Starting phenix.real_space_refine on Sat Mar 7 04:14:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jfo_22308/03_2026/7jfo_22308.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jfo_22308/03_2026/7jfo_22308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jfo_22308/03_2026/7jfo_22308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jfo_22308/03_2026/7jfo_22308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jfo_22308/03_2026/7jfo_22308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jfo_22308/03_2026/7jfo_22308.map" } resolution = 2.13 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 23904 2.51 5 N 6680 2.21 5 O 8094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38958 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "C" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "E" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "G" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "I" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "K" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "M" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "N" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "O" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3407 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 21, 'TRANS': 422} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'TRP:plan': 2, 'SMC:plan-1': 1} Unresolved non-hydrogen planarities: 25 Chain: "P" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "q" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "r" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "s" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "t" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "u" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "v" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "w" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "x" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 183 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "E" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "I" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 111 Classifications: {'water': 111} Link IDs: {None: 110} Chain: "J" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "K" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "M" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "N" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 108 Classifications: {'water': 108} Link IDs: {None: 107} Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Time building chain proxies: 9.51, per 1000 atoms: 0.24 Number of scatterers: 38958 At special positions: 0 Unit cell: (142.135, 142.135, 139.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 8094 8.00 N 6680 7.00 C 23904 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=0, symmetry=0 Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.7 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8864 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 32 sheets defined 46.7% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 153 through 163 removed outlier: 4.388A pdb=" N VAL A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 297 through 303 removed outlier: 3.761A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.578A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 452 removed outlier: 6.358A pdb=" N GLY A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASP A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.856A pdb=" N VAL A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 54 through 60 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 123 through 127 Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 153 through 163 removed outlier: 4.390A pdb=" N VAL C 157 " --> pdb=" O HIS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 195 Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 297 through 303 removed outlier: 3.759A pdb=" N ILE C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.577A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 412 through 433 Processing helix chain 'C' and resid 436 through 452 removed outlier: 6.348A pdb=" N GLY C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASP C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 461 removed outlier: 3.863A pdb=" N VAL C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 54 through 60 Processing helix chain 'D' and resid 86 through 100 Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 112 through 122 Processing helix chain 'E' and resid 123 through 127 Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 153 through 163 removed outlier: 4.390A pdb=" N VAL E 157 " --> pdb=" O HIS E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 195 Processing helix chain 'E' and resid 213 through 233 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.756A pdb=" N ILE E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.578A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 351 Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 386 through 395 Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 412 through 433 Processing helix chain 'E' and resid 436 through 452 removed outlier: 6.385A pdb=" N GLY E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 443 " --> pdb=" O ARG E 439 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 461 removed outlier: 3.837A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 47 through 51 removed outlier: 4.484A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 47 through 51' Processing helix chain 'F' and resid 54 through 60 Processing helix chain 'F' and resid 85 through 100 removed outlier: 4.500A pdb=" N VAL F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 60 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 123 through 127 Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 153 through 163 removed outlier: 4.393A pdb=" N VAL G 157 " --> pdb=" O HIS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 195 Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 246 through 261 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 297 through 303 removed outlier: 3.754A pdb=" N ILE G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.576A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 351 Processing helix chain 'G' and resid 357 through 361 Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 404 through 409 Processing helix chain 'G' and resid 412 through 433 Processing helix chain 'G' and resid 436 through 452 removed outlier: 6.377A pdb=" N GLY G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ASP G 443 " --> pdb=" O ARG G 439 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 461 removed outlier: 3.836A pdb=" N VAL G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 47 through 51 removed outlier: 4.508A pdb=" N TYR H 51 " --> pdb=" O SER H 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 47 through 51' Processing helix chain 'H' and resid 54 through 60 Processing helix chain 'H' and resid 86 through 100 Processing helix chain 'I' and resid 49 through 60 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 112 through 122 Processing helix chain 'I' and resid 123 through 127 Processing helix chain 'I' and resid 141 through 146 Processing helix chain 'I' and resid 153 through 163 removed outlier: 4.393A pdb=" N VAL I 157 " --> pdb=" O HIS I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 195 Processing helix chain 'I' and resid 213 through 233 Processing helix chain 'I' and resid 246 through 261 Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 273 through 288 Processing helix chain 'I' and resid 297 through 303 removed outlier: 3.755A pdb=" N ILE I 301 " --> pdb=" O MET I 297 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG I 303 " --> pdb=" O ALA I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 322 removed outlier: 3.582A pdb=" N LEU I 314 " --> pdb=" O HIS I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 351 Processing helix chain 'I' and resid 357 through 361 Processing helix chain 'I' and resid 386 through 395 Processing helix chain 'I' and resid 404 through 409 Processing helix chain 'I' and resid 412 through 433 Processing helix chain 'I' and resid 436 through 452 removed outlier: 6.378A pdb=" N GLY I 442 " --> pdb=" O ALA I 438 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP I 443 " --> pdb=" O ARG I 439 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 461 removed outlier: 3.853A pdb=" N VAL I 461 " --> pdb=" O ALA I 457 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 54 through 60 Processing helix chain 'J' and resid 85 through 100 removed outlier: 4.476A pdb=" N VAL J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 60 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 122 Processing helix chain 'K' and resid 123 through 127 Processing helix chain 'K' and resid 141 through 146 Processing helix chain 'K' and resid 153 through 163 removed outlier: 4.392A pdb=" N VAL K 157 " --> pdb=" O HIS K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 195 Processing helix chain 'K' and resid 213 through 233 Processing helix chain 'K' and resid 246 through 261 Processing helix chain 'K' and resid 269 through 273 Processing helix chain 'K' and resid 273 through 288 Processing helix chain 'K' and resid 297 through 303 removed outlier: 3.755A pdb=" N ILE K 301 " --> pdb=" O MET K 297 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG K 303 " --> pdb=" O ALA K 299 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 322 removed outlier: 3.577A pdb=" N LEU K 314 " --> pdb=" O HIS K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 351 Processing helix chain 'K' and resid 357 through 361 Processing helix chain 'K' and resid 386 through 395 Processing helix chain 'K' and resid 404 through 409 Processing helix chain 'K' and resid 412 through 433 Processing helix chain 'K' and resid 436 through 452 removed outlier: 6.409A pdb=" N GLY K 442 " --> pdb=" O ALA K 438 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASP K 443 " --> pdb=" O ARG K 439 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 461 removed outlier: 3.820A pdb=" N VAL K 461 " --> pdb=" O ALA K 457 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 47 through 51 removed outlier: 4.471A pdb=" N TYR L 51 " --> pdb=" O SER L 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 47 through 51' Processing helix chain 'L' and resid 54 through 60 Processing helix chain 'L' and resid 86 through 100 Processing helix chain 'M' and resid 49 through 60 Processing helix chain 'M' and resid 104 through 108 Processing helix chain 'M' and resid 112 through 122 Processing helix chain 'M' and resid 123 through 127 Processing helix chain 'M' and resid 141 through 146 Processing helix chain 'M' and resid 153 through 163 removed outlier: 4.389A pdb=" N VAL M 157 " --> pdb=" O HIS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 195 Processing helix chain 'M' and resid 213 through 233 Processing helix chain 'M' and resid 246 through 261 Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 273 through 288 Processing helix chain 'M' and resid 297 through 303 removed outlier: 3.749A pdb=" N ILE M 301 " --> pdb=" O MET M 297 