (ttt) outliers start: 105 outliers final: 62 residues processed: 417 average time/residue: 0.1805 time to fit residues: 122.5583 Evaluate side-chains 376 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 308 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 696 ASP 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 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 642 SER 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 C residue 822 GLN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 318 GLU 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 644 SER 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 744 VAL 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 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 275 LEU Chi-restraints excluded: chain F residue 293 MET 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 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 749 PHE 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: 9.9990 chunk 56 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 359 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 806 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS C 692 GLN ** C 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN D 692 GLN E 427 GLN F 378 HIS F 641 HIS F 858 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.105059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079912 restraints weight = 75253.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081724 restraints weight = 43136.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.082895 restraints weight = 25057.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.083074 restraints weight = 21175.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.083185 restraints weight = 19306.666| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 29305 Z= 0.203 Angle : 0.661 12.150 39594 Z= 0.331 Chirality : 0.045 0.227 4479 Planarity : 0.005 0.064 5168 Dihedral : 7.043 105.293 4097 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.12 % Allowed : 14.73 % Favored : 82.15 % 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 (0.11), residues: 2004 sheet: -2.35 (0.22), residues: 434 loop : -1.20 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 645 TYR 0.017 0.002 TYR F 671 PHE 0.022 0.002 PHE D 729 TRP 0.014 0.001 TRP E 543 HIS 0.021 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (29297) covalent geometry : angle 0.66054 / 0.33 (39594) hydrogen bonds : bond 0.04576 / 3.14 ( 1470) hydrogen bonds : angle 5.32292 / 3.72 ( 4326) Misc. bond : bond 0.00310 / 0.14 ( 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: 94 poor density : 340 time to evaluate : 1.165 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: 0.4812 (tpp) cc_final: 0.3887 (tpp) REVERT: A 566 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7890 (mm) REVERT: A 622 MET cc_start: 0.7026 (ppp) cc_final: 0.6712 (ppp) REVERT: A 629 MET cc_start: 0.6467 (ptm) cc_final: 0.5982 (ppp) REVERT: A 737 MET cc_start: 0.7117 (tpp) cc_final: 0.6731 (tpt) REVERT: B 392 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7723 (t0) REVERT: B 562 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7922 (ttt) REVERT: B 710 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8003 (mtt90) REVERT: B 737 MET cc_start: 0.8994 (ttm) cc_final: 0.8715 (ttp) REVERT: C 186 GLU cc_start: 0.7845 (mp0) cc_final: 0.7566 (mp0) REVERT: C 413 ASP cc_start: 0.8730 (t0) cc_final: 0.8257 (t0) REVERT: C 453 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7333 (ttp80) REVERT: C 562 MET cc_start: 0.8749 (ttt) cc_final: 0.8059 (ttt) REVERT: C 634 MET cc_start: 0.8283 (mmm) cc_final: 0.7708 (mmm) REVERT: C 644 SER cc_start: 0.9343 (m) cc_final: 0.9081 (p) REVERT: C 700 THR cc_start: 0.9178 (m) cc_final: 0.8639 (p) REVERT: C 750 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7061 (mtm110) REVERT: D 418 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8239 (tpt90) REVERT: D 424 LEU cc_start: 0.9204 (mt) cc_final: 0.8767 (tt) REVERT: D 562 MET cc_start: 0.8875 (tpt) cc_final: 0.8587 (tpt) REVERT: D 696 ASP cc_start: 0.8024 (t0) cc_final: 0.7712 (t70) REVERT: E 588 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6682 (ttm170) REVERT: E 685 ASP cc_start: 0.8283 (p0) cc_final: 0.8016 (p0) REVERT: F 217 