Starting phenix.real_space_refine on Sat Mar 7 04:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jsx_22462/03_2026/7jsx_22462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jsx_22462/03_2026/7jsx_22462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jsx_22462/03_2026/7jsx_22462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jsx_22462/03_2026/7jsx_22462.map" model { file = "/net/cci-nas-00/data/ceres_data/7jsx_22462/03_2026/7jsx_22462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jsx_22462/03_2026/7jsx_22462.cif" } resolution = 2.06 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= 0.015 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 23856 2.51 5 N 6632 2.21 5 O 8045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 136 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: 38813 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: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "r" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "s" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "t" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "u" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "v" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "w" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "x" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 172 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 2, 'TRANS': 19} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Classifications: {'water': 106} Link IDs: {None: 105} 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: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} 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: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 102 Classifications: {'water': 102} Link IDs: {None: 101} 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: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} 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: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 104 Classifications: {'water': 104} Link IDs: {None: 103} Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "O" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "P" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Time building chain proxies: 8.93, per 1000 atoms: 0.23 Number of scatterers: 38813 At special positions: 0 Unit cell: (142.636, 142.636, 139.26, 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 8045 8.00 N 6632 7.00 C 23856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS C 247 " distance=2.19 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS G 247 " distance=2.20 Simple disulfide: pdb=" SG CYS I 247 " - pdb=" SG CYS K 247 " distance=2.20 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS O 247 " distance=2.15 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: 3.27 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 46.8% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 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: 4.218A pdb=" N VAL A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 195 removed outlier: 3.662A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) 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: 3.760A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 3.752A 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 47 through 51 removed outlier: 4.463A pdb=" N TYR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 51' 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: 3.505A 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: 3.864A 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: 4.363A 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: 4.501A 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: 3.753A 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: 3.577A 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: 3.514A 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: 6.387A 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: 3.750A 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 125 through 135 Processing helix chain 'r' and resid 125 through 135 Processing helix chain 's' and resid 125 through 135 Processing helix chain 't' and resid 125 through 135 Processing helix chain 'u' and resid 125 through 135 Processing helix chain 'v' and resid 125 through 135 Processing helix chain 'w' and resid 125 through 135 Processing helix chain 'x' and resid 125 through 135 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.408A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.533A 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: 6.811A 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: 6.727A 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: 6.826A 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: 6.265A pdb=" N LEU A 170 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS A 201 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N CYS A 172 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.157A 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: 7.306A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.334A 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: 6.665A 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: 6.798A 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: 4.409A 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: 8.165A 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: 6.588A 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: 7.306A 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: 6.400A 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: 4.650A 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: 6.808A 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: 6.969A 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: 8.278A 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: 6.683A 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: 6.873A 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: 4.390A 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: 8.281A 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: 8.021A pdb=" N SER G 379 " --> pdb=" O LEU G 326 " (cutoff:3.500A) removed outlier: 6.398A 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: 4.652A 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: 3.986A 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: 5.709A 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: 3.896A 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: 6.810A 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: 8.086A pdb=" N LYS I 201 " --> pdb=" O LEU I 170 " (cutoff:3.500A) removed outlier: 6.975A 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: 6.328A 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: 6.386A pdb=" N GLN J 124 " --> pdb=" O ALA J 103 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL J 105 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU J 122 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.612A 