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) Processing helix chain 'M' and resid 310 through 322 removed outlier: 3.574A pdb=" N LEU M 314 " --> pdb=" O HIS M 310 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 351 Processing helix chain 'M' and resid 357 through 361 Processing helix chain 'M' and resid 386 through 395 Processing helix chain 'M' and resid 404 through 409 Processing helix chain 'M' and resid 412 through 433 Processing helix chain 'M' and resid 436 through 452 removed outlier: 6.388A pdb=" N GLY M 442 " --> pdb=" O ALA M 438 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASP M 443 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 452 through 461 removed outlier: 3.882A pdb=" N VAL M 461 " --> pdb=" O ALA M 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 36 Processing helix chain 'N' and resid 47 through 51 removed outlier: 4.523A pdb=" N TYR N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 47 through 51' Processing helix chain 'N' and resid 54 through 60 Processing helix chain 'N' and resid 86 through 100 Processing helix chain 'O' and resid 49 through 60 Processing helix chain 'O' and resid 104 through 108 Processing helix chain 'O' and resid 112 through 122 Processing helix chain 'O' and resid 123 through 127 Processing helix chain 'O' and resid 141 through 146 Processing helix chain 'O' and resid 153 through 163 removed outlier: 4.389A pdb=" N VAL O 157 " --> pdb=" O HIS O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 195 Processing helix chain 'O' and resid 213 through 233 Processing helix chain 'O' and resid 246 through 261 Processing helix chain 'O' and resid 269 through 273 Processing helix chain 'O' and resid 273 through 288 Processing helix chain 'O' and resid 297 through 303 removed outlier: 3.751A pdb=" N ILE O 301 " --> pdb=" O MET O 297 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG O 303 " --> pdb=" O ALA O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 322 removed outlier: 3.573A pdb=" N LEU O 314 " --> pdb=" O HIS O 310 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 351 Processing helix chain 'O' and resid 357 through 361 Processing helix chain 'O' and resid 386 through 395 Processing helix chain 'O' and resid 404 through 409 Processing helix chain 'O' and resid 412 through 433 Processing helix chain 'O' and resid 436 through 452 removed outlier: 6.349A pdb=" N GLY O 442 " --> pdb=" O ALA O 438 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP O 443 " --> pdb=" O ARG O 439 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 452 through 461 removed outlier: 3.835A pdb=" N VAL O 461 " --> pdb=" O ALA O 457 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 36 Processing helix chain 'P' and resid 48 through 50 No H-bonds generated for 'chain 'P' and resid 48 through 50' Processing helix chain 'P' and resid 54 through 60 Processing helix chain 'P' and resid 86 through 100 Processing helix chain 'q' and resid 62 through 72 removed outlier: 3.559A pdb=" N SER q 69 " --> pdb=" O GLN q 65 " (cutoff:3.500A) Processing helix chain 'r' and resid 62 through 72 removed outlier: 3.557A pdb=" N SER r 69 " --> pdb=" O GLN r 65 " (cutoff:3.500A) Processing helix chain 's' and resid 62 through 72 removed outlier: 3.559A pdb=" N SER s 69 " --> pdb=" O GLN s 65 " (cutoff:3.500A) Processing helix chain 't' and resid 62 through 72 removed outlier: 3.559A pdb=" N SER t 69 " --> pdb=" O GLN t 65 " (cutoff:3.500A) Processing helix chain 'u' and resid 62 through 72 removed outlier: 3.559A pdb=" N SER u 69 " --> pdb=" O GLN u 65 " (cutoff:3.500A) Processing helix chain 'v' and resid 62 through 72 removed outlier: 3.559A pdb=" N SER v 69 " --> pdb=" O GLN v 65 " (cutoff:3.500A) Processing helix chain 'w' and resid 62 through 72 removed outlier: 3.559A pdb=" N SER w 69 " --> pdb=" O GLN w 65 " (cutoff:3.500A) Processing helix chain 'x' and resid 62 through 72 removed outlier: 3.558A pdb=" N SER x 69 " --> pdb=" O GLN x 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.704A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU A 37 " --> pdb=" O ASP A 137 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP A 137 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA A 39 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU A 135 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG A 41 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 133 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 43 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 173 removed outlier: 6.363A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS A 294 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N SER A 379 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N PHE A 402 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY A 171 " --> pdb=" O PHE A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA B 103 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLN B 124 " --> pdb=" O ALA B 103 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 105 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU B 122 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 107 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY B 120 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 109 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.702A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU C 37 " --> pdb=" O ASP C 137 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 137 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA C 39 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU C 135 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG C 41 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU C 133 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR C 43 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 173 removed outlier: 6.357A pdb=" N LEU C 170 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS C 201 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS C 172 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS C 294 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 326 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N SER C 379 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N SER C 328 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N PHE C 402 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY C 171 " --> pdb=" O PHE C 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA8, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.651A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ALA D 103 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN D 124 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL D 105 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU D 122 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU D 107 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY D 120 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA D 109 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 89 removed outlier: 5.706A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU E 37 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP E 137 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA E 39 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEU E 135 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ARG E 41 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU E 133 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR E 43 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 173 removed outlier: 6.368A pdb=" N LEU E 170 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS E 201 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS E 172 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N THR E 200 " --> pdb=" O TYR E 239 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN E 241 " --> pdb=" O THR E 200 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS E 238 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ASP E 268 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 265 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N HIS E 294 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS E 267 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 326 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N SER E 379 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE E 402 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY E 171 " --> pdb=" O PHE E 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.656A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA F 103 " --> pdb=" O GLN F 124 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN F 124 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL F 105 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU F 122 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU F 107 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY F 120 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA F 109 " --> pdb=" O ILE F 118 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 83 through 89 removed outlier: 5.710A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU G 37 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP G 137 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA G 39 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU G 135 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG G 41 " --> pdb=" O LEU G 133 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU G 133 " --> pdb=" O ARG G 41 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR G 43 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 169 through 173 removed outlier: 6.361A pdb=" N LEU G 170 " --> pdb=" O PHE G 199 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS G 201 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS G 172 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N HIS G 294 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU G 326 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N SER G 379 " --> pdb=" O LEU G 326 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE G 402 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY G 171 " --> pdb=" O PHE G 402 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.653A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA H 103 " --> pdb=" O GLN H 124 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLN H 124 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL H 105 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU H 122 " --> pdb=" O VAL H 105 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 107 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY H 120 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA H 109 " --> pdb=" O ILE H 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 83 through 89 removed outlier: 5.708A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU I 37 " --> pdb=" O ASP I 137 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP I 137 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA I 39 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LEU I 135 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG I 41 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU I 133 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR I 43 " --> pdb=" O ARG I 