GLU cc_start: 0.8263 (pt0) cc_final: 0.7925 (pt0) REVERT: F 257 GLU cc_start: 0.8729 (tt0) cc_final: 0.8329 (tm-30) REVERT: F 320 ARG cc_start: 0.9112 (ptm160) cc_final: 0.8890 (ptm160) REVERT: F 337 PHE cc_start: 0.7635 (t80) cc_final: 0.7398 (t80) REVERT: F 575 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7809 (mm-30) REVERT: F 629 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6215 (mtm) REVERT: F 737 MET cc_start: 0.6196 (tpt) cc_final: 0.5336 (mmp) REVERT: F 844 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7216 (mp) outliers start: 94 outliers final: 61 residues processed: 404 average time/residue: 0.1768 time to fit residues: 116.1904 Evaluate side-chains 372 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 303 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 566 LEU Chi-restraints excluded: chain A residue 571 ILE 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 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 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 548 VAL Chi-restraints excluded: chain C residue 580 VAL 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 C residue 754 ILE Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 779 LEU Chi-restraints excluded: chain C residue 822 GLN 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 318 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 641 HIS Chi-restraints excluded: chain D residue 644 SER 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 318 GLU 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 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 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 719 ASN 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: 6.9990 chunk 351 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 299 optimal weight: 0.0870 chunk 96 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS C 264 ASN C 421 GLN C 641 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.105093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.079793 restraints weight = 75238.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082458 restraints weight = 39752.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.083005 restraints weight = 23523.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.083591 restraints weight = 19134.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083637 restraints weight = 17444.848| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29305 Z= 0.173 Angle : 0.642 18.269 39594 Z= 0.318 Chirality : 0.044 0.238 4479 Planarity : 0.005 0.065 5168 Dihedral : 6.961 104.923 4097 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.36 % Allowed : 15.29 % Favored : 81.35 % 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: -0.42 (0.14), residues: 3561 helix: 0.74 (0.12), residues: 1998 sheet: -2.37 (0.22), residues: 424 loop : -1.11 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 645 TYR 0.018 0.002 TYR C 734 PHE 0.020 0.002 PHE D 729 TRP 0.010 0.001 TRP E 543 HIS 0.019 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (29297) covalent geometry : angle 0.64162 / 0.32 (39594) hydrogen bonds : bond 0.04395 / 3.01 ( 1470) hydrogen bonds : angle 5.22053 / 3.64 ( 4326) Misc. bond : bond 0.00294 / 0.13 ( 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 435 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 334 time to evaluate : 1.158 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 562 MET cc_start: 0.4803 (tpp) cc_final: 0.3884 (tpp) REVERT: A 566 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7902 (mm) REVERT: A 621 PHE cc_start: 0.7181 (m-10) cc_final: 0.6973 (m-10) REVERT: A 627 GLU cc_start: 0.7720 (pm20) cc_final: 0.7428 (pp20) REVERT: A 629 MET cc_start: 0.6495 (ptm) cc_final: 0.6143 (ppp) REVERT: B 325 LYS cc_start: 0.8585 (mptt) cc_final: 0.8223 (mmtm) REVERT: B 392 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7610 (t0) REVERT: B 710 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8032 (mtt90) REVERT: B 737 MET cc_start: 0.8953 (ttm) cc_final: 0.8672 (ttp) REVERT: C 413 ASP cc_start: 0.8752 (t0) cc_final: 0.8300 (t0) REVERT: C 453 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7452 (ttp80) REVERT: C 634 MET cc_start: 0.8232 (mmm) cc_final: 0.7618 (mmm) REVERT: C 645 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8654 (ptm160) REVERT: C 646 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8549 (pp) REVERT: C 700 THR cc_start: 0.9152 (m) cc_final: 0.8579 (p) REVERT: C 737 MET cc_start: 0.8367 (tpp) cc_final: 0.8127 (tpp) REVERT: C 750 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6971 (mtm110) REVERT: D 418 ARG cc_start: 0.8480 (mmm160) cc_final: 0.8216 (tpt90) REVERT: D 424 LEU cc_start: 0.9170 (mt) cc_final: 0.8739 (tt) REVERT: D 562 MET cc_start: 0.8810 (tpt) cc_final: 0.8589 (tpt) REVERT: D 696 ASP cc_start: 0.8028 (t0) cc_final: 0.7730 (t70) REVERT: E 588 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6478 (ttm170) REVERT: E 685 ASP cc_start: 0.8264 (p0) cc_final: 0.7978 (p0) REVERT: F 217 GLU cc_start: 0.8365 (pt0) cc_final: 0.8042 (pt0) REVERT: F 257 GLU cc_start: 0.8719 (tt0) cc_final: 0.8315 (tm-30) REVERT: F 293 MET cc_start: 0.3756 (tmm) cc_final: 0.3523 (tmm) REVERT: F 337 PHE cc_start: 0.7663 (t80) cc_final: 0.7402 (t80) REVERT: F 575 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7800 (mm-30) REVERT: F 629 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.6185 (mtm) REVERT: F 634 MET cc_start: 0.1814 (tpp) cc_final: 0.1565 (tpp) REVERT: F 737 MET cc_start: 0.6477 (tpt) cc_final: 0.5647 (mmp) REVERT: F 844 ILE cc_start: 0.7647 (OUTLIER) cc_final: 0.7193 (mp) outliers start: 101 outliers final: 64 residues processed: 407 average time/residue: 0.1905 time to fit residues: 125.7230 Evaluate side-chains 372 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 299 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE 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 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 710 ARG Chi-restraints excluded: chain B residue 712 THR Chi-restraints excluded: chain B residue 716 MET 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 641 HIS Chi-restraints excluded: chain C residue 645 ARG Chi-restraints excluded: chain C residue 646 LEU 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 C residue 822 GLN 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 318 GLU 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 644 SER 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 318 GLU 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 656 TYR Chi-restraints excluded: chain E residue 692 GLN Chi-restraints excluded: chain E residue 803 LEU 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 615 CYS Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 741 VAL 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: 10.0000 chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 350 optimal weight: 3.9990 chunk 352 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 187 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 747 HIS C 421 GLN C 641 HIS C 692 GLN C 794 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.103533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078279 restraints weight = 76071.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.080896 restraints weight = 40888.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081312 restraints weight = 24045.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.081900 restraints weight = 20873.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.081942 restraints weight = 18089.053| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29305 Z= 0.211 Angle : 0.673 16.589 39594 Z= 0.335 Chirality : 0.045 0.212 4479 Planarity : 0.005 0.066 5168 Dihedral : 7.020 106.210 4097 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.49 % Allowed : 15.72 % Favored : 80.78 % 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: -0.42 (0.14), residues: 3561 helix: 0.75 (0.12), residues: 2008 sheet: -2.36 (0.22), residues: 426 loop : -1.12 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 710 TYR 0.017 0.002 TYR F 671 PHE 0.018 0.002 PHE D 729 TRP 0.012 0.001 TRP E 462 HIS 0.008 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.21 (29297) covalent geometry : angle 0.67315 / 0.33 (39594) hydrogen bonds : bond 0.04493 / 3.07 ( 1470) hydrogen bonds : angle 5.24488 / 3.67 ( 4326) Misc. bond : bond 0.00322 / 0.15 ( 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 412 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 307 time to evaluate : 1.002 