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: 3.905A 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: 6.805A 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: 6.430A 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: 8.715A 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: 6.690A 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: 4.950A 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: 6.845A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU M 37 " --> pdb=" O ASP M 137 " (cutoff:3.500A) removed outlier: 6.810A 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: 4.392A 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: 8.018A 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: 6.869A 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: 6.808A pdb=" N LEU O 37 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 6.810A 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: 8.085A 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: 6.539A 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: 8.023A 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: 7.303A 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: 6.275A pdb=" N ALA P 109 " --> pdb=" O ILE P 118 " (cutoff:3.500A) 1691 hydrogen bonds defined for protein. 4638 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: 7.33 Time building geometry restraints manager: 4.33 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: 6504 1.30 - 1.44: 10625 1.44 - 1.58: 20677 1.58 - 1.72: 351 1.72 - 1.86: 427 Bond restraints: 38584 Sorted by residual: 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 bond pdb=" SD MET G 266 " pdb=" CE MET G 266 " ideal model delta sigma weight residual 1.791 1.657 0.134 2.50e-02 1.60e+03 2.88e+01 ... (remaining 38579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 46805 2.53 - 5.06: 4609 5.06 - 7.59: 719 7.59 - 10.12: 154 10.12 - 12.65: 25 Bond angle restraints: 52312 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 111.36 124.01 -12.65 1.09e+00 8.42e-01 1.35e+02 angle pdb=" N TRP M 66 " pdb=" CA TRP M 66 " pdb=" C TRP M 66 " ideal model delta sigma weight residual 111.36 123.73 -12.37 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 52307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.24: 20477 14.24 - 28.49: 2049 28.49 - 42.73: 306 42.73 - 56.97: 88 56.97 - 71.21: 44 Dihedral angle restraints: 22964 sinusoidal: 9084 harmonic: 13880 Sorted by residual: dihedral pdb=" CB CYS M 247 " pdb=" SG CYS M 247 " pdb=" SG CYS O 247 " pdb=" CB CYS O 247 " ideal model delta sinusoidal sigma weight residual -86.00 -36.93 -49.07 1 1.00e+01 1.00e-02 3.31e+01 dihedral pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " pdb=" SG CYS C 247 " pdb=" CB CYS C 247 " ideal model delta sinusoidal sigma weight residual -86.00 -37.59 -48.41 1 1.00e+01 1.00e-02 3.23e+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 ... (remaining 22961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 4358 0.114 - 0.228: 949 0.228 - 0.342: 193 0.342 - 0.456: 68 0.456 - 0.569: 8 Chirality restraints: 5576 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 7.92e+00 ... (remaining 5573 not shown) Planarity restraints: 6856 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 6853 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4236 2.74 - 3.28: 40259 3.28 - 3.82: 74449 3.82 - 4.36: 92125 4.36 - 4.90: 145123 Nonbonded interactions: 356192 Sorted by model distance: 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 2.205 3.120 nonbonded pdb=" NE2 GLN C 156 " pdb=" OD2 ASP C 160 " model vdw 2.206 3.120 nonbonded pdb=" NE2 GLN E 156 " pdb=" OD2 ASP E 160 " model vdw 2.206 3.120 ... (remaining 356187 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: 0.01 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 33.890 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 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 0.167 38588 Z= 1.005 Angle : 1.679 14.181 52320 Z= 0.984 Chirality : 0.110 0.569 5576 Planarity : 0.014 0.064 6856 Dihedral : 11.972 71.215 14088 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.26 % Allowed : 4.01 % Favored : 94.73 % 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: -1.03 (0.11), residues: 4760 helix: -0.73 (0.10), residues: 1872 sheet: -0.23 (0.19), residues: 784 loop : -0.64 (0.13), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.005 ARG G 350 TYR 0.083 0.011 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 0.02152 (38584) covalent geometry : angle 1.67143 (52312) SS BOND : bond 0.15509 ( 4) SS BOND : angle 13.20364 ( 8) hydrogen bonds : bond 0.18604 ( 1691) hydrogen bonds : angle 7.40728 ( 4638) *********************** 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 854 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 805 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: q 131 GLU cc_start: 0.4096 (OUTLIER) cc_final: 0.3686 (tp30) REVERT: r 131 GLU cc_start: 0.4148 (OUTLIER) cc_final: 0.3553 (tp30) REVERT: s 131 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3457 (tp30) REVERT: u 131 GLU cc_start: 0.4235 (OUTLIER) cc_final: 0.3671 (tp30) REVERT: v 131 GLU cc_start: 0.4077 (OUTLIER) cc_final: 0.3505 (tp30) REVERT: w 131 GLU cc_start: 0.4451 (OUTLIER) cc_final: 0.3970 (tp30) REVERT: x 131 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.3541 (tp30) outliers start: 49 outliers final: 3 residues processed: 848 average time/residue: 0.8270 time to fit residues: 829.1899 Evaluate side-chains 610 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 600 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain q residue 131 GLU Chi-restraints excluded: chain r residue 131 GLU Chi-restraints excluded: chain s residue 131 GLU Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain u residue 131 GLU Chi-restraints excluded: chain v residue 131 GLU Chi-restraints excluded: chain w residue 131 GLU Chi-restraints excluded: chain x residue 131 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 470 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN A 207 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 8 ASN B 9 ASN B 29 GLN B 36 ASN C 115 ASN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN C 207 ASN C 238 HIS C 241 ASN C 267 HIS C 277 ASN ** C 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 ASN D 8 ASN D 9 ASN D 29 GLN D 36 ASN E 96 GLN E 115 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 207 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 8 ASN F 9 ASN F 29 GLN F 36 ASN G 115 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 207 ASN G 238 HIS G 241 ASN G 267 HIS G 277 ASN G 432 ASN H 8 ASN H 9 ASN H 29 GLN H 36 ASN H 115 GLN I 115 ASN I 123 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN I 207 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 8 ASN J 9 ASN J 29 GLN J 36 ASN J 124 GLN K 96 GLN K 115 ASN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 ASN K 207 