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 169 through 173 removed outlier: 6.363A pdb=" N LEU I 170 " --> pdb=" O PHE I 199 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS I 201 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N CYS I 172 " --> pdb=" O LYS I 201 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR I 200 " --> pdb=" O TYR I 239 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN I 241 " --> pdb=" O THR I 200 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N HIS I 238 " --> pdb=" O ILE I 264 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET I 266 " --> pdb=" O HIS I 238 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU I 240 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASP I 268 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE I 265 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS I 294 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS I 267 " --> pdb=" O HIS I 294 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU I 326 " --> pdb=" O VAL I 377 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N SER I 379 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N SER I 328 " --> pdb=" O SER I 379 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU I 169 " --> pdb=" O LEU I 400 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE I 402 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY I 171 " --> pdb=" O PHE I 402 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 353 through 354 Processing sheet with id=AC2, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.660A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA J 103 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN J 124 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL J 105 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N LEU J 122 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU J 107 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY J 120 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA J 109 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 83 through 89 removed outlier: 5.705A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU K 37 " --> pdb=" O ASP K 137 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP K 137 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA K 39 " --> pdb=" O LEU K 135 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU K 135 " --> pdb=" O ALA K 39 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG K 41 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU K 133 " --> pdb=" O ARG K 41 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N THR K 43 " --> pdb=" O ARG K 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 169 through 173 removed outlier: 6.373A pdb=" N LEU K 170 " --> pdb=" O PHE K 199 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS K 201 " --> pdb=" O LEU K 170 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N CYS K 172 " --> pdb=" O LYS K 201 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR K 200 " --> pdb=" O TYR K 239 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN K 241 " --> pdb=" O THR K 200 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS K 238 " --> pdb=" O ILE K 264 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET K 266 " --> pdb=" O HIS K 238 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU K 240 " --> pdb=" O MET K 266 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ASP K 268 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE K 265 " --> pdb=" O HIS K 292 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N HIS K 294 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N HIS K 267 " --> pdb=" O HIS K 294 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU K 326 " --> pdb=" O VAL K 377 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER K 379 " --> pdb=" O LEU K 326 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N SER K 328 " --> pdb=" O SER K 379 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N GLN K 401 " --> pdb=" O PRO K 376 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA K 378 " --> pdb=" O GLN K 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU K 169 " --> pdb=" O LEU K 400 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE K 402 " --> pdb=" O LEU K 169 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLY K 171 " --> pdb=" O PHE K 402 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 353 through 354 Processing sheet with id=AC6, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.648A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA L 103 " --> pdb=" O GLN L 124 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN L 124 " --> pdb=" O ALA L 103 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL L 105 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N LEU L 122 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU L 107 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY L 120 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA L 109 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 83 through 89 removed outlier: 5.710A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU M 37 " --> pdb=" O ASP M 137 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP M 137 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA M 39 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU M 135 " --> pdb=" O ALA M 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ARG M 41 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU M 133 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR M 43 " --> pdb=" O ARG M 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 169 through 173 removed outlier: 6.370A pdb=" N LEU M 170 " --> pdb=" O PHE M 199 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS M 201 " --> pdb=" O LEU M 170 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS M 172 " --> pdb=" O LYS M 201 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR M 200 " --> pdb=" O TYR M 239 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN M 241 " --> pdb=" O THR M 200 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS M 238 " --> pdb=" O ILE M 264 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N MET M 266 " --> pdb=" O HIS M 238 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU M 240 " --> pdb=" O MET M 266 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP M 268 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE M 265 " --> pdb=" O HIS M 292 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N HIS M 294 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N HIS M 267 " --> pdb=" O HIS M 294 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU M 326 " --> pdb=" O VAL M 377 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N SER M 379 " --> pdb=" O LEU M 326 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N SER M 328 " --> pdb=" O SER M 379 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN M 401 " --> pdb=" O PRO M 376 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA M 378 " --> pdb=" O GLN M 401 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU M 169 " --> pdb=" O LEU M 400 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE M 402 " --> pdb=" O LEU M 169 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY M 171 " --> pdb=" O PHE M 402 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 353 through 354 Processing sheet with id=AD1, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.645A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA N 103 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLN N 124 " --> pdb=" O ALA N 103 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL N 105 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU N 122 " --> pdb=" O VAL N 105 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU N 107 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY N 120 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA N 109 " --> pdb=" O ILE N 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 83 through 89 removed outlier: 5.710A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU O 37 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP O 137 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA O 39 " --> pdb=" O LEU O 135 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU O 135 " --> pdb=" O ALA O 39 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG O 41 " --> pdb=" O LEU O 133 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU O 133 " --> pdb=" O ARG O 41 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR O 43 " --> pdb=" O ARG O 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 169 through 173 removed outlier: 6.366A pdb=" N LEU O 170 " --> pdb=" O PHE O 199 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LYS O 201 " --> pdb=" O LEU O 170 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N CYS O 172 " --> pdb=" O LYS O 201 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR O 200 " --> pdb=" O TYR O 239 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN O 241 " --> pdb=" O THR O 200 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS O 238 " --> pdb=" O ILE O 264 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N MET O 266 " --> pdb=" O HIS O 238 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU O 240 " --> pdb=" O MET O 266 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N ASP O 268 " --> pdb=" O LEU O 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE O 265 " --> pdb=" O HIS O 292 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N HIS O 294 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS O 267 " --> pdb=" O HIS O 294 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU O 326 " --> pdb=" O VAL O 377 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N SER O 379 " --> pdb=" O LEU O 326 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N SER O 328 " --> pdb=" O SER O 379 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU O 169 " --> pdb=" O LEU O 400 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE O 402 " --> pdb=" O LEU O 169 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY O 171 " --> pdb=" O PHE O 402 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 353 through 354 Processing sheet with id=AD5, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.649A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA P 103 " --> pdb=" O GLN P 124 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN P 124 " --> pdb=" O ALA P 103 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL P 105 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU P 122 " --> pdb=" O VAL P 105 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU P 107 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY P 120 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA P 109 " --> pdb=" O ILE P 118 " (cutoff:3.500A) 1682 hydrogen bonds defined for protein. 