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 217 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 562 MET cc_start: 0.4852 (tpp) cc_final: 0.3996 (tpp) REVERT: A 566 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7921 (mm) REVERT: A 627 GLU cc_start: 0.7775 (pm20) cc_final: 0.7461 (pp20) REVERT: A 629 MET cc_start: 0.6714 (ptm) cc_final: 0.6466 (ppp) REVERT: A 737 MET cc_start: 0.7151 (tpp) cc_final: 0.6813 (tpt) REVERT: B 392 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7840 (t0) REVERT: B 562 MET cc_start: 0.8317 (ttm) cc_final: 0.7594 (ttt) REVERT: B 633 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.8212 (t70) REVERT: B 641 HIS cc_start: 0.8945 (OUTLIER) cc_final: 0.8693 (p-80) REVERT: B 710 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8040 (mtt90) REVERT: B 737 MET cc_start: 0.8958 (ttm) cc_final: 0.8674 (ttp) REVERT: C 413 ASP cc_start: 0.8808 (t0) cc_final: 0.8393 (t0) REVERT: C 453 ARG cc_start: 0.7740 (ttp80) cc_final: 0.7376 (ttp80) REVERT: C 645 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8686 (ptm160) REVERT: C 700 THR cc_start: 0.9205 (m) cc_final: 0.8614 (p) REVERT: C 737 MET cc_start: 0.8424 (tpp) cc_final: 0.8149 (tpp) REVERT: C 750 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.6982 (mtm110) REVERT: D 418 ARG cc_start: 0.8526 (mmm160) cc_final: 0.8253 (tpt90) REVERT: D 424 LEU cc_start: 0.9171 (mt) cc_final: 0.8738 (tt) REVERT: D 822 GLN cc_start: 0.8677 (tt0) cc_final: 0.8367 (mm-40) REVERT: E 320 ARG cc_start: 0.8770 (ptm-80) cc_final: 0.8558 (ptm-80) REVERT: E 588 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6446 (ttm170) REVERT: E 685 ASP cc_start: 0.8267 (p0) cc_final: 0.7856 (p0) REVERT: F 257 GLU cc_start: 0.8714 (tt0) cc_final: 0.8304 (tm-30) REVERT: F 293 MET cc_start: 0.4213 (tmm) cc_final: 0.3993 (tmm) REVERT: F 320 ARG cc_start: 0.9114 (ptm160) cc_final: 0.8565 (ptp-110) REVERT: F 575 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7883 (mm-30) REVERT: F 629 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6192 (mtm) REVERT: F 737 MET cc_start: 0.6637 (tpt) cc_final: 0.5874 (mmp) REVERT: F 844 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7273 (mp) outliers start: 105 outliers final: 74 residues processed: 383 average time/residue: 0.1899 time to fit residues: 118.3603 Evaluate side-chains 373 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 288 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 566 LEU Chi-restraints excluded: chain A residue 571 ILE 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 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 633 ASP 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 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 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 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 641 HIS Chi-restraints excluded: chain C residue 642 SER Chi-restraints excluded: chain C residue 645 ARG 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 C residue 822 GLN 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 318 GLU 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 644 SER 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 280 LEU Chi-restraints excluded: chain E residue 318 GLU 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 644 SER 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 760 VAL Chi-restraints excluded: chain E residue 803 LEU 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 403 MET Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 761 VAL Chi-restraints excluded: chain F residue 834 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: 0.7980 chunk 300 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 328 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 203 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 HIS ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS C 641 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.105311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.080354 restraints weight = 74793.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.082994 restraints weight = 39648.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083531 restraints weight = 23256.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084054 restraints weight = 19888.