ASN K 238 HIS K 241 ASN K 267 HIS K 277 ASN ** K 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 ASN L 8 ASN L 9 ASN L 29 GLN L 115 GLN M 96 GLN M 115 ASN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 163 ASN M 207 ASN M 238 HIS M 241 ASN M 267 HIS M 277 ASN ** M 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 432 ASN N 8 ASN N 9 ASN N 29 GLN N 36 ASN O 115 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 163 ASN O 207 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 8 ASN P 9 ASN P 29 GLN P 36 ASN P 115 GLN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.165562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.127504 restraints weight = 26403.823| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.31 r_work: 0.2999 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38588 Z= 0.174 Angle : 0.674 5.890 52320 Z= 0.362 Chirality : 0.045 0.189 5576 Planarity : 0.005 0.035 6856 Dihedral : 6.001 41.772 5370 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.54 % Allowed : 6.82 % Favored : 92.64 % 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: 0.48 (0.12), residues: 4760 helix: 0.84 (0.11), residues: 1960 sheet: 0.27 (0.19), residues: 696 loop : -0.02 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.014 0.002 TYR M 226 PHE 0.037 0.003 PHE I 345 TRP 0.017 0.002 TRP w 126 HIS 0.009 0.002 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00365 (38584) covalent geometry : angle 0.67083 (52312) SS BOND : bond 0.01199 ( 4) SS BOND : angle 5.32712 ( 8) hydrogen bonds : bond 0.04550 ( 1691) hydrogen bonds : angle 5.67973 ( 4638) *********************** 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 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 714 time to evaluate : 1.420 Fit side-chains REVERT: A 52 GLU cc_start: 0.8167 (tt0) cc_final: 0.7894 (tt0) REVERT: A 128 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7969 (mmtm) REVERT: A 339 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7380 (ttm170) REVERT: B 66 LEU cc_start: 0.8578 (mt) cc_final: 0.8318 (mt) REVERT: B 68 TYR cc_start: 0.8426 (m-80) cc_final: 0.8217 (m-80) REVERT: C 52 GLU cc_start: 0.8168 (tt0) cc_final: 0.7870 (tt0) REVERT: C 128 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7944 (mmtm) REVERT: D 66 LEU cc_start: 0.8614 (mt) cc_final: 0.8336 (mt) REVERT: D 68 TYR cc_start: 0.8403 (m-80) cc_final: 0.8187 (m-80) REVERT: E 52 GLU cc_start: 0.8166 (tt0) cc_final: 0.7898 (tt0) REVERT: F 66 LEU cc_start: 0.8608 (mt) cc_final: 0.8309 (mt) REVERT: F 68 TYR cc_start: 0.8467 (m-80) cc_final: 0.8250 (m-80) REVERT: G 52 GLU cc_start: 0.8177 (tt0) cc_final: 0.7890 (tt0) REVERT: G 128 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7928 (mmtm) REVERT: G 252 LYS cc_start: 0.8765 (mtpm) cc_final: 0.8453 (mmtm) REVERT: G 339 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7486 (ttm170) REVERT: H 66 LEU cc_start: 0.8615 (mt) cc_final: 0.8318 (mt) REVERT: I 52 GLU cc_start: 0.8122 (tt0) cc_final: 0.7857 (tt0) REVERT: I 252 LYS cc_start: 0.8772 (mtpm) cc_final: 0.8461 (mmtm) REVERT: J 66 LEU cc_start: 0.8635 (mt) cc_final: 0.8353 (mt) REVERT: K 52 GLU cc_start: 0.8155 (tt0) cc_final: 0.7864 (tt0) REVERT: K 128 LYS cc_start: 0.8325 (mmtt) cc_final: 0.7929 (mmtm) REVERT: K 252 LYS cc_start: 0.8791 (mtpm) cc_final: 0.8462 (mmtm) REVERT: K 339 ARG cc_start: 0.8002 (ttp80) cc_final: 0.7725 (ttp-110) REVERT: L 92 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8349 (mm-30) REVERT: M 52 GLU cc_start: 0.8204 (tt0) cc_final: 0.7917 (tt0) REVERT: M 128 LYS cc_start: 0.8312 (mmtt) cc_final: 0.7903 (mmtm) REVERT: N 34 VAL cc_start: 0.8510 (t) cc_final: 0.8270 (m) REVERT: N 66 LEU cc_start: 0.8639 (mt) cc_final: 0.8363 (mt) REVERT: O 52 GLU cc_start: 0.8210 (tt0) cc_final: 0.7926 (tt0) REVERT: O 128 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7988 (mmtm) REVERT: O 252 LYS cc_start: 0.8768 (mtpm) cc_final: 0.8462 (mmtm) outliers start: 21 outliers final: 9 residues processed: 714 average time/residue: 0.8331 time to fit residues: 702.1287 Evaluate side-chains 664 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 655 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain E residue 447 SER Chi-restraints excluded: chain G residue 447 SER Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 47 SER Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain M residue 447 SER Chi-restraints excluded: chain O residue 447 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 94 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 317 optimal weight: 6.9990 chunk 341 optimal weight: 4.9990 chunk 189 optimal weight: 9.9990 chunk 277 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN A 429 GLN B 36 ASN B 115 GLN C 45 GLN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 420 ASN D 8 ASN D 36 ASN D 115 GLN D 124 GLN E 45 GLN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 420 ASN E 429 GLN F 36 ASN F 115 GLN F 124 GLN G 45 GLN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN G 420 ASN G 429 GLN H 8 ASN H 36 ASN H 124 GLN I 45 GLN I 123 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 429 GLN J 36 ASN J 115 GLN J 124 GLN K 45 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 429 GLN L 8 ASN L 36 ASN M 45 GLN M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 420 ASN M 429 GLN N 36 ASN N 115 GLN N 124 GLN O 45 GLN O 96 GLN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 229 GLN O 420 ASN O 429 GLN P 8 ASN P 36 ASN P 124 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.113312 restraints weight = 25785.381| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 0.97 r_work: 0.2900 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 38588 Z= 0.286 Angle : 0.771 7.943 52320 Z= 0.414 Chirality : 0.050 0.220 5576 Planarity : 0.006 0.044 6856 Dihedral : 5.867 27.116 5344 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.82 % Allowed : 7.56 % Favored : 91.62 % 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: 0.55 (0.12), residues: 4760 helix: 0.98 (0.11), residues: 1952 sheet: -0.13 (0.18), residues: 752 loop : 0.13 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 253 TYR 0.021 0.003 TYR D 67 PHE 0.037 0.004 PHE O 345 TRP 0.018 0.002 TRP C 368 HIS 0.018 0.004 HIS K 153 Details of bonding type rmsd covalent geometry : bond 0.00596 (38584) covalent geometry : angle 0.76692 (52312) SS BOND : bond 0.02679 ( 4) SS BOND : angle 6.10239 ( 8) hydrogen bonds : bond 0.05414 ( 1691) hydrogen bonds : angle 5.85215 ( 4638) *********************** 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 747 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 715 time to evaluate : 1.244 Fit side-chains REVERT: A 52 GLU cc_start: 0.8156 (tt0) cc_final: 0.7868 (tt0) REVERT: A 128 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8027 (mmtm) REVERT: B 36 ASN cc_start: 0.9029 (m-40) cc_final: 0.8814 (m110) REVERT: B 92 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8427 (mm-30) REVERT: C 128 