4611 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: 9.57 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6506 1.30 - 1.44: 10659 1.44 - 1.58: 20717 1.58 - 1.72: 362 1.72 - 1.86: 428 Bond restraints: 38672 Sorted by residual: bond pdb=" SD MET G 266 " pdb=" CE MET G 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.92e+01 bond pdb=" SD MET E 266 " pdb=" CE MET E 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET O 266 " pdb=" CE MET O 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.91e+01 bond pdb=" SD MET K 266 " pdb=" CE MET K 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" SD MET M 266 " pdb=" CE MET M 266 " ideal model delta sigma weight residual 1.791 1.656 0.135 2.50e-02 1.60e+03 2.90e+01 ... (remaining 38667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 46884 2.52 - 5.05: 4646 5.05 - 7.57: 730 7.57 - 10.10: 147 10.10 - 12.62: 25 Bond angle restraints: 52432 Sorted by residual: angle pdb=" N TRP I 66 " pdb=" CA TRP I 66 " pdb=" C TRP I 66 " ideal model delta sigma weight residual 111.36 123.98 -12.62 1.09e+00 8.42e-01 1.34e+02 angle pdb=" N TRP M 66 " pdb=" CA TRP M 66 " pdb=" C TRP M 66 " ideal model delta sigma weight residual 111.36 123.74 -12.38 1.09e+00 8.42e-01 1.29e+02 angle pdb=" N TRP O 66 " pdb=" CA TRP O 66 " pdb=" C TRP O 66 " ideal model delta sigma weight residual 111.36 123.51 -12.15 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N TRP A 66 " pdb=" CA TRP A 66 " pdb=" C TRP A 66 " ideal model delta sigma weight residual 111.36 119.71 -8.35 1.09e+00 8.42e-01 5.87e+01 angle pdb=" N TRP K 66 " pdb=" CA TRP K 66 " pdb=" C TRP K 66 " ideal model delta sigma weight residual 111.36 119.63 -8.27 1.09e+00 8.42e-01 5.76e+01 ... (remaining 52427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 20504 14.24 - 28.49: 2053 28.49 - 42.73: 324 42.73 - 56.97: 83 56.97 - 71.21: 44 Dihedral angle restraints: 23008 sinusoidal: 9128 harmonic: 13880 Sorted by residual: dihedral pdb=" CA PHE F 60 " pdb=" C PHE F 60 " pdb=" N GLY F 61 " pdb=" CA GLY F 61 " ideal model delta harmonic sigma weight residual 180.00 152.39 27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PHE H 60 " pdb=" C PHE H 60 " pdb=" N GLY H 61 " pdb=" CA GLY H 61 " ideal model delta harmonic sigma weight residual 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA PHE P 60 " pdb=" C PHE P 60 " pdb=" N GLY P 61 " pdb=" CA GLY P 61 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 23005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4369 0.114 - 0.228: 945 0.228 - 0.342: 194 0.342 - 0.456: 68 0.456 - 0.569: 8 Chirality restraints: 5584 Sorted by residual: chirality pdb=" CB ILE G 301 " pdb=" CA ILE G 301 " pdb=" CG1 ILE G 301 " pdb=" CG2 ILE G 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.11e+00 chirality pdb=" CB ILE K 301 " pdb=" CA ILE K 301 " pdb=" CG1 ILE K 301 " pdb=" CG2 ILE K 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.93e+00 chirality pdb=" CB ILE E 301 " pdb=" CA ILE E 301 " pdb=" CG1 ILE E 301 " pdb=" CG2 ILE E 301 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 5581 not shown) Planarity restraints: 6880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS I 153 " 0.066 2.00e-02 2.50e+03 5.82e-02 5.08e+01 pdb=" CG HIS I 153 " -0.102 2.00e-02 2.50e+03 pdb=" ND1 HIS I 153 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS I 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS I 153 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 HIS I 153 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS G 153 " -0.066 2.00e-02 2.50e+03 5.81e-02 5.07e+01 pdb=" CG HIS G 153 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS G 153 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS G 153 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 HIS G 153 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS G 153 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 153 " 0.065 2.00e-02 2.50e+03 5.78e-02 5.02e+01 pdb=" CG HIS E 153 " -0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS E 153 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 HIS E 153 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS E 153 " -0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS E 153 " 0.067 2.00e-02 2.50e+03 ... (remaining 6877 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4065 2.74 - 3.28: 40522 3.28 - 3.82: 74812 3.82 - 4.36: 92442 4.36 - 4.90: 145802 Nonbonded interactions: 357643 Sorted by model distance: nonbonded pdb=" NE2 GLN A 156 " pdb=" OD2 ASP A 160 " model vdw 2.198 3.120 nonbonded pdb=" NE2 GLN G 156 " pdb=" OD2 ASP G 160 " model vdw 2.201 3.120 nonbonded pdb=" NE2 GLN O 156 " pdb=" OD2 ASP O 160 " model vdw 2.203 3.120 nonbonded pdb=" NE2 GLN I 156 " pdb=" OD2 ASP I 160 " model vdw 2.204 3.120 nonbonded pdb=" NE2 GLN C 156 " pdb=" OD2 ASP C 160 " model vdw 2.206 3.120 ... (remaining 357638 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.760 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 37.700 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.180 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:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.022 0.162 38672 Z= 1.005 Angle : 1.666 12.619 52432 Z= 0.976 Chirality : 0.109 0.569 5584 Planarity : 0.014 0.064 6880 Dihedral : 12.066 71.215 14144 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.23 % Allowed : 4.59 % Favored : 94.17 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.11), residues: 4760 helix: -0.72 (0.10), residues: 1856 sheet: -0.22 (0.20), residues: 752 loop : -0.52 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.005 ARG G 350 TYR 0.083 0.012 TYR O 363 PHE 0.103 0.012 PHE I 148 TRP 0.039 0.008 TRP M 214 HIS 0.050 0.011 HIS M 153 Details of bonding type rmsd covalent geometry : bond 0.02162 (38672) covalent geometry : angle 1.66607 (52432) hydrogen bonds : bond 0.19020 ( 1682) hydrogen bonds : angle 7.46118 ( 4611) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 644 time to evaluate : 1.528 Fit side-chains REVERT: B 80 MET cc_start: 0.7538 (mtm) cc_final: 0.7202 (mpp) REVERT: D 80 MET cc_start: 0.7558 (mtm) cc_final: 0.7179 (mpp) REVERT: E 297 MET cc_start: 0.8201 (ttp) cc_final: 0.7759 (ttp) REVERT: I 297 MET cc_start: 0.8278 (ttp) cc_final: 0.7837 (ttp) REVERT: L 49 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7954 (mmtm) REVERT: L 80 MET cc_start: 0.7561 (mtm) cc_final: 0.7218 (mpp) REVERT: M 205 ASN cc_start: 0.7781 (p0) cc_final: 0.7413 (p0) REVERT: N 80 MET cc_start: 0.7555 (mtm) cc_final: 0.7195 (mpp) REVERT: P 80 MET cc_start: 0.7495 (mtm) cc_final: 0.7142 (mpp) REVERT: P 122 LEU cc_start: 0.9057 (tp) cc_final: 0.8824 (tp) REVERT: v 56 ARG cc_start: 0.5811 (OUTLIER) cc_final: 0.5591 (tpp-160) outliers start: 48 outliers final: 7 residues processed: 682 average time/residue: 0.8300 time to fit residues: 672.7370 Evaluate side-chains 609 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 601 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 268 ASP Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 56 ARG Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 96 GLN A 115 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN A 163 ASN A 238 HIS A 241 ASN A 267 HIS A 277 ASN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN B 9 ASN B 29 GLN B 36 ASN C 45 GLN C 96 GLN C 115 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 163 ASN C 238 HIS C 241 ASN C 267 HIS C 277 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 432 ASN D 9 ASN D 29 GLN D 36 ASN E 45 GLN E 96 GLN E 115 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 238 HIS E 241 ASN E 267 HIS E 277 ASN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN F 9 ASN F 29 GLN F 36 ASN G 45 GLN G 96 GLN G 115 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 163 ASN G 238 HIS G 241 ASN G 267 HIS G 277 ASN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 432 ASN H 9 ASN H 29 GLN H 36 ASN I 45 GLN I 96 GLN I 115 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN I 238 HIS I 241 ASN I 267 HIS I 277 ASN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN J 9 ASN J 29 GLN J 36 ASN K 45 GLN K 96 GLN K 115 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 163 ASN K 238 HIS K 241 ASN K 267 HIS K 277 ASN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 432 ASN L 9 ASN L 29 GLN L 36 ASN M 45 GLN M 96 GLN M 115 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 163 ASN M 238 HIS M 241 ASN M 267 HIS M 277 ASN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN M 432 ASN N 9 ASN N 29 GLN N 36 ASN O 45 GLN O 96 GLN O 115 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 163 ASN O 238 HIS O 241 ASN O 267 HIS O 277 ASN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 432 ASN P 9 ASN P 29 GLN P 36 ASN Total number of N/Q/H flips: 105 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.201136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.162272 restraints weight = 212913.329| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 6.14 r_work: 0.2964 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 38672 Z= 0.132 Angle : 0.617 5.691 52432 Z= 0.337 Chirality : 0.044 0.171 5584 Planarity : 0.005 0.044 6880 Dihedral : 5.694 25.840 5372 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.69 % Allowed : 7.39 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.12), residues: 4760 helix: 1.19 (0.12), residues: 1880 sheet: -0.19 (0.18), residues: 792 loop : -0.01 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 339 TYR 0.015 0.002 TYR G 269 PHE 0.036 0.002 PHE O 345 TRP 0.009 0.001 TRP P 38 HIS 0.010 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00268 (38672) covalent geometry : angle 0.61680 (52432) hydrogen bonds : bond 0.04747 ( 1682) hydrogen bonds : angle 5.54595 ( 4611) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 708 time to evaluate : 1.552 Fit side-chains REVERT: A 33 ASP cc_start: 0.8144 (m-30) cc_final: 0.7717 (p0) REVERT: A 339 ARG cc_start: 0.6839 (ttm110) cc_final: 0.6629 (ttm170) REVERT: A 392 GLU cc_start: 0.7620 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 13 GLU cc_start: 0.7785 (mm-30) cc_final: 0.6962 (mm-30) REVERT: B 46 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7015 (mp0) REVERT: B 80 MET cc_start: 0.8283 (mtm) cc_final: 0.7710 (mpp) REVERT: C 33 ASP cc_start: 0.8131 (m-30) cc_final: 0.7717 (p0) REVERT: C 339 ARG cc_start: 0.6926 (ttm110) cc_final: 0.6722 (ttm170) REVERT: D 46 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7178 (mt-10) REVERT: D 80 MET cc_start: 0.8323 (mtm) cc_final: 0.7693 (mpp) REVERT: D 122 LEU cc_start: 0.8829 (tp) cc_final: 0.8590 (tp) REVERT: E 33 ASP cc_start: 0.8129 (m-30) cc_final: 0.7727 (p0) REVERT: E 339 ARG cc_start: 0.6810 (ttm110) cc_final: 0.5979 (ttp-170) REVERT: F 46 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7103 (mt-10) REVERT: F 122 LEU cc_start: 0.8824 (tp) cc_final: 0.8560 (tp) REVERT: G 33 ASP cc_start: 0.8074 (m-30) cc_final: 0.7565 (p0) REVERT: G 339 ARG cc_start: 0.6775 (ttm110) cc_final: 0.5935 (ttp-170) REVERT: H 46 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7036 (mt-10) REVERT: I 33 ASP cc_start: 0.8118 (m-30) cc_final: 0.7597 (p0) REVERT: J 97 THR cc_start: 0.8005 (p) cc_final: 0.7697 (t) REVERT: J 122 LEU cc_start: 0.8873 (tp) cc_final: 0.8606 (tp) REVERT: K 392 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7134 (tm-30) REVERT: L 13 GLU cc_start: 0.7775 (mm-30) cc_final: 0.6954 (mm-30) REVERT: L 46 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7060 (mt-10) REVERT: L 80 MET cc_start: 