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084115 restraints weight = 17113.769| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29305 Z= 0.131 Angle : 0.629 17.620 39594 Z= 0.310 Chirality : 0.043 0.245 4479 Planarity : 0.004 0.065 5168 Dihedral : 6.867 104.304 4097 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.86 % Allowed : 16.62 % Favored : 80.52 % 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: -0.16 (0.14), residues: 3561 helix: 0.95 (0.12), residues: 1993 sheet: -2.28 (0.22), residues: 433 loop : -0.96 (0.19), residues: 1135 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 0.019 0.001 PHE A 623 TRP 0.011 0.001 TRP E 462 HIS 0.016 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (29297) covalent geometry : angle 0.62895 / 0.31 (39594) hydrogen bonds : bond 0.04133 / 2.81 ( 1470) hydrogen bonds : angle 5.07851 / 3.54 ( 4326) Misc. bond : bond 0.00261 / 0.12 ( 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 414 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 328 time to evaluate : 1.037 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 242 MET cc_start: 0.8133 (mtm) cc_final: 0.7931 (mtm) REVERT: A 562 MET cc_start: 0.4716 (tpp) cc_final: 0.3991 (tpp) REVERT: A 566 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 622 MET cc_start: 0.7051 (ppp) cc_final: 0.6762 (ppp) REVERT: A 627 GLU cc_start: 0.7813 (pm20) cc_final: 0.7562 (pp20) REVERT: A 629 MET cc_start: 0.6612 (ptm) cc_final: 0.6380 (ppp) REVERT: A 737 MET cc_start: 0.7152 (tpp) cc_final: 0.6837 (tpt) REVERT: B 325 LYS cc_start: 0.8651 (mptt) cc_final: 0.8356 (mmtm) REVERT: B 392 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7715 (t0) REVERT: B 562 MET cc_start: 0.8269 (ttm) cc_final: 0.7378 (ttt) REVERT: B 633 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8105 (t70) REVERT: B 641 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.8626 (p-80) REVERT: B 737 MET cc_start: 0.8958 (ttm) cc_final: 0.8630 (ttp) REVERT: C 186 GLU cc_start: 0.7899 (mp0) cc_final: 0.7536 (mp0) REVERT: C 408 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7961 (mttp) REVERT: C 413 ASP cc_start: 0.8761 (t0) cc_final: 0.8336 (t0) REVERT: C 453 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7467 (ttp80) REVERT: C 562 MET cc_start: 0.8893 (ttt) cc_final: 0.8239 (ttt) REVERT: C 645 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8726 (ptm160) REVERT: C 700 THR cc_start: 0.9174 (m) cc_final: 0.8656 (p) REVERT: C 737 MET cc_start: 0.8390 (tpp) cc_final: 0.8113 (tpp) REVERT: C 750 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6930 (mtm110) REVERT: D 418 ARG cc_start: 0.8479 (mmm160) cc_final: 0.8222 (tpt90) REVERT: D 424 LEU cc_start: 0.9195 (mt) cc_final: 0.8767 (tt) REVERT: D 822 GLN cc_start: 0.8624 (tt0) cc_final: 0.8318 (mm-40) REVERT: E 293 MET cc_start: 0.2118 (tpp) cc_final: 0.1821 (tpp) REVERT: E 685 ASP cc_start: 0.8262 (p0) cc_final: 0.7855 (p0) REVERT: E 737 MET cc_start: 0.7860 (tpp) cc_final: 0.7595 (tpp) REVERT: F 257 GLU cc_start: 0.8786 (tt0) cc_final: 0.8347 (tm-30) REVERT: F 305 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7866 (mmt90) REVERT: F 562 MET cc_start: 0.7118 (ppp) cc_final: 0.6647 (ppp) REVERT: F 575 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7805 (mm-30) REVERT: F 629 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.6095 (mtm) REVERT: F 737 MET cc_start: 0.6632 (tpt) cc_final: 0.5865 (mmp) REVERT: F 827 ASN cc_start: 0.8599 (m-40) cc_final: 0.8275 (m110) REVERT: F 844 ILE cc_start: 0.7697 (OUTLIER) cc_final: 0.7243 (mp) outliers start: 86 outliers final: 55 residues processed: 387 average time/residue: 0.1896 time to fit residues: 119.7991 Evaluate side-chains 372 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 543 TRP Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 571 ILE 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 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 633 ASP 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 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 284 VAL 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 750 ARG Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain C residue 822 GLN 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 538 GLU Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 