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8030 (mmtm) REVERT: C 305 ARG cc_start: 0.8292 (tpt170) cc_final: 0.7878 (tpt90) REVERT: C 339 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7747 (ttm110) REVERT: D 55 GLU cc_start: 0.7677 (pm20) cc_final: 0.7391 (pm20) REVERT: D 92 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8475 (mm-30) REVERT: E 305 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7414 (tpp80) REVERT: F 92 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8437 (mm-30) REVERT: G 45 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8389 (mm-40) REVERT: G 128 LYS cc_start: 0.8484 (mmtt) cc_final: 0.7914 (mmtm) REVERT: G 252 LYS cc_start: 0.8881 (mtpm) cc_final: 0.8521 (mmtm) REVERT: G 305 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7407 (tpp80) REVERT: H 36 ASN cc_start: 0.9032 (m-40) cc_final: 0.8819 (m110) REVERT: H 88 GLN cc_start: 0.7920 (mt0) cc_final: 0.7338 (tp-100) REVERT: I 45 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8387 (mm-40) REVERT: I 252 LYS cc_start: 0.8854 (mtpm) cc_final: 0.8518 (mmtm) REVERT: J 36 ASN cc_start: 0.9024 (m-40) cc_final: 0.8820 (m110) REVERT: J 92 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8421 (mm-30) REVERT: K 45 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8399 (mm-40) REVERT: K 128 LYS cc_start: 0.8488 (mmtt) cc_final: 0.7935 (mmtm) REVERT: K 252 LYS cc_start: 0.8870 (mtpm) cc_final: 0.8524 (mmtm) REVERT: K 339 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7750 (ttm-80) REVERT: L 36 ASN cc_start: 0.9018 (m-40) cc_final: 0.8805 (m110) REVERT: L 55 GLU cc_start: 0.7672 (pm20) cc_final: 0.7387 (pm20) REVERT: M 128 LYS cc_start: 0.8477 (mmtt) cc_final: 0.7990 (mmtm) REVERT: N 92 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8449 (mm-30) REVERT: O 128 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8019 (mmtm) REVERT: O 252 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8512 (mmtm) REVERT: P 36 ASN cc_start: 0.9047 (m-40) cc_final: 0.8813 (m110) outliers start: 32 outliers final: 18 residues processed: 729 average time/residue: 0.8810 time to fit residues: 754.8174 Evaluate side-chains 700 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 682 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 447 SER Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 447 SER Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 167 optimal weight: 9.9990 chunk 408 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 30.0000 chunk 272 optimal weight: 0.7980 chunk 279 optimal weight: 0.0030 chunk 327 optimal weight: 10.0000 chunk 62 optimal weight: 0.0040 chunk 398 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.7604 ------------------------------------------------------------------------------- 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 GLN C 96 GLN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN C 429 GLN D 36 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 123 ASN ** I 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 36 ASN O 45 GLN O 96 GLN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 229 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.160263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.117516 restraints weight = 26142.229| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.00 r_work: 0.2986 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 38588 Z= 0.117 Angle : 0.555 5.365 52320 Z= 0.296 Chirality : 0.042 0.169 5576 Planarity : 0.004 0.030 6856 Dihedral : 5.133 24.082 5344 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.44 % Allowed : 8.18 % Favored : 91.38 % 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: 1.02 (0.12), residues: 4760 helix: 1.64 (0.12), residues: 1912 sheet: -0.18 (0.18), residues: 736 loop : 0.23 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.012 0.001 TYR A 269 PHE 0.033 0.002 PHE G 345 TRP 0.007 0.001 TRP x 126 HIS 0.006 0.001 HIS I 153 Details of bonding type rmsd covalent geometry : bond 0.00241 (38584) covalent geometry : angle 0.55313 (52312) SS BOND : bond 0.01737 ( 4) SS BOND : angle 3.95011 ( 8) hydrogen bonds : bond 0.03762 ( 1691) hydrogen bonds : angle 5.25806 ( 4638) *********************** 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 723 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 706 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8460 (mmtt) cc_final: 0.8003 (mmtm) REVERT: A 339 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.7543 (ttp-110) REVERT: B 53 SER cc_start: 0.8462 (p) cc_final: 0.8226 (t) REVERT: B 66 LEU cc_start: 0.8478 (mt) cc_final: 0.8259 (mt) REVERT: B 92 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8405 (mm-30) REVERT: C 128 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7973 (mmtm) REVERT: C 305 ARG cc_start: 0.8306 (tpt170) cc_final: 0.7882 (tpt170) REVERT: C 339 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7652 (ttm110) REVERT: C 375 MET cc_start: 0.8970 (tpp) cc_final: 0.8764 (tpp) REVERT: D 55 GLU cc_start: 0.7501 (pm20) cc_final: 0.7090 (pm20) REVERT: D 66 LEU cc_start: 0.8521 (mt) cc_final: 0.8305 (mt) REVERT: D 92 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8484 (mm-30) REVERT: E 305 ARG cc_start: 0.8310 (tpt170) cc_final: 0.7563 (mmp-170) REVERT: E 338 GLU cc_start: 0.7469 (mp0) cc_final: 0.7218 (mp0) REVERT: F 53 SER cc_start: 0.8513 (p) cc_final: 0.8313 (p) REVERT: F 66 LEU cc_start: 0.8498 (mt) cc_final: 0.8259 (mt) REVERT: F 92 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8385 (mm-30) REVERT: G 128 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7969 (mmtm) REVERT: G 252 LYS cc_start: 0.8827 (mtpm) cc_final: 0.8480 (mmtm) REVERT: G 305 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7519 (tpp80) REVERT: G 338 GLU cc_start: 0.7541 (mp0) cc_final: 0.7340 (mp0) REVERT: I 252 LYS cc_start: 0.8768 (mtpm) cc_final: 0.8422 (mmtm) REVERT: J 92 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8431 (mm-30) REVERT: K 252 LYS cc_start: 0.8775 (mtpm) cc_final: 0.8427 (mmtm) REVERT: K 339 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7755 (ttm-80) REVERT: K 446 ARG cc_start: 0.8536 (mtm-85) cc_final: 0.8320 (mtm-85) REVERT: L 55 GLU cc_start: 0.7490 (pm20) cc_final: 0.7071 (pm20) REVERT: M 128 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7927 (mmtm) REVERT: M 355 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8171 (tp30) REVERT: M 387 MET cc_start: 0.8853 (tpp) cc_final: 0.8600 (tpp) REVERT: N 53 SER cc_start: 0.8498 (p) cc_final: 0.8243 (t) REVERT: N 66 LEU cc_start: 0.8523 (mt) cc_final: 0.8305 (mt) REVERT: N 92 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8447 (mm-30) REVERT: O 128 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8060 (mmtm) REVERT: O 252 LYS cc_start: 0.8760 (mtpm) cc_final: 0.8412 (mmtm) REVERT: O 375 MET cc_start: 0.8957 (tpp) cc_final: 0.8756 (tpp) outliers start: 17 outliers final: 2 residues processed: 708 average time/residue: 0.8591 time