0.8316 (mtm) cc_final: 0.7745 (mpp) REVERT: L 122 LEU cc_start: 0.8767 (tp) cc_final: 0.8545 (tp) REVERT: M 339 ARG cc_start: 0.6788 (ttm110) cc_final: 0.5973 (ttp-170) REVERT: M 382 ILE cc_start: 0.4422 (OUTLIER) cc_final: 0.4222 (mm) REVERT: N 13 GLU cc_start: 0.7790 (mm-30) cc_final: 0.6993 (mm-30) REVERT: N 46 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6926 (mp0) REVERT: N 80 MET cc_start: 0.8295 (mtm) cc_final: 0.7727 (mpp) REVERT: O 33 ASP cc_start: 0.8104 (m-30) cc_final: 0.7680 (p0) REVERT: O 339 ARG cc_start: 0.6824 (ttm110) cc_final: 0.6612 (ttm170) REVERT: O 392 GLU cc_start: 0.7625 (tt0) cc_final: 0.7296 (tm-30) REVERT: O 443 ASP cc_start: 0.7413 (m-30) cc_final: 0.6938 (t70) REVERT: P 13 GLU cc_start: 0.7813 (mm-30) cc_final: 0.6972 (mm-30) REVERT: P 80 MET cc_start: 0.8291 (mtm) cc_final: 0.7735 (mpp) REVERT: P 122 LEU cc_start: 0.8803 (tp) cc_final: 0.8555 (tp) outliers start: 27 outliers final: 16 residues processed: 725 average time/residue: 0.7783 time to fit residues: 672.9342 Evaluate side-chains 675 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 658 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain r residue 68 GLU Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain w residue 68 GLU Chi-restraints excluded: chain x residue 68 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 chunk 456 optimal weight: 0.7980 chunk 464 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 258 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 96 GLN A 153 HIS A 156 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN B 8 ASN B 36 ASN C 45 GLN C 96 GLN C 153 HIS C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 ASN D 36 ASN D 124 GLN E 45 GLN E 96 GLN E 153 HIS E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 ASN F 8 ASN F 36 ASN G 45 GLN G 96 GLN G 153 HIS G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN H 8 ASN H 36 ASN H 124 GLN I 45 GLN I 96 GLN I 153 HIS I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN J 8 ASN J 36 ASN J 124 GLN K 45 GLN K 96 GLN K 153 HIS K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 36 ASN M 45 GLN M 96 GLN M 153 HIS M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 8 ASN N 36 ASN N 124 GLN O 45 GLN O 96 GLN O 153 HIS O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 ASN P 8 ASN P 36 ASN P 124 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.196828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.157058 restraints weight = 214382.970| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 6.17 r_work: 0.2902 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 38672 Z= 0.188 Angle : 0.681 5.940 52432 Z= 0.370 Chirality : 0.047 0.192 5584 Planarity : 0.006 0.052 6880 Dihedral : 5.754 25.375 5365 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.13 % Allowed : 8.29 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.12), residues: 4760 helix: 1.46 (0.12), residues: 1880 sheet: -0.14 (0.18), residues: 744 loop : 0.13 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 285 TYR 0.020 0.002 TYR E 269 PHE 0.036 0.003 PHE O 345 TRP 0.009 0.002 TRP O 368 HIS 0.016 0.002 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00394 (38672) covalent geometry : angle 0.68077 (52432) hydrogen bonds : bond 0.05208 ( 1682) hydrogen bonds : angle 5.46324 ( 4611) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 655 time to evaluate : 1.390 Fit side-chains REVERT: A 33 ASP cc_start: 0.8213 (m-30) cc_final: 0.7726 (p0) REVERT: A 297 MET cc_start: 0.8416 (ttp) cc_final: 0.8090 (ttp) REVERT: A 339 ARG cc_start: 0.6599 (ttm110) cc_final: 0.6397 (ttm170) REVERT: A 392 GLU cc_start: 0.7657 (tt0) cc_final: 0.7297 (tm-30) REVERT: B 80 MET cc_start: 0.8246 (mtm) cc_final: 0.7718 (mpp) REVERT: C 33 ASP cc_start: 0.8269 (m-30) cc_final: 0.7797 (p0) REVERT: C 297 MET cc_start: 0.8409 (ttp) cc_final: 0.8098 (ttp) REVERT: C 339 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6446 (ttm170) REVERT: D 46 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7060 (mp0) REVERT: D 80 MET cc_start: 0.8227 (mtm) cc_final: 0.7570 (mpp) REVERT: E 33 ASP cc_start: 0.8292 (m-30) cc_final: 0.7800 (p0) REVERT: E 297 MET cc_start: 0.8331 (ttp) cc_final: 0.8028 (ttp) REVERT: E 339 ARG cc_start: 0.6547 (ttm110) cc_final: 0.6280 (ttm170) REVERT: F 46 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7372 (mt-10) REVERT: F 122 LEU cc_start: 0.8840 (tp) cc_final: 0.8627 (tp) REVERT: G 33 ASP cc_start: 0.8224 (m-30) cc_final: 0.7633 (p0) REVERT: G 297 MET cc_start: 0.8344 (ttp) cc_final: 0.8027 (ttp) REVERT: G 339 ARG cc_start: 0.6556 (ttm110) cc_final: 0.6350 (ttm170) REVERT: H 46 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7104 (mp0) REVERT: I 33 ASP cc_start: 0.8192 (m-30) cc_final: 0.7603 (p0) REVERT: I 297 MET cc_start: 0.8419 (ttp) cc_final: 0.8082 (ttp) REVERT: J 97 THR cc_start: 0.7918 (p) cc_final: 0.7615 (t) REVERT: J 122 LEU cc_start: 0.8886 (tp) cc_final: 0.8633 (tp) REVERT: K 297 MET cc_start: 0.8371 (ttp) cc_final: 0.8062 (ttp) REVERT: L 80 MET cc_start: 0.8176 (mtm) cc_final: 0.7643 (mpp) REVERT: M 297 MET cc_start: 0.8369 (ttp) cc_final: 0.8061 (ttp) REVERT: M 339 ARG cc_start: 0.6585 (ttm110) cc_final: 0.6339 (ttm170) REVERT: N 80 MET cc_start: 0.8236 (mtm) cc_final: 0.7710 (mpp) REVERT: O 33 ASP cc_start: 0.8188 (m-30) cc_final: 0.7694 (p0) REVERT: O 297 MET cc_start: 0.8416 (ttp) cc_final: 0.8093 (ttp) REVERT: O 339 ARG cc_start: 0.6669 (ttm110) cc_final: 0.6405 (ttm170) REVERT: O 392 GLU cc_start: 0.7573 (tt0) cc_final: 0.7222 (tm-30) REVERT: P 80 MET cc_start: 0.8185 (mtm) cc_final: 0.7634 (mpp) REVERT: P 122 LEU cc_start: 0.8864 (tp) cc_final: 0.8626 (tp) outliers start: 44 outliers final: 20 residues processed: 682 average time/residue: 0.8395 time to fit residues: 680.4258 Evaluate side-chains 657 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 637 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain r residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 144 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 316 optimal weight: 9.9990 chunk 409 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 465 optimal weight: 0.5980 chunk 272 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 chunk 414 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 45 GLN E 96 GLN E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN G 156 GLN ** G 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN N 124 GLN O 96 GLN O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 420 ASN P 36 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.195925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.156373 restraints weight = 214748.804| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 6.33 r_work: 0.2897 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38672 Z= 0.212 Angle : 0.706 6.136 52432 Z= 0.384 Chirality : 0.049 0.196 5584 Planarity : 0.006 0.058 6880 Dihedral : 5.810 25.147 5362 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.16 % Allowed : 8.60 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.12), residues: 4760 helix: 1.48 (0.12), residues: 1880 sheet: -0.13 (0.18), residues: 744 loop : 0.10 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 285 TYR 0.022 0.003 TYR E 269 PHE 0.035 0.003 PHE O 345 TRP 0.010 0.002 TRP M 214 HIS 0.012 0.002 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.00448 (38672) covalent geometry : angle 0.70650 (52432) hydrogen bonds : bond 0.05366 ( 1682) hydrogen bonds : angle 5.49541 ( 4611) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 664 time to evaluate : 1.556 Fit side-chains REVERT: A 33 ASP cc_start: 0.8209 (m-30) cc_final: 0.7696 (p0) REVERT: A 297 MET cc_start: 0.8504 (ttp) cc_final: 0.8208 (ttp) REVERT: A 339 ARG cc_start: 0.6710 (ttm110) cc_final: 0.6508 (ttm170) REVERT: A 392 GLU cc_start: 0.7715 (tt0) cc_final: 0.7350 (tm-30) REVERT: B 80 MET cc_start: 0.8240 (mtm) cc_final: 0.7708 (mpp) REVERT: C 33 ASP cc_start: 0.8309 (m-30) cc_final: 0.7823 (p0) REVERT: C 297 MET cc_start: 0.8452 (ttp) cc_final: 0.8164 (ttp) REVERT: C 339 ARG cc_start: 0.6744 (ttm110) cc_final: 0.6509 (ttm170) REVERT: D 46 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7099 (mp0) REVERT: D 80 MET cc_start: 0.8266 (mtm) cc_final: 0.7748 (mpp) REVERT: E 33 ASP cc_start: 0.8290 (m-30) cc_final: 0.7792 (p0) REVERT: E 297 MET cc_start: 0.8370 (ttp) cc_final: 0.8011 (ttp) REVERT: E 339 ARG cc_start: 0.6606 (ttm110) cc_final: 0.6372 (ttm170) REVERT: E 431 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6655 (tmm-80) REVERT: F 1 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6747 (ttp) REVERT: F 46 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7326 (mt-10) REVERT: F 80 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7979 (mpp) REVERT: F 122 LEU cc_start: 0.8871 (tp) cc_final: 0.8638 (tp) REVERT: G 33 ASP cc_start: 0.8211 (m-30) cc_final: 0.7604 (p0) REVERT: G 297 MET cc_start: 0.8386 (ttp) cc_final: 0.8021 (ttp) REVERT: G 339 ARG cc_start: 0.6617 (ttm110) cc_final: 0.6414 (ttm170) REVERT: H 46 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7158 (mp0) REVERT: H 125 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7013 (mtt180) REVERT: I 33 ASP cc_start: 0.8146 (m-30) cc_final: 0.7551 (p0) REVERT: I 297 MET cc_start: 0.8459 (ttp) cc_final: 0.8150 (ttp) REVERT: J 97 THR cc_start: 0.7932 (p) cc_final: 0.7633 (t) REVERT: J 122 LEU cc_start: 0.8904 (tp) cc_final: 0.8666 (tp) REVERT: K 297 MET cc_start: 0.8471 (ttp) cc_final: 0.8190 (ttp) REVERT: L 13 GLU cc_start: 0.7854 (mm-30) cc_final: 0.6982 (mm-30) REVERT: L 46 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7005 (mp0) REVERT: L 80 MET cc_start: 0.8349 (mtm) cc_final: 0.7727 (mpp) REVERT: M 297 MET cc_start: 0.8419 (ttp) cc_final: 0.8063 (ttp) REVERT: M 339 ARG cc_start: 0.6672 (ttm110) cc_final: 0.6411 (ttm170) REVERT: N 80 MET cc_start: 0.8305 (mtm) cc_final: 0.7788 (mpp) REVERT: O 33 ASP cc_start: 0.8186 (m-30) cc_final: 0.7666 (p0) REVERT: O 297 MET cc_start: 0.8457 (ttp) cc_final: 0.8080 (ttp) REVERT: O 339 ARG cc_start: 0.6690 (ttm110) cc_final: 0.6455 (ttm170) REVERT: O 392 GLU cc_start: 0.7589 (tt0) cc_final: 0.7265 (tm-30) REVERT: P 13 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7090 (mm-30) REVERT: P 80 MET cc_start: 0.8234 (mtm) cc_final: 0.7712 (mpp) REVERT: P 122 LEU cc_start: 0.8871 (tp) cc_final: 0.8651 (tp) outliers start: 45 outliers final: 28 residues processed: 690 average time/residue: 0.8674 time to fit residues: 709.2368 Evaluate side-chains 688 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 657 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain q residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 308 optimal weight: 0.7980 chunk 461 optimal weight: 30.0000 chunk 75 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 373 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 460 optimal weight: 10.0000 chunk 435 optimal weight: 9.9990 chunk 350 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 156 GLN ** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 ASN H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 123 ASN K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 123 ASN