641 HIS 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 638 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 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 336 VAL Chi-restraints excluded: chain F residue 543 TRP Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 719 ASN 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: 0.9980 chunk 6 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 291 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 344 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 189 optimal weight: 0.0050 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 726 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.081563 restraints weight = 74692.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083789 restraints weight = 40342.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.084767 restraints weight = 24359.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.085261 restraints weight = 19395.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085353 restraints weight = 16928.118| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29305 Z= 0.128 Angle : 0.638 17.118 39594 Z= 0.312 Chirality : 0.043 0.229 4479 Planarity : 0.004 0.065 5168 Dihedral : 6.757 101.909 4097 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.09 % Allowed : 17.69 % Favored : 80.22 % 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: -0.03 (0.14), residues: 3561 helix: 1.04 (0.12), residues: 2001 sheet: -2.20 (0.23), residues: 417 loop : -0.91 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 710 TYR 0.019 0.001 TYR F 671 PHE 0.018 0.001 PHE A 255 TRP 0.004 0.001 TRP C 462 HIS 0.007 0.001 HIS A 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (29297) covalent geometry : angle 0.63778 / 0.31 (39594) hydrogen bonds : bond 0.03991 / 2.72 ( 1470) hydrogen bonds : angle 4.96224 / 3.45 ( 4326) Misc. bond : bond 0.00253 / 0.12 ( 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 391 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 328 time to evaluate : 1.149 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: A 310 CYS cc_start: 0.8713 (t) cc_final: 0.8507 (p) REVERT: A 562 MET cc_start: 0.4693 (tpp) cc_final: 0.4002 (tpp) REVERT: A 566 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (mm) REVERT: A 622 MET cc_start: 0.7135 (ppp) cc_final: 0.6817 (ppp) REVERT: A 627 GLU cc_start: 0.7901 (pm20) cc_final: 0.7629 (pp20) REVERT: A 629 MET cc_start: 0.6643 (ptm) cc_final: 0.6414 (ppp) REVERT: A 737 MET cc_start: 0.7143 (tpp) cc_final: 0.6804 (tpt) REVERT: B 298 MET cc_start: 0.8668 (ttm) cc_final: 0.8428 (ttm) REVERT: B 325 LYS cc_start: 0.8662 (mptt) cc_final: 0.8360 (mmtm) REVERT: B 562 MET cc_start: 0.8350 (ttm) cc_final: 0.7537 (ttt) REVERT: B 633 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8104 (t70) REVERT: B 635 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8820 (t) REVERT: B 641 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8610 (p-80) REVERT: B 737 MET cc_start: 0.8966 (ttm) cc_final: 0.8641 (ttp) REVERT: C 186 GLU cc_start: 0.7896 (mp0) cc_final: 0.7584 (mp0) REVERT: C 413 ASP cc_start: 0.8789 (t0) cc_final: 0.8395 (t0) REVERT: C 453 ARG cc_start: 0.7807 (ttp80) cc_final: 0.7477 (ttp80) REVERT: C 562 MET cc_start: 0.8876 (ttt) cc_final: 0.8242 (ttt) REVERT: C 565 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7624 (tm-30) REVERT: C 700 THR cc_start: 0.9141 (m) cc_final: 0.8876 (p) REVERT: C 750 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6890 (mtm110) REVERT: D 418 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8191 (tpt90) REVERT: D 424 LEU cc_start: 0.9199 (mt) cc_final: 0.8756 (tt) REVERT: D 822 GLN cc_start: 0.8597 (tt0) cc_final: 0.8271 (mm-40) REVERT: E 551 MET cc_start: 0.4161 (ppp) cc_final: 0.3908 (ppp) REVERT: E 685 ASP cc_start: 0.8266 (p0) cc_final: 0.7828 (p0) REVERT: E 701 ASP cc_start: 0.8110 (p0) cc_final: 0.7695 (p0) REVERT: E 737 MET cc_start: 0.7930 (tpp) cc_final: 0.7655 (tpp) REVERT: F 178 ASP cc_start: 0.8212 (m-30) cc_final: 0.7813 (m-30) REVERT: F 257 GLU cc_start: 0.8795 (tt0) cc_final: 0.8311 (tm-30) REVERT: F 320 ARG cc_start: 0.8923 (ptm160) cc_final: 0.8486 (ptp-110) REVERT: F 562 MET cc_start: 0.7082 (ppp) cc_final: 0.6628 (ppp) REVERT: F 575 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7809 (mm-30) REVERT: F 629 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5592 (mtm) REVERT: F 737 MET cc_start: 0.6380 (tpt) cc_final: 0.5703 (mmp) REVERT: F 827 ASN cc_start: 0.8552 (m-40) cc_final: 0.8303 (m110) REVERT: F 844 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7275 (mp) outliers start: 63 outliers final: 49 residues processed: 371 average time/residue: 0.1919 time to fit residues: 116.3261 Evaluate side-chains 369 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 313 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 566 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 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 242 MET 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 679 VAL Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU Chi-restraints excluded: chain D residue 641 HIS 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 656 TYR Chi-restraints excluded: chain E residue 803 LEU 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 240 LEU 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 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 679 VAL Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 761 VAL 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: 7.9990 chunk 190 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 353 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 320 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 HIS C 688 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 857 GLN ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082717 restraints weight = 74612.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084718 restraints weight = 38912.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085654 restraints weight = 24495.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.086184 restraints weight = 19689.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086223 restraints weight = 16766.324| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29305 Z= 0.125 Angle : 0.635 17.275 39594 Z= 0.309 Chirality : 0.043 0.249 4479 Planarity : 0.004 0.064 5168 Dihedral : 6.704 99.971 4097 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.93 % Allowed : 17.69 % Favored : 80.39 % 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: 0.07 (0.14), residues: 3561 helix: 1.10 (0.12), residues: 2012 sheet: -2.12 (0.23), residues: 425 loop : -0.86 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 710 TYR 0.019 0.001 TYR F 671 PHE 0.019 0.001 PHE A 255 TRP 0.005 0.001 TRP C 462 HIS 0.009 0.001 HIS C 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (29297) covalent geometry : angle 0.63490 / 0.31 (39594) hydrogen bonds : bond 0.03893 / 2.65 ( 1470) hydrogen bonds : angle 4.89709 / 3.40 ( 4326) Misc. bond : bond 0.00218 / 0.10 ( 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 386 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 328 time to evaluate : 1.152 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: A 283 MET cc_start: 0.8158 (ppp) cc_final: 0.7955 (ptm) REVERT: A 562 MET cc_start: 0.4677 (tpp) cc_final: 0.4392 (tpp) REVERT: A 566 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 622 MET cc_start: 0.6922 (ppp) cc_final: 0.6591 (ppp) REVERT: A 627 GLU cc_start: 0.7905 (pm20) cc_final: 0.7662 (pp20) REVERT: A 629 MET cc_start: 0.6647 (ptm) cc_final: 0.6411 (ppp) REVERT: A 737 MET cc_start: 0.7222 (tpp) cc_final: 0.6899 (tpt) REVERT: B 298 MET cc_start: 0.8669 (ttm) cc_final: 0.8394 (ttm) REVERT: B 325 LYS cc_start: 0.8678 (mptt) cc_final: 0.8451 (mmtm) REVERT: B 562 MET cc_start: 0.8356 (ttm) cc_final: 0.7794 (ttm) REVERT: B 633 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.8119 (t70) REVERT: B 635 SER cc_start: 0.9098 (OUTLIER) cc_final: 0.8836 (t) REVERT: B 737 MET cc_start: 0.8953 (ttm) cc_final: 0.8619 (ttp) REVERT: C 186 GLU cc_start: 0.7880 (mp0) cc_final: 0.7635 (mp0) REVERT: C 413 ASP cc_start: 0.8764 (t0) cc_final: 0.8405 (t0) REVERT: C 453 ARG cc_start: 0.7818 (ttp80) cc_final: 0.7477 (ttp80) REVERT: C 562 MET cc_start: 0.8857 (ttt) cc_final: 0.8286 (ttt) REVERT: C 565 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 657 GLU cc_start: 0.7305 (tm-30) cc_final: 0.7096 (tp30) REVERT: C 700 THR cc_start: 0.9118 (m) cc_final: 0.8869 (p) REVERT: C 737 