to fit residues: 715.7776 Evaluate side-chains 664 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 662 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 271 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 254 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 377 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 96 GLN A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN B 36 ASN C 95 ASN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN E 96 GLN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 96 GLN I 123 ASN I 153 HIS I 156 GLN I 229 GLN I 401 GLN J 36 ASN K 95 ASN K 96 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN K 401 GLN L 36 ASN M 95 ASN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 229 GLN M 401 GLN N 36 ASN O 96 GLN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN P 36 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.157334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.114122 restraints weight = 25792.057| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.00 r_work: 0.2936 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38588 Z= 0.178 Angle : 0.634 6.122 52320 Z= 0.337 Chirality : 0.045 0.202 5576 Planarity : 0.005 0.045 6856 Dihedral : 5.336 24.763 5344 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.44 % Allowed : 8.77 % Favored : 90.79 % 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: 1.00 (0.12), residues: 4760 helix: 1.55 (0.12), residues: 1912 sheet: -0.11 (0.19), residues: 736 loop : 0.26 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 339 TYR 0.015 0.002 TYR C 269 PHE 0.032 0.003 PHE O 345 TRP 0.011 0.001 TRP G 368 HIS 0.014 0.002 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00372 (38584) covalent geometry : angle 0.63094 (52312) SS BOND : bond 0.02382 ( 4) SS BOND : angle 4.95215 ( 8) hydrogen bonds : bond 0.04412 ( 1691) hydrogen bonds : angle 5.38704 ( 4638) *********************** 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 708 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 691 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8311 (m) REVERT: A 339 ARG cc_start: 0.8014 (ttm-80) cc_final: 0.7655 (ttp-110) REVERT: B 92 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8442 (mm-30) REVERT: C 128 LYS cc_start: 0.8348 (mmtt) cc_final: 0.7957 (mmtm) REVERT: C 305 ARG cc_start: 0.8266 (tpt170) cc_final: 0.7456 (tpp80) REVERT: C 339 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7723 (ttm110) REVERT: D 92 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8518 (mm-30) REVERT: E 305 ARG cc_start: 0.8264 (tpt170) cc_final: 0.7529 (mmp-170) REVERT: F 66 LEU cc_start: 0.8599 (mt) cc_final: 0.8351 (mt) REVERT: F 92 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8415 (mm-30) REVERT: G 252 LYS cc_start: 0.8864 (mtpm) cc_final: 0.8511 (mmtm) REVERT: G 305 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7537 (tpp80) REVERT: I 252 LYS cc_start: 0.8856 (mtpm) cc_final: 0.8503 (mmtm) REVERT: I 305 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7503 (tpp80) REVERT: J 92 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8395 (mm-30) REVERT: K 252 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8506 (mmtm) REVERT: K 339 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7772 (ttm-80) REVERT: M 53 CYS cc_start: 0.8582 (m) cc_final: 0.8370 (m) REVERT: M 128 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7896 (mmtm) REVERT: M 305 ARG cc_start: 0.8265 (tpt170) cc_final: 0.7482 (tpp80) REVERT: N 92 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8434 (mm-30) REVERT: O 53 CYS cc_start: 0.8561 (m) cc_final: 0.8349 (m) REVERT: O 128 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8003 (mmtm) REVERT: O 252 LYS cc_start: 0.8850 (mtpm) cc_final: 0.8499 (mmtm) REVERT: O 305 ARG cc_start: 0.8240 (tpt170) cc_final: 0.7310 (tpp80) outliers start: 17 outliers final: 13 residues processed: 707 average time/residue: 0.8512 time to fit residues: 708.7428 Evaluate side-chains 681 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 667 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 37 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 389 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 330 optimal weight: 8.9990 chunk 393 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 GLN D 36 ASN E 96 GLN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 95 ASN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 95 ASN I 96 GLN I 123 ASN I 156 GLN J 36 ASN K 95 ASN K 96 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 36 ASN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN M 401 GLN N 36 ASN O 96 GLN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 401 GLN P 36 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.112819 restraints weight = 25793.793| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.15 r_work: 0.2924 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 38588 Z= 0.218 Angle : 0.679 6.319 52320 Z= 0.363 Chirality : 0.046 0.213 5576 Planarity : 0.005 0.047 6856 Dihedral : 5.531 25.913 5344 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.77 % Allowed : 8.74 % Favored : 90.48 % 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: 1.35 (0.12), residues: 1912 sheet: -0.27 (0.19), residues: 744 loop : 0.41 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 339 TYR 0.017 0.002 TYR E 269 PHE 0.034 0.003 PHE I 345 TRP 0.012 0.001 TRP E 368 HIS 0.014 0.002 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00454 (38584) covalent geometry : angle 0.67622 (52312) SS BOND : bond 0.02572 ( 4) SS BOND : angle 5.43571 ( 8) hydrogen bonds : bond 0.04710 ( 1691) hydrogen bonds : angle 5.51396 ( 4638) *********************** 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 739 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 709 time to evaluate : 1.343 Fit side-chains REVERT: A 53 CYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 128 LYS cc_start: 0.8394 (mmtt) cc_final: 0.7969 (mmtm) REVERT: A 339 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7663 (ttp-110) REVERT: B 92 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8439 (mm-30) REVERT: C 128 LYS cc_start: 0.8378 (mmtt) cc_final: 0.7968 (mmtm) REVERT: C 305 ARG cc_start: 0.8287 (tpt170) cc_final: 0.7480 (tpp80) REVERT: C 339 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7678 (ttm110) REVERT: D 92 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8471 (mm-30) REVERT: E 305 ARG cc_start: 0.8307 (tpt170) cc_final: 0.7506 (tpp80) REVERT: F 92 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8395 (mm-30) REVERT: G 128 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7885 (mmtm) REVERT: G 252 LYS cc_start: 0.8866 (mtpm) cc_final: 0.8507 (mmtm) REVERT: G 305 ARG cc_start: 0.8319 (tpt170) cc_final: 0.7548 (tpp80) REVERT: G 358 ARG cc_start: 0.8324 (mmm-85) cc_final: 0.8087 (mmm160) REVERT: H 68 TYR cc_start: 0.8476 (m-80) cc_final: 0.8267 (m-80) REVERT: I 252 LYS