M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.198034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.158750 restraints weight = 214604.732| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 6.08 r_work: 0.2926 rms_B_bonded: 5.10 restraints_weight: 2.0000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38672 Z= 0.141 Angle : 0.603 5.485 52432 Z= 0.327 Chirality : 0.044 0.180 5584 Planarity : 0.005 0.043 6880 Dihedral : 5.447 21.778 5361 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.92 % Allowed : 9.19 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 4760 helix: 1.74 (0.12), residues: 1880 sheet: -0.21 (0.18), residues: 824 loop : 0.27 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 305 TYR 0.016 0.002 TYR E 269 PHE 0.033 0.002 PHE E 345 TRP 0.013 0.001 TRP B 132 HIS 0.008 0.001 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00292 (38672) covalent geometry : angle 0.60281 (52432) hydrogen bonds : bond 0.04506 ( 1682) hydrogen bonds : angle 5.26528 ( 4611) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 663 time to evaluate : 1.507 Fit side-chains REVERT: A 33 ASP cc_start: 0.8208 (m-30) cc_final: 0.7750 (p0) REVERT: A 297 MET cc_start: 0.8488 (ttp) cc_final: 0.8168 (ttp) REVERT: A 339 ARG cc_start: 0.6656 (ttm110) cc_final: 0.6436 (ttm170) REVERT: A 392 GLU cc_start: 0.7635 (tt0) cc_final: 0.7327 (tm-30) REVERT: B 13 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7041 (mm-30) REVERT: B 46 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7468 (mt-10) REVERT: B 80 MET cc_start: 0.8260 (mtm) cc_final: 0.7723 (mpp) REVERT: C 33 ASP cc_start: 0.8278 (m-30) cc_final: 0.7844 (p0) REVERT: C 297 MET cc_start: 0.8481 (ttp) cc_final: 0.8192 (ttp) REVERT: C 339 ARG cc_start: 0.6712 (ttm110) cc_final: 0.6453 (ttm170) REVERT: D 13 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7076 (mm-30) REVERT: D 46 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7015 (mp0) REVERT: D 80 MET cc_start: 0.8356 (mtm) cc_final: 0.7792 (mpp) REVERT: E 33 ASP cc_start: 0.8225 (m-30) cc_final: 0.7776 (p0) REVERT: E 297 MET cc_start: 0.8414 (ttp) cc_final: 0.8117 (ttp) REVERT: E 339 ARG cc_start: 0.6584 (ttm110) cc_final: 0.6101 (ttm110) REVERT: E 431 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.6568 (tmm-80) REVERT: F 13 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7007 (mm-30) REVERT: F 46 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7304 (mt-10) REVERT: F 80 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7901 (mpp) REVERT: F 122 LEU cc_start: 0.8864 (tp) cc_final: 0.8662 (tp) REVERT: G 33 ASP cc_start: 0.8184 (m-30) cc_final: 0.7630 (p0) REVERT: G 297 MET cc_start: 0.8427 (ttp) cc_final: 0.8123 (ttp) REVERT: H 13 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7090 (mm-30) REVERT: H 46 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7060 (mp0) REVERT: H 80 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7793 (mpp) REVERT: I 33 ASP cc_start: 0.8164 (m-30) cc_final: 0.7606 (p0) REVERT: I 297 MET cc_start: 0.8492 (ttp) cc_final: 0.8170 (ttp) REVERT: J 13 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7006 (mm-30) REVERT: J 46 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7478 (mt-10) REVERT: J 80 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8007 (mpp) REVERT: J 97 THR cc_start: 0.7971 (p) cc_final: 0.7674 (t) REVERT: J 122 LEU cc_start: 0.8866 (tp) cc_final: 0.8643 (tp) REVERT: K 297 MET cc_start: 0.8462 (ttp) cc_final: 0.8161 (ttp) REVERT: L 13 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7047 (mm-30) REVERT: L 46 GLU cc_start: 0.7627 (mm-30) cc_final: 0.6956 (mp0) REVERT: L 80 MET cc_start: 0.8183 (mtm) cc_final: 0.7638 (mpp) REVERT: M 297 MET cc_start: 0.8447 (ttp) cc_final: 0.8143 (ttp) REVERT: M 339 ARG cc_start: 0.6602 (ttm110) cc_final: 0.6074 (ttm110) REVERT: N 13 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7023 (mm-30) REVERT: N 46 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7242 (mt-10) REVERT: N 80 MET cc_start: 0.8323 (mtm) cc_final: 0.7806 (mpp) REVERT: O 33 ASP cc_start: 0.8190 (m-30) cc_final: 0.7723 (p0) REVERT: O 88 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6651 (pt0) REVERT: O 297 MET cc_start: 0.8483 (ttp) cc_final: 0.8173 (ttp) REVERT: O 339 ARG cc_start: 0.6628 (ttm110) cc_final: 0.6396 (ttm170) REVERT: O 392 GLU cc_start: 0.7511 (tt0) cc_final: 0.7205 (tm-30) REVERT: P 13 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7071 (mm-30) REVERT: P 80 MET cc_start: 0.8286 (mtm) cc_final: 0.7772 (mpp) REVERT: P 122 LEU cc_start: 0.8859 (tp) cc_final: 0.8651 (tp) outliers start: 36 outliers final: 17 residues processed: 683 average time/residue: 0.9085 time to fit residues: 731.5979 Evaluate side-chains 671 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 650 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 241 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 327 optimal weight: 20.0000 chunk 467 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 282 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 123 ASN A 156 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN B 36 ASN C 96 GLN C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 123 ASN E 156 GLN E 386 HIS ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN G 123 ASN G 156 GLN G 386 HIS ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 123 ASN I 156 GLN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 156 GLN ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 123 ASN M 156 GLN ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN O 123 ASN O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.197289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.157687 restraints weight = 213614.300| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 6.15 r_work: 0.2912 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38672 Z= 0.171 Angle : 0.644 5.716 52432 Z= 0.349 Chirality : 0.046 0.188 5584 Planarity : 0.005 0.048 6880 Dihedral : 5.535 21.397 5360 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 9.50 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 4760 helix: 1.71 (0.12), residues: 1880 sheet: -0.19 (0.18), residues: 824 loop : 0.30 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 305 TYR 0.018 0.002 TYR E 269 PHE 0.033 0.003 PHE O 345 TRP 0.014 0.002 TRP B 132 HIS 0.011 0.002 HIS M 153 Details of bonding type rmsd covalent geometry : bond 0.00359 (38672) covalent geometry : angle 0.64353 (52432) hydrogen bonds : bond 0.04871 ( 1682) hydrogen bonds : angle 5.32013 ( 4611) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 664 time to evaluate : 1.527 Fit side-chains REVERT: A 33 ASP cc_start: 0.8207 (m-30) cc_final: 0.7713 (p0) REVERT: A 297 MET cc_start: 0.8497 (ttp) cc_final: 0.8204 (ttp) REVERT: A 339 ARG cc_start: 0.6721 (ttm110) cc_final: 0.6490 (ttm170) REVERT: A 392 GLU cc_start: 0.7625 (tt0) cc_final: 0.7313 (tm-30) REVERT: B 13 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 46 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7110 (mp0) REVERT: B 80 MET cc_start: 0.8294 (mtm) cc_final: 0.7748 (mpp) REVERT: C 33 ASP cc_start: 0.8166 (m-30) cc_final: 0.7715 (p0) REVERT: C 297 MET cc_start: 0.8453 (ttp) cc_final: 0.8169 (ttp) REVERT: C 339 ARG cc_start: 0.6705 (ttm110) cc_final: 0.6437 (ttm170) REVERT: D 13 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7004 (mm-30) REVERT: D 46 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7000 (mp0) REVERT: D 80 MET cc_start: 0.8279 (mtm) cc_final: 0.7688 (mpp) REVERT: E 33 ASP cc_start: 0.8184 (m-30) cc_final: 0.7725 (p0) REVERT: E 297 MET cc_start: 0.8394 (ttp) cc_final: 0.8027 (ttp) REVERT: E 339 ARG cc_start: 0.6594 (ttm110) cc_final: 0.6340 (ttm170) REVERT: E 431 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.6540 (tmm-80) REVERT: F 13 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7036 (mm-30) REVERT: F 46 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7132 (mp0) REVERT: F 80 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8012 (mpp) REVERT: F 122 LEU cc_start: 0.8877 (tp) cc_final: 0.8677 (tp) REVERT: G 33 ASP cc_start: 0.8194 (m-30) cc_final: 0.7613 (p0) REVERT: G 297 MET cc_start: 0.8394 (ttp) cc_final: 0.8019 (ttp) REVERT: H 13 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7018 (mm-30) REVERT: H 46 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7088 (mp0) REVERT: H 80 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7831 (mpp) REVERT: I 33 ASP cc_start: 0.8149 (m-30) cc_final: 0.7567 (p0) REVERT: I 297 MET cc_start: 0.8478 (ttp) cc_final: 0.8172 (ttp) REVERT: J 13 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7038 (mm-30) REVERT: J 97 THR cc_start: 0.7962 (p) cc_final: 0.7658 (t) REVERT: J 122 LEU cc_start: 0.8903 (tp) cc_final: 0.8692 (tp) REVERT: K 297 MET cc_start: 0.8451 (ttp) cc_final: 0.8094 (ttp) REVERT: K 431 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.6613 (tmm-80) REVERT: L 13 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7107 (mm-30) REVERT: L 46 GLU cc_start: 0.7637 (mm-30) cc_final: 0.6976 (mp0) REVERT: L 80 MET cc_start: 0.8295 (mtm) cc_final: 0.7741 (mpp) REVERT: M 297 MET cc_start: 0.8409 (ttp) cc_final: 0.8042 (ttp) REVERT: M 339 ARG cc_start: 0.6666 (ttm110) cc_final: 0.6132 (ttm110) REVERT: N 13 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7103 (mm-30) REVERT: N 46 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7256 (mt-10) REVERT: N 80 MET cc_start: 0.8250 (mtm) cc_final: 0.7705 (mpp) REVERT: O 33 ASP cc_start: 0.8173 (m-30) cc_final: 0.7691 (p0) REVERT: O 88 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6634 (pt0) REVERT: O 297 MET cc_start: 0.8456 (ttp) cc_final: 0.8087 (ttp) REVERT: O 339 ARG cc_start: 0.6674 (ttm110) cc_final: 0.6465 (ttm170) REVERT: O 392 GLU cc_start: 0.7497 (tt0) cc_final: 0.7194 (tm-30) REVERT: O 431 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.6563 (tmm-80) REVERT: P 13 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7057 (mm-30) REVERT: P 80 MET cc_start: 0.8257 (mtm) cc_final: 0.7704 (mpp) REVERT: P 122 LEU cc_start: 0.8871 (tp) cc_final: 0.8662 (tp) outliers start: 42 outliers final: 25 residues processed: 691 average time/residue: 0.9028 time to fit residues: 735.8634 Evaluate side-chains 679 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 649 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 244 optimal weight: 10.0000 chunk 226 optimal weight: 5.9990 chunk 443 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 412 optimal weight: 1.9990 chunk 470 optimal weight: 9.9990 chunk 280 optimal weight: 5.9990 chunk 468 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN A 386 HIS ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN C 123 ASN C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 123 ASN K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 156 GLN ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.197042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.157300 restraints weight = 213932.936| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 6.13 r_work: 0.2911 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38672 Z= 0.170 Angle : 0.639 5.692 52432 Z= 0.346 Chirality : 0.046 0.187 5584 Planarity : 0.005 0.048 6880 Dihedral : 5.519 21.267 5360 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.10 % Allowed : 9.75 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.12), residues: 4760 helix: 1.72 (0.12), residues: 1880 sheet: -0.19 (0.18), residues: 824 loop : 0.33 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 305 TYR 0.018 0.002 TYR E 269 PHE 0.033 0.003 PHE O 345 TRP 0.017 0.002 TRP B 132 HIS 0.011 0.002 HIS M 153 Details of bonding type rmsd covalent geometry : bond 0.00356 (38672) covalent geometry : angle 0.63946 (52432) hydrogen bonds : bond 0.04824 ( 1682) hydrogen bonds : angle 5.29756 ( 4611) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 663 time to evaluate : 1.594 Fit side-chains REVERT: A 33 ASP cc_start: 0.8192 (m-30) cc_final: 0.7707 (p0) REVERT: A 297 MET cc_start: 0.8490 (ttp) cc_final: 0.8192 (ttp) REVERT: A 339 ARG cc_start: 0.6660 (ttm110) cc_final: 0.6450 (ttm170) REVERT: A 392 GLU cc_start: 0.7666 (tt0) cc_final: 0.7355 (tm-30) REVERT: B 13 GLU cc_start: 0.7821 (mm-30) cc_final: 0.6993 (mm-30) REVERT: B 46 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7076 (mp0) REVERT: B 80 MET cc_start: 0.8281 (mtm) cc_final: 0.7711 (mpp) REVERT: C 33 ASP cc_start: 0.8221 (m-30) cc_final: 0.7777 (p0) REVERT: C 297 MET cc_start: 0.8484 (ttp) cc_final: 0.8214 (ttp) REVERT: C 339 ARG cc_start: 0.6631 (ttm110) cc_final: 0.6354 (ttm170) REVERT: D 13 GLU cc_start: 0.7816 (mm-30) cc_final: 0.6964 (mm-30) REVERT: D 46 GLU cc_start: 0.7612 (mm-30) cc_final: 0.6987 (mp0) REVERT: D 80 MET cc_start: 0.8312 (mtm) cc_final: 0.7876 (mpp) REVERT: E 33 ASP cc_start: 0.8196 (m-30) cc_final: 0.7725 (p0) REVERT: E 297 MET cc_start: 0.8416 (ttp) cc_final: 0.8063 (ttp) REVERT: E 339 ARG cc_start: 0.6524 (ttm110) cc_final: 0.6274 (ttm170) REVERT: E 431 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.6532 (tmm-80) REVERT: F 13 GLU cc_start: 0.7826 (mm-30) cc_final: 0.6997 (mm-30) REVERT: F 46 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7086 (mp0) REVERT: F 80 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7915 (mpp) REVERT: F 122 LEU cc_start: 0.8870 (tp) cc_final: 0.8662 (tp) REVERT: G 33 ASP cc_start: 0.8159 (m-30) cc_final: 0.7575 (p0) REVERT: G 297 MET cc_start: 0.8390 (ttp) cc_final: 0.8025 (ttp) REVERT: H 13 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6982 (mm-30) REVERT: H 46 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7071 (mp0) REVERT: H 80 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: I 33 ASP cc_start: 0.8210 (m-30) cc_final: 0.7619 (p0) REVERT: I 297 MET cc_start: 0.8480 (ttp) cc_final: 0.8184 (ttp) REVERT: J 13 GLU cc_start: 0.7836 (mm-30) cc_final: 0.6995 (mm-30) REVERT: J 46 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7467 (mt-10) REVERT: J 97 THR cc_start: 0.7955 (p) cc_final: 0.7648 (t) REVERT: J 122 LEU cc_start: 0.8898 (tp) cc_final: 0.8677 (tp) REVERT: K 297 MET cc_start: 0.8456 (ttp) cc_final: 0.8176 (ttp) REVERT: K 431 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.6518 (tmm-80) REVERT: L 13 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7077 (mm-30) REVERT: L 46 GLU cc_start: 0.7632 (mm-30) cc_final: 0.6962 (mp0) REVERT: L 80 MET cc_start: 0.8200 (mtm) cc_final: 0.7553 (mpp) REVERT: M 297 MET cc_start: 0.8418 (ttp) cc_final: 0.8065 (ttp) REVERT: M 339 ARG cc_start: 0.6511 (ttm110) cc_final: 0.5995 (ttm110) REVERT: N 13 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7077 (mm-30) REVERT: N 46 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7214 (mt-10) REVERT: N 80 MET cc_start: 0.8193 (mtm) cc_final: 0.7625 (mpp) REVERT: O 33 ASP cc_start: 0.8149 (m-30) cc_final: 0.7662 (p0) REVERT: O 88 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6528 (pt0) REVERT: O 297 MET cc_start: 0.8495 (ttp) cc_final: 0.8132 (ttp) REVERT: O 339 ARG cc_start: 0.6528 (ttm110) cc_final: 0.6311 (ttm170) REVERT: O 392 GLU cc_start: 0.7525 (tt0) cc_final: 0.7234 (tm-30) REVERT: O 431 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.6549 (tmm-80) REVERT: P 13 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7036 (mm-30) REVERT: P 80 MET cc_start: 0.8175 (mtm) cc_final: 0.7658 (mpp) REVERT: P 122 LEU cc_start: 0.8864 (tp) cc_final: 0.8659 (tp) outliers start: 43 outliers final: 30 residues processed: 691 average time/residue: 0.9068 time to fit residues: 739.1290 Evaluate side-chains 691 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 656 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 51 ARG Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 51 ARG Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 47 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 430 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 363 optimal weight: 7.9990 chunk 422 optimal weight: 5.9990 chunk 401 optimal weight: 0.9980 chunk 342 optimal weight: 10.0000 chunk 320 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 313 optimal weight: 0.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 123 ASN I 156 GLN ** I 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 156 GLN ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN O 156 GLN ** O 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.196427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.156681 restraints weight = 212776.854| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 6.20 r_work: 0.2906 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 38672 Z= 0.194 Angle : 0.675 5.854 52432 Z= 0.365 Chirality : 0.047 0.194 5584 Planarity : 0.006 0.056 6880 Dihedral : 5.631 21.907 5360 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.03 % Allowed : 10.14 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4760 helix: 1.66 (0.12), residues: 1880 sheet: -0.17 (0.18), residues: 744 loop : 0.29 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 305 TYR 0.020 0.002 TYR E 269 PHE 0.034 0.003 PHE O 345 TRP 0.020 0.002 TRP B 132 HIS 0.013 0.002 HIS E 153 Details of bonding type rmsd covalent geometry : bond 0.00408 (38672) covalent geometry : angle 0.67466 (52432) hydrogen bonds : bond 0.05093 ( 1682) hydrogen bonds : angle 5.37370 ( 4611) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 661 time to evaluate : 1.556 Fit side-chains REVERT: A 33 ASP cc_start: 0.8181 (m-30) cc_final: 0.7678 (p0) REVERT: A 297 MET cc_start: 0.8509 (ttp) cc_final: 0.8222 (ttp) REVERT: A 339 ARG cc_start: 0.6689 (ttm110) cc_final: 0.6483 (ttm170) REVERT: A 392 GLU cc_start: 0.7577 (tt0) cc_final: 0.7258 (tm-30) REVERT: B 13 GLU cc_start: 0.7807 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 46 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7061 (mp0) REVERT: B 80 MET cc_start: 0.8330 (mtm) cc_final: 0.7690 (mpp) REVERT: C 33 ASP cc_start: 0.8172 (m-30) cc_final: 0.7716 (p0) REVERT: C 297 MET cc_start: 0.8458 (ttp) cc_final: 0.8101 (ttp) REVERT: C 339 ARG cc_start: 0.6778 (ttm110) cc_final: 0.6513 (ttm170) REVERT: D 46 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6952 (mp0) REVERT: D 80 MET cc_start: 0.8318 (mtm) cc_final: 0.7765 (mpp) REVERT: E 33 ASP cc_start: 0.8189 (m-30) cc_final: 0.7726 (p0) REVERT: E 297 MET cc_start: 0.8397 (ttp) cc_final: 0.8036 (ttp) REVERT: E 339 ARG cc_start: 0.6633 (ttm110) cc_final: 0.6123 (ttm110) REVERT: E 431 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.6562 (tmm-80) REVERT: F 13 GLU cc_start: 0.7820 (mm-30) cc_final: 0.6992 (mm-30) REVERT: F 46 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7055 (mp0) REVERT: F 80 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8009 (mpp) REVERT: G 33 ASP cc_start: 0.8136 (m-30) cc_final: 0.7533 (p0) REVERT: G 297 MET cc_start: 0.8405 (ttp) cc_final: 0.8043 (ttp) REVERT: H 46 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7088 (mp0) REVERT: H 80 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.7938 (mpp) REVERT: I 33 ASP cc_start: 0.8157 (m-30) cc_final: 0.7551 (p0) REVERT: I 297 MET cc_start: 0.8451 (ttp) cc_final: 0.8097 (ttp) REVERT: J 13 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7011 (mm-30) REVERT: J 46 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7105 (mp0) REVERT: J 80 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8020 (mpp) REVERT: J 97 THR cc_start: 0.7956 (p) cc_final: 0.7652 (t) REVERT: J 122 LEU cc_start: 0.8918 (tp) cc_final: 0.8706 (tp) REVERT: K 297 MET cc_start: 0.8452 (ttp) cc_final: 0.8189 (ttp) REVERT: K 431 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.6565 (tmm-80) REVERT: L 13 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7105 (mm-30) REVERT: L 46 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7053 (mp0) REVERT: L 80 MET cc_start: 0.8287 (mtm) cc_final: 0.7631 (mpp) REVERT: M 297 MET cc_start: 0.8433 (ttp) cc_final: 0.8092 (ttp) REVERT: M 339 ARG cc_start: 0.6694 (ttm110) cc_final: 0.6182 (ttm110) REVERT: N 13 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7115 (mm-30) REVERT: N 46 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7268 (mt-10) REVERT: N 80 MET cc_start: 0.8385 (mtm) cc_final: 0.7891 (mpp) REVERT: O 33 ASP cc_start: 0.8132 (m-30) cc_final: 0.7654 (p0) REVERT: O 88 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6591 (pt0) REVERT: O 297 MET cc_start: 0.8473 (ttp) cc_final: 0.8110 (ttp) REVERT: O 339 ARG cc_start: 0.6717 (ttm110) cc_final: 0.6497 (ttm170) REVERT: O 392 GLU cc_start: 0.7510 (tt0) cc_final: 0.7217 (tm-30) REVERT: O 431 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.6550 (tmm-80) REVERT: P 13 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7050 (mm-30) REVERT: P 80 MET cc_start: 0.8254 (mtm) cc_final: 0.7722 (mpp) outliers start: 40 outliers final: 30 residues processed: 688 average time/residue: 0.8766 time to fit residues: 713.1187 Evaluate side-chains 681 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 645 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain P residue 47 SER Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 51 ARG Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 51 ARG Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 252 optimal weight: 3.9990 chunk 423 optimal weight: 2.9990 chunk 444 optimal weight: 0.9980 chunk 170 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 373 optimal weight: 0.0170 chunk 166 optimal weight: 0.9990 chunk 360 optimal weight: 2.9990 chunk 445 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 123 ASN E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 96 GLN G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 123 ASN K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 123 ASN M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN O 123 ASN O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.199582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.160629 restraints weight = 216154.909| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 6.26 r_work: 0.2951 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 38672 Z= 0.118 Angle : 0.563 5.181 52432 Z= 0.304 Chirality : 0.043 0.172 5584 Planarity : 0.004 0.048 6880 Dihedral : 5.212 19.852 5360 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.92 % Allowed : 10.29 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4760 helix: 1.79 (0.12), residues: 1928 sheet: -0.03 (0.18), residues: 776 loop : 0.25 (0.15), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 305 TYR 0.014 0.001 TYR A 269 PHE 0.032 0.002 PHE E 345 TRP 0.023 0.001 TRP B 132 HIS 0.007 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00242 (38672) covalent geometry : angle 0.56306 (52432) hydrogen bonds : bond 0.04026 ( 1682) hydrogen bonds : angle 5.10934 ( 4611) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 669 time to evaluate : 1.319 Fit side-chains REVERT: A 33 ASP cc_start: 0.8135 (m-30) cc_final: 0.7681 (p0) REVERT: A 339 ARG cc_start: 0.6604 (ttm110) cc_final: 0.6131 (ttm110) REVERT: A 392 GLU cc_start: 0.7650 (tt0) cc_final: 0.7314 (tm-30) REVERT: B 13 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7029 (mm-30) REVERT: B 46 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7387 (mt-10) REVERT: B 80 MET cc_start: 0.8279 (mtm) cc_final: 0.7761 (mpp) REVERT: C 33 ASP cc_start: 0.8206 (m-30) cc_final: 0.7773 (p0) REVERT: C 339 ARG cc_start: 0.6692 (ttm110) cc_final: 0.6421 (ttm170) REVERT: C 392 GLU cc_start: 0.7544 (tt0) cc_final: 0.7247 (tm-30) REVERT: D 13 GLU cc_start: 0.7756 (mm-30) cc_final: 0.6994 (mm-30) REVERT: D 46 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7181 (mt-10) REVERT: D 80 MET cc_start: 0.8279 (mtm) cc_final: 0.7883 (mpp) REVERT: E 33 ASP cc_start: 0.8196 (m-30) cc_final: 0.7757 (p0) REVERT: E 327 HIS cc_start: 0.8402 (m-70) cc_final: 0.8160 (m90) REVERT: E 339 ARG cc_start: 0.6475 (ttm110) cc_final: 0.6010 (ttm110) REVERT: E 431 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.6548 (tmm-80) REVERT: F 13 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7103 (mm-30) REVERT: F 46 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7228 (mt-10) REVERT: F 80 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7928 (mpp) REVERT: G 33 ASP cc_start: 0.8144 (m-30) cc_final: 0.7606 (p0) REVERT: H 13 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7016 (mm-30) REVERT: H 46 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7140 (mt-10) REVERT: H 80 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7915 (mpp) REVERT: I 33 ASP cc_start: 0.8162 (m-30) cc_final: 0.7635 (p0) REVERT: I 297 MET cc_start: 0.8453 (ttp) cc_final: 0.8142 (ttp) REVERT: J 13 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7027 (mm-30) REVERT: J 46 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7402 (mt-10) REVERT: J 80 MET cc_start: 0.8372 (mtp) cc_final: 0.7992 (mpp) REVERT: J 97 THR cc_start: 0.7986 (p) cc_final: 0.7672 (t) REVERT: K 88 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6671 (pt0) REVERT: K 297 MET cc_start: 0.8426 (ttp) cc_final: 0.8124 (ttp) REVERT: K 431 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6587 (tmm-80) REVERT: L 13 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7008 (mm-30) REVERT: L 46 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6866 (mp0) REVERT: L 80 MET cc_start: 0.8274 (mtm) cc_final: 0.7757 (mpp) REVERT: M 339 ARG cc_start: 0.6479 (ttm110) cc_final: 0.6003 (ttm110) REVERT: N 13 GLU cc_start: 0.7774 (mm-30) cc_final: 0.6996 (mm-30) REVERT: N 46 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7191 (mt-10) REVERT: N 80 MET cc_start: 0.8320 (mtm) cc_final: 0.7820 (mpp) REVERT: O 33 ASP cc_start: 0.8105 (m-30) cc_final: 0.7653 (p0) REVERT: O 88 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6610 (pt0) REVERT: O 339 ARG cc_start: 0.6657 (ttm110) cc_final: 0.6442 (ttm170) REVERT: O 392 GLU cc_start: 0.7482 (tt0) cc_final: 0.7185 (tm-30) REVERT: O 396 ASP cc_start: 0.8318 (m-30) cc_final: 0.7751 (m-30) REVERT: O 431 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.6523 (tmm-80) REVERT: P 13 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7018 (mm-30) REVERT: P 46 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7349 (mt-10) REVERT: P 80 MET cc_start: 0.8249 (mtm) cc_final: 0.7736 (mpp) outliers start: 36 outliers final: 24 residues processed: 697 average time/residue: 0.8875 time to fit residues: 730.9752 Evaluate side-chains 684 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 655 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain N residue 47 SER Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 469 optimal weight: 30.0000 chunk 290 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 411 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 278 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 123 ASN A 156 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 96 GLN C 156 GLN ** C 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 45 GLN E 96 GLN ** E 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 45 GLN G 96 GLN G 123 ASN G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN I 386 HIS ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN ** K 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN ** M 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN ** O 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.194706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.154714 restraints weight = 211019.160| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 6.05 r_work: 0.2885 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 38672 Z= 0.320 Angle : 0.822 8.277 52432 Z= 0.447 Chirality : 0.055 0.225 5584 Planarity : 0.008 0.078 6880 Dihedral : 5.960 24.007 5360 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.85 % Allowed : 10.63 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4760 helix: 1.27 (0.12), residues: 1928 sheet: -0.17 (0.18), residues: 744 loop : 0.12 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 187 TYR 0.028 0.004 TYR G 269 PHE 0.036 0.005 PHE E 345 TRP 0.016 0.003 TRP M 214 HIS 0.018 0.004 HIS M 153 Details of bonding type rmsd covalent geometry : bond 0.00689 (38672) covalent geometry : angle 0.82204 (52432) hydrogen bonds : bond 0.06037 ( 1682) hydrogen bonds : angle 5.60701 ( 4611) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 639 time to evaluate : 1.562 Fit side-chains REVERT: A 33 ASP cc_start: 0.8238 (m-30) cc_final: 0.7713 (p0) REVERT: A 297 MET cc_start: 0.8470 (ttp) cc_final: 0.8158 (ttp) REVERT: A 339 ARG cc_start: 0.6752 (ttm110) cc_final: 0.6539 (ttm170) REVERT: A 392 GLU cc_start: 0.7614 (tt0) cc_final: 0.7314 (tm-30) REVERT: B 46 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7140 (mp0) REVERT: B 80 MET cc_start: 0.8387 (mtm) cc_final: 0.7751 (mpp) REVERT: C 33 ASP cc_start: 0.8224 (m-30) cc_final: 0.7728 (p0) REVERT: C 297 MET cc_start: 0.8466 (ttp) cc_final: 0.8176 (ttp) REVERT: C 339 ARG cc_start: 0.6793 (ttm110) cc_final: 0.6526 (ttm170) REVERT: D 46 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7129 (mp0) REVERT: D 80 MET cc_start: 0.8353 (mtm) cc_final: 0.7855 (mpp) REVERT: E 33 ASP cc_start: 0.8239 (m-30) cc_final: 0.7762 (p0) REVERT: E 297 MET cc_start: 0.8396 (ttp) cc_final: 0.8114 (ttp) REVERT: E 339 ARG cc_start: 0.6771 (ttm110) cc_final: 0.6261 (ttm110) REVERT: E 431 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6684 (tmm-80) REVERT: G 297 MET cc_start: 0.8403 (ttp) cc_final: 0.8109 (ttp) REVERT: H 46 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7182 (mp0) REVERT: I 297 MET cc_start: 0.8477 (ttp) cc_final: 0.8124 (ttp) REVERT: J 97 THR cc_start: 0.7927 (p) cc_final: 0.7622 (t) REVERT: K 297 MET cc_start: 0.8479 (ttp) cc_final: 0.8128 (ttp) REVERT: K 431 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.6682 (tmm-80) REVERT: L 80 MET cc_start: 0.8284 (mtm) cc_final: 0.7647 (mpp) REVERT: M 297 MET cc_start: 0.8414 (ttp) cc_final: 0.8132 (ttp) REVERT: M 339 ARG cc_start: 0.6718 (ttm110) cc_final: 0.6163 (ttm110) REVERT: N 80 MET cc_start: 0.8296 (mtm) cc_final: 0.7663 (mpp) REVERT: O 33 ASP cc_start: 0.8199 (m-30) cc_final: 0.7682 (p0) REVERT: O 88 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6604 (pt0) REVERT: O 297 MET cc_start: 0.8465 (ttp) cc_final: 0.8186 (ttp) REVERT: O 339 ARG cc_start: 0.6777 (ttm110) cc_final: 0.6539 (ttm170) REVERT: O 392 GLU cc_start: 0.7504 (tt0) cc_final: 0.7237 (tm-30) REVERT: O 431 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.6739 (tmm-80) REVERT: P 80 MET cc_start: 0.8220 (mtm) cc_final: 0.7578 (mpp) outliers start: 33 outliers final: 22 residues processed: 665 average time/residue: 0.8958 time to fit residues: 703.3539 Evaluate side-chains 658 residues out of total 3984 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 633 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain E residue 382 ILE Chi-restraints excluded: chain E residue 431 ARG Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain H residue 47 SER Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 431 ARG Chi-restraints excluded: chain L residue 47 SER Chi-restraints excluded: chain M residue 63 THR Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 382 ILE Chi-restraints excluded: chain O residue 382 ILE Chi-restraints excluded: chain O residue 431 ARG Chi-restraints excluded: chain r residue 55 THR Chi-restraints excluded: chain s residue 51 ARG Chi-restraints excluded: chain s residue 55 THR Chi-restraints excluded: chain u residue 51 ARG Chi-restraints excluded: chain u residue 55 THR Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain w residue 55 THR Chi-restraints excluded: chain x residue 55 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 448 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 chunk 361 optimal weight: 0.8980 chunk 63 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN A 156 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 123 ASN C 156 GLN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 45 GLN E 96 GLN E 156 GLN ** E 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN G 45 GLN G 96 GLN G 156 GLN ** G 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 ASN I 96 GLN I 156 GLN ** I 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 36 ASN K 96 GLN K 156 GLN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 ASN M 96 GLN M 123 ASN M 156 GLN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 96 GLN O 156 GLN ** O 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 36 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.196351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.156527 restraints weight = 212914.700| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 6.06 r_work: 0.2900 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 38672 Z= 0.210 Angle : 0.699 6.312 52432 Z= 0.379 Chirality : 0.048 0.194 5584 Planarity : 0.006 0.064 6880 Dihedral : 5.740 22.334 5360 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.69 % Allowed : 10.88 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 4760 helix: 1.55 (0.12), residues: 1880 sheet: -0.17 (0.18), residues: 744 loop : 0.16 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 305 TYR 0.021 0.003 TYR E 269 PHE 0.034 0.003 PHE E 345 TRP 0.021 0.002 TRP N 132 HIS 0.014 0.002 HIS C 153 Details of bonding type rmsd covalent geometry : bond 0.00446 (38672) covalent geometry : angle 0.69869 (52432) hydrogen bonds : bond 0.05218 ( 1682) hydrogen bonds : angle 5.44827 ( 4611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16490.09 seconds wall clock time: 281 minutes 51.79 seconds (16911.79 seconds total)