MET cc_start: 0.8704 (tpp) cc_final: 0.8496 (tpp) REVERT: C 750 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6906 (mtm110) REVERT: D 418 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8126 (tpt90) REVERT: D 424 LEU cc_start: 0.9207 (mt) cc_final: 0.8772 (tt) REVERT: D 701 ASP cc_start: 0.8629 (p0) cc_final: 0.8384 (p0) REVERT: D 822 GLN cc_start: 0.8569 (tt0) cc_final: 0.8236 (mm-40) REVERT: E 551 MET cc_start: 0.4105 (ppp) cc_final: 0.3894 (ppp) REVERT: E 701 ASP cc_start: 0.8094 (p0) cc_final: 0.7688 (p0) REVERT: E 737 MET cc_start: 0.7942 (tpp) cc_final: 0.7698 (tpp) REVERT: F 257 GLU cc_start: 0.8825 (tt0) cc_final: 0.8331 (tm-30) REVERT: F 320 ARG cc_start: 0.8976 (ptm160) cc_final: 0.8458 (ptp-110) REVERT: F 322 TYR cc_start: 0.8363 (m-80) cc_final: 0.8078 (m-10) REVERT: F 562 MET cc_start: 0.7204 (ppp) cc_final: 0.6783 (ppp) REVERT: F 575 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7819 (mm-30) REVERT: F 629 MET cc_start: 0.6191 (OUTLIER) cc_final: 0.5645 (mtm) REVERT: F 737 MET cc_start: 0.6473 (tpt) cc_final: 0.5837 (mmp) REVERT: F 844 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7257 (mp) outliers start: 58 outliers final: 47 residues processed: 370 average time/residue: 0.1850 time to fit residues: 111.8132 Evaluate side-chains 362 residues out of total 3026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 298 MET Chi-restraints excluded: chain A residue 566 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 560 LEU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 633 ASP Chi-restraints excluded: chain B residue 635 SER Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 242 MET 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 747 HIS Chi-restraints excluded: chain C residue 750 ARG Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 446 GLU Chi-restraints excluded: chain D residue 538 GLU 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 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 641 HIS Chi-restraints excluded: chain E residue 646 LEU Chi-restraints excluded: chain E residue 656 TYR Chi-restraints excluded: chain E residue 803 LEU 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 240 LEU 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 553 GLU Chi-restraints excluded: chain F residue 615 CYS Chi-restraints excluded: chain F residue 620 ASN Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain F residue 761 VAL 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: 6.9990 chunk 18 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 339 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 288 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 200 ASN A 334 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 747 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 747 HIS ** C 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN F 827 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078714 restraints weight = 76560.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.081073 restraints weight = 40004.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.081892 restraints weight = 24092.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.082246 restraints weight = 20206.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082299 restraints weight = 17657.102| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29305 Z= 0.225 Angle : 0.719 15.998 39594 Z= 0.355 Chirality : 0.046 0.264 4479 Planarity : 0.005 0.064 5168 Dihedral : 6.931 104.556 4097 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.23 % Allowed : 17.82 % Favored : 79.95 % 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: -0.07 (0.14), residues: 3561 helix: 1.01 (0.12), residues: 2003 sheet: -2.19 (0.23), residues: 429 loop : -0.93 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 710 TYR 0.020 0.002 TYR E 656 PHE 0.018 0.002 PHE A 255 TRP 0.014 0.001 TRP E 543 HIS 0.029 0.001 HIS C 747 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (29297) covalent geometry : angle 0.71861 / 0.36 (39594) hydrogen bonds : bond 0.04439 / 3.03 ( 1470) hydrogen bonds : angle 5.09636 / 3.54 ( 4326) Misc. bond : bond 0.00324 / 0.15 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4661.82 seconds wall clock time: 81 minutes 41.78 seconds (4901.78 seconds total)