cc_start: 0.8853 (mtpm) cc_final: 0.8500 (mmtm) REVERT: I 305 ARG cc_start: 0.8290 (tpt170) cc_final: 0.7446 (tpp80) REVERT: I 358 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8158 (mmm160) REVERT: J 92 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8432 (mm-30) REVERT: K 128 LYS cc_start: 0.8319 (mmtt) cc_final: 0.7880 (mmtm) REVERT: K 252 LYS cc_start: 0.8863 (mtpm) cc_final: 0.8501 (mmtm) REVERT: K 305 ARG cc_start: 0.8282 (tpt170) cc_final: 0.7444 (tpp80) REVERT: K 339 ARG cc_start: 0.8107 (ttp80) cc_final: 0.7764 (ttm-80) REVERT: L 36 ASN cc_start: 0.8932 (m-40) cc_final: 0.8727 (m110) REVERT: M 53 CYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8372 (m) REVERT: M 128 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7885 (mmtm) REVERT: M 305 ARG cc_start: 0.8295 (tpt170) cc_final: 0.7430 (tpp80) REVERT: N 92 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8417 (mm-30) REVERT: O 53 CYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (m) REVERT: O 128 LYS cc_start: 0.8399 (mmtt) cc_final: 0.7965 (mmtm) REVERT: O 252 LYS cc_start: 0.8856 (mtpm) cc_final: 0.8497 (mmtm) REVERT: O 305 ARG cc_start: 0.8274 (tpt170) cc_final: 0.7458 (tpp80) outliers start: 30 outliers final: 24 residues processed: 736 average time/residue: 0.8658 time to fit residues: 751.8953 Evaluate side-chains 713 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 686 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain M residue 53 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain O residue 53 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 345 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 210 optimal weight: 9.9990 chunk 461 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN C 401 GLN D 36 ASN E 95 ASN E 96 GLN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 95 ASN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 95 ASN I 96 GLN I 123 ASN I 156 GLN I 401 GLN J 36 ASN K 95 ASN K 96 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 36 ASN O 96 GLN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN O 401 GLN P 36 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.156239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.114758 restraints weight = 25685.714| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 0.93 r_work: 0.2940 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work: 0.2643 rms_B_bonded: 4.65 restraints_weight: 0.1250 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 38588 Z= 0.209 Angle : 0.669 7.840 52320 Z= 0.357 Chirality : 0.046 0.205 5576 Planarity : 0.005 0.036 6856 Dihedral : 5.497 26.104 5344 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.77 % Allowed : 8.74 % Favored : 90.48 % 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: 1.25 (0.12), residues: 1960 sheet: -0.37 (0.19), residues: 744 loop : 0.42 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 319 TYR 0.017 0.002 TYR F 32 PHE 0.035 0.003 PHE C 345 TRP 0.011 0.001 TRP C 368 HIS 0.013 0.002 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00437 (38584) covalent geometry : angle 0.66536 (52312) SS BOND : bond 0.02528 ( 4) SS BOND : angle 5.41753 ( 8) hydrogen bonds : bond 0.04616 ( 1691) hydrogen bonds : angle 5.46768 ( 4638) *********************** 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 724 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 694 time to evaluate : 1.272 Fit side-chains REVERT: A 53 CYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8559 (m) REVERT: B 92 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8561 (mm-30) REVERT: C 128 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8151 (mmtm) REVERT: C 305 ARG cc_start: 0.8490 (tpt170) cc_final: 0.7661 (tpp80) REVERT: C 339 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7827 (ttm110) REVERT: D 92 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8600 (mm-30) REVERT: E 305 ARG cc_start: 0.8487 (tpt170) cc_final: 0.7677 (tpp80) REVERT: F 92 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8517 (mm-30) REVERT: G 128 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8062 (mmtm) REVERT: G 252 LYS cc_start: 0.8994 (mtpm) cc_final: 0.8602 (mmtm) REVERT: G 305 ARG cc_start: 0.8521 (tpt170) cc_final: 0.7710 (tpp80) REVERT: G 358 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.8192 (mmm160) REVERT: H 55 GLU cc_start: 0.7770 (pm20) cc_final: 0.7533 (pm20) REVERT: H 68 TYR cc_start: 0.8594 (m-80) cc_final: 0.8387 (m-80) REVERT: I 252 LYS cc_start: 0.8976 (mtpm) cc_final: 0.8595 (mmtm) REVERT: I 305 ARG cc_start: 0.8453 (tpt170) cc_final: 0.7594 (tpp80) REVERT: I 358 ARG cc_start: 0.8490 (mmm-85) cc_final: 0.8257 (mmm160) REVERT: J 92 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8543 (mm-30) REVERT: K 128 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8061 (mmtm) REVERT: K 252 LYS cc_start: 0.8981 (mtpm) cc_final: 0.8593 (mmtm) REVERT: K 305 ARG cc_start: 0.8491 (tpt170) cc_final: 0.7684 (tpp80) REVERT: K 339 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7904 (ttm-80) REVERT: L 36 ASN cc_start: 0.9011 (m-40) cc_final: 0.8739 (m110) REVERT: M 128 LYS cc_start: 0.8463 (mmtt) cc_final: 0.8245 (mmmm) REVERT: M 305 ARG cc_start: 0.8499 (tpt170) cc_final: 0.7606 (tpp80) REVERT: N 92 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8555 (mm-30) REVERT: O 128 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8137 (mmtm) REVERT: O 252 LYS cc_start: 0.8982 (mtpm) cc_final: 0.8591 (mmtm) REVERT: O 305 ARG cc_start: 0.8473 (tpt170) cc_final: 0.7597 (tpp80) REVERT: O 436 ASP cc_start: 0.8619 (t0) cc_final: 0.8411 (t70) outliers start: 30 outliers final: 25 residues processed: 721 average time/residue: 0.8575 time to fit residues: 728.0207 Evaluate side-chains 704 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 678 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 69 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 463 optimal weight: 8.9990 chunk 252 optimal weight: 1.9990 chunk 467 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 151 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 36 ASN E 95 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 95 ASN G 96 GLN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 95 ASN I 123 ASN I 156 GLN I 401 GLN K 96 GLN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 36 ASN O 95 ASN O 96 GLN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114087 restraints weight = 25663.514| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.03 r_work: 0.2935 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 38588 Z= 0.182 Angle : 0.640 6.380 52320 Z= 0.341 Chirality : 0.045 0.199 5576 Planarity : 0.004 0.035 6856 Dihedral : 5.390 25.517 5344 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.75 % Allowed : 9.05 % Favored : 90.20 % 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: 0.95 (0.12), residues: 4760 helix: 1.35 (0.12), residues: 1960 sheet: -0.34 (0.18), residues: 736 loop : 0.48 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O 319 TYR 0.017 0.002 TYR F 32 PHE 0.034 0.003 PHE A 345 TRP 0.010 0.001 TRP C 368 HIS 0.012 0.002 HIS A 153 Details of bonding type rmsd covalent geometry : bond 0.00380 (38584) covalent geometry : angle 0.63655 (52312) SS BOND : bond 0.02395 ( 4) SS BOND : angle 5.12531 ( 8) hydrogen bonds : bond 0.04381 ( 1691) hydrogen bonds : angle 5.36619 ( 4638) *********************** 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 717 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 688 time to evaluate : 1.467 Fit side-chains REVERT: A 53 CYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8341 (m) REVERT: A 128 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7756 (mmtm) REVERT: A 339 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7682 (ttp-110) REVERT: B 92 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8433 (mm-30) REVERT: C 128 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8013 (mmtm) REVERT: C 305 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7511 (tpp80) REVERT: C 339 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7681 (ttm170) REVERT: D 92 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8448 (mm-30) REVERT: E 305 ARG cc_start: 0.8293 (tpt170) cc_final: 0.7542 (mmp-170) REVERT: F 92 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8406 (mm-30) REVERT: G 128 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7944 (mmtm) REVERT: G 252 LYS cc_start: 0.8875 (mtpm) cc_final: 0.8519 (mmtm) REVERT: G 305 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7546 (mmp-170) REVERT: H 68 TYR cc_start: 0.8498 (m-80) cc_final: 0.8279 (m-80) REVERT: I 252 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8511 (mmtm) REVERT: I 305 ARG cc_start: 0.8260 (tpt170) cc_final: 0.7422 (tpp80) REVERT: I 358 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8177 (mmm160) REVERT: J 92 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8378 (mm-30) REVERT: K 128 LYS cc_start: 0.8298 (mmtt) cc_final: 0.8097 (mmmm) REVERT: K 252 LYS cc_start: 0.8866 (mtpm) cc_final: 0.8511 (mmtm) REVERT: K 305 ARG cc_start: 0.8294 (tpt170) cc_final: 0.7461 (tpp80) REVERT: K 339 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7781 (ttm-80) REVERT: L 36 ASN cc_start: 0.8926 (m-40) cc_final: 0.8701 (m110) REVERT: M 128 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8094 (mmmm) REVERT: M 305 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7410 (tpp80) REVERT: N 92 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8428 (mm-30) REVERT: O 128 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8043 (mmtm) REVERT: O 252 LYS cc_start: 0.8860 (mtpm) cc_final: 0.8504 (mmtm) REVERT: O 305 ARG cc_start: 0.8296 (tpt170) cc_final: 0.7449 (tpp80) REVERT: O 436 ASP cc_start: 0.8571 (t0) cc_final: 0.8336 (t70) outliers start: 29 outliers final: 28 residues processed: 716 average time/residue: 0.8423 time to fit residues: 712.3890 Evaluate side-chains 699 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 670 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 429 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 412 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 273 optimal weight: 0.4980 chunk 147 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 363 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 36 ASN E 95 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN F 124 GLN G 95 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 95 ASN I 123 ASN I 156 GLN I 401 GLN K 95 ASN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 36 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.155619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112874 restraints weight = 25747.487| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 0.97 r_work: 0.2900 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 38588 Z= 0.234 Angle : 0.705 8.452 52320 Z= 0.376 Chirality : 0.047 0.218 5576 Planarity : 0.005 0.036 6856 Dihedral : 5.603 26.540 5344 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.93 % Allowed : 9.00 % Favored : 90.07 % 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: 0.88 (0.12), residues: 4760 helix: 1.31 (0.12), residues: 1912 sheet: -0.47 (0.18), residues: 744 loop : 0.50 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 319 TYR 0.019 0.003 TYR F 32 PHE 0.036 0.003 PHE C 345 TRP 0.013 0.001 TRP G 368 HIS 0.014 0.003 HIS K 153 Details of bonding type rmsd covalent geometry : bond 0.00490 (38584) covalent geometry : angle 0.70153 (52312) SS BOND : bond 0.02683 ( 4) SS BOND : angle 5.67555 ( 8) hydrogen bonds : bond 0.04817 ( 1691) hydrogen bonds : angle 5.51333 ( 4638) *********************** 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 718 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 682 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8397 (m) REVERT: A 128 LYS cc_start: 0.8207 (mmpt) cc_final: 0.7775 (mmtm) REVERT: A 339 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7673 (ttp-110) REVERT: B 92 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8453 (mm-30) REVERT: B 98 LYS cc_start: 0.8947 (ttmm) cc_final: 0.8728 (ttmt) REVERT: C 128 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8017 (mmtm) REVERT: C 305 ARG cc_start: 0.8329 (tpt170) cc_final: 0.7520 (tpp80) REVERT: D 92 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8478 (mm-30) REVERT: E 305 ARG cc_start: 0.8324 (tpt170) cc_final: 0.7539 (tpp80) REVERT: F 92 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8434 (mm-30) REVERT: G 252 LYS cc_start: 0.8890 (mtpm) cc_final: 0.8533 (mmtm) REVERT: G 305 ARG cc_start: 0.8346 (tpt170) cc_final: 0.7556 (tpp80) REVERT: H 68 TYR cc_start: 0.8513 (m-80) cc_final: 0.8290 (m-80) REVERT: I 252 LYS cc_start: 0.8872 (mtpm) cc_final: 0.8525 (mmtm) REVERT: I 305 ARG cc_start: 0.8299 (tpt170) cc_final: 0.7468 (tpp80) REVERT: J 92 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8420 (mm-30) REVERT: K 128 LYS cc_start: 0.8347 (mmtt) cc_final: 0.8102 (mmmm) REVERT: K 252 LYS cc_start: 0.8884 (mtpm) cc_final: 0.8529 (mmtm) REVERT: K 305 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7517 (tpp80) REVERT: K 339 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7773 (ttm-80) REVERT: L 36 ASN cc_start: 0.8967 (m-40) cc_final: 0.8751 (m110) REVERT: M 53 CYS cc_start: 0.8606 (m) cc_final: 0.8391 (m) REVERT: M 128 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8110 (mmmm) REVERT: M 305 ARG cc_start: 0.8316 (tpt170) cc_final: 0.7469 (tpp80) REVERT: N 92 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8453 (mm-30) REVERT: O 53 CYS cc_start: 0.8604 (m) cc_final: 0.8401 (m) REVERT: O 128 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8017 (mmtm) REVERT: O 252 LYS cc_start: 0.8876 (mtpm) cc_final: 0.8519 (mmtm) REVERT: O 305 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7487 (tpp80) REVERT: O 436 ASP cc_start: 0.8589 (t0) cc_final: 0.8350 (t70) outliers start: 36 outliers final: 33 residues processed: 717 average time/residue: 0.8399 time to fit residues: 711.9965 Evaluate side-chains 709 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 675 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 137 LYS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 137 LYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 137 LYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain q residue 115 VAL Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain s residue 115 VAL Chi-restraints excluded: chain t residue 115 VAL Chi-restraints excluded: chain u residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain w residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 403 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 0.0980 chunk 324 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 362 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 331 optimal weight: 2.9990 chunk 428 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 36 ASN E 95 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 95 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 95 ASN I 123 ASN I 156 GLN K 95 ASN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 36 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.157026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.115134 restraints weight = 25893.654| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 0.95 r_work: 0.2949 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38588 Z= 0.157 Angle : 0.620 6.210 52320 Z= 0.330 Chirality : 0.044 0.191 5576 Planarity : 0.004 0.034 6856 Dihedral : 5.322 25.031 5344 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.67 % Allowed : 9.28 % Favored : 90.05 % 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: 0.98 (0.12), residues: 4760 helix: 1.42 (0.12), residues: 1960 sheet: -0.38 (0.18), residues: 736 loop : 0.48 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 339 TYR 0.019 0.002 TYR F 32 PHE 0.035 0.002 PHE E 345 TRP 0.009 0.001 TRP E 368 HIS 0.012 0.002 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00331 (38584) covalent geometry : angle 0.61712 (52312) SS BOND : bond 0.02257 ( 4) SS BOND : angle 4.89136 ( 8) hydrogen bonds : bond 0.04148 ( 1691) hydrogen bonds : angle 5.29624 ( 4638) ********************** 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 706 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 680 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 CYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8336 (m) REVERT: A 128 LYS cc_start: 0.8152 (mmpt) cc_final: 0.7747 (mmtm) REVERT: A 339 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7683 (ttp-110) REVERT: B 92 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8419 (mm-30) REVERT: C 305 ARG cc_start: 0.8281 (tpt170) cc_final: 0.7741 (ttt90) REVERT: C 339 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.7682 (ttp-110) REVERT: D 92 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8431 (mm-30) REVERT: E 305 ARG cc_start: 0.8275 (tpt170) cc_final: 0.7505 (mmp-170) REVERT: F 66 LEU cc_start: 0.8589 (mt) cc_final: 0.8326 (mt) REVERT: F 92 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8421 (mm-30) REVERT: G 252 LYS cc_start: 0.8902 (mtpm) cc_final: 0.8536 (mmtm) REVERT: G 305 ARG cc_start: 0.8347 (tpt170) cc_final: 0.7560 (mmp-170) REVERT: H 87 MET cc_start: 0.8516 (tpt) cc_final: 0.8307 (tpt) REVERT: I 252 LYS cc_start: 0.8886 (mtpm) cc_final: 0.8529 (mmtm) REVERT: I 305 ARG cc_start: 0.8280 (tpt170) cc_final: 0.7421 (tpp80) REVERT: I 358 ARG cc_start: 0.8411 (mmm-85) cc_final: 0.8205 (mmm160) REVERT: J 92 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8361 (mm-30) REVERT: K 128 LYS cc_start: 0.8305 (mmtt) cc_final: 0.8080 (mmmm) REVERT: K 252 LYS cc_start: 0.8903 (mtpm) cc_final: 0.8539 (mmtm) REVERT: K 305 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7445 (tpp80) REVERT: K 339 ARG cc_start: 0.8082 (ttp80) cc_final: 0.7751 (ttm-80) REVERT: M 53 CYS cc_start: 0.8572 (m) cc_final: 0.8363 (m) REVERT: M 128 LYS cc_start: 0.8318 (mmtt) cc_final: 0.8115 (mmmm) REVERT: M 305 ARG cc_start: 0.8270 (tpt170) cc_final: 0.7391 (tpp80) REVERT: N 92 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8411 (mm-30) REVERT: O 252 LYS cc_start: 0.8878 (mtpm) cc_final: 0.8519 (mmtm) REVERT: O 305 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7403 (tpp80) outliers start: 26 outliers final: 20 residues processed: 705 average time/residue: 0.8481 time to fit residues: 705.4595 Evaluate side-chains 694 residues out of total 3976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 673 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain L residue 137 LYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 THR Chi-restraints excluded: chain N residue 137 LYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 THR Chi-restraints excluded: chain P residue 137 LYS Chi-restraints excluded: chain r residue 115 VAL Chi-restraints excluded: chain v residue 115 VAL Chi-restraints excluded: chain x residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 397 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 304 optimal weight: 0.5980 chunk 418 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 123 ASN ** C 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 GLN D 36 ASN E 95 ASN E 123 ASN ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 GLN F 36 ASN G 123 ASN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 156 GLN I 95 ASN I 123 ASN I 156 GLN K 95 ASN K 123 ASN ** K 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 156 GLN L 36 ASN M 96 GLN M 123 ASN ** M 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 156 GLN N 36 ASN O 123 ASN ** O 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 156 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.157025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.113775 restraints weight = 25797.477| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.11 r_work: 0.2928 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 38588 Z= 0.175 Angle : 0.642 8.004 52320 Z= 0.342 Chirality : 0.045 0.201 5576 Planarity : 0.004 0.034 6856 Dihedral : 5.360 25.180 5344 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.69 % Allowed : 9.36 % Favored : 89.94 % 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: 0.96 (0.12), residues: 4760 helix: 1.39 (0.12), residues: 1960 sheet: -0.38 (0.18), residues: 736 loop : 0.47 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 319 TYR 0.018 0.002 TYR N 32 PHE 0.036 0.003 PHE A 345 TRP 0.011 0.001 TRP C 368 HIS 0.012 0.002 HIS O 153 Details of bonding type rmsd covalent geometry : bond 0.00367 (38584) covalent geometry : angle 0.63949 (52312) SS BOND : bond 0.02364 ( 4) SS BOND : angle 5.04375 ( 8) hydrogen bonds : bond 0.04320 ( 1691) hydrogen bonds : angle 5.30767 ( 4638) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21066.45 seconds wall clock time: 357 minutes 29.64 seconds (21449.64 seconds total)