Starting phenix.real_space_refine on Thu Sep 26 03:26:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/09_2024/3j6f_5896.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/09_2024/3j6f_5896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/09_2024/3j6f_5896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/09_2024/3j6f_5896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/09_2024/3j6f_5896.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/09_2024/3j6f_5896.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 ------------------------------------------------------------------------------- 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= 0.528 sd= 1.926 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: 6 Type Number sf(0) Gaussians P 45 5.49 5 Mg 9 5.21 5 S 414 5.16 5 C 38214 2.51 5 N 10395 2.21 5 O 11826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 378 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 60903 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: D, F, H, J, L, N, P, R, C, E, G, I, K, M, O, Q Time building chain proxies: 14.41, per 1000 atoms: 0.24 Number of scatterers: 60903 At special positions: 0 Unit cell: (170.52, 88.74, 290.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 414 16.00 P 45 15.00 Mg 9 11.99 O 11826 8.00 N 10395 7.00 C 38214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 356 " distance=2.02 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: 12.26 Conformation dependent library (CDL) restraints added in 6.0 seconds 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14202 Finding SS restraints... Secondary structure from input PDB file: 333 helices and 45 sheets defined 52.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.98 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.543A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 110 through 129 removed outlier: 3.856A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 238 removed outlier: 4.190A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 402 removed outlier: 3.784A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 437 Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.595A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 81 removed outlier: 3.808A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.614A pdb=" N PHE B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 244 removed outlier: 4.037A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.676A pdb=" N ARG B 284 " --> pdb=" O GLN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 384 through 402 removed outlier: 3.612A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 414 through 437 Processing helix chain 'C' and resid 10 through 29 Processing helix chain 'C' and resid 71 through 80 removed outlier: 4.544A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 110 through 129 removed outlier: 3.856A pdb=" N ILE C 114 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 161 removed outlier: 3.537A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 223 through 238 removed outlier: 4.190A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 324 through 338 Processing helix chain 'C' and resid 383 through 402 removed outlier: 3.784A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 437 Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.595A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG D 48 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 71 through 81 removed outlier: 3.807A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 161 Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 196 through 198 No H-bonds generated for 'chain 'D' and resid 196 through 198' Processing helix chain 'D' and resid 205 through 216 removed outlier: 3.614A pdb=" N PHE D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 244 removed outlier: 4.037A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 279 through 284 removed outlier: 3.676A pdb=" N ARG D 284 " --> pdb=" O GLN D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 384 through 402 removed outlier: 3.612A pdb=" N PHE D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 414 through 437 Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.544A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 110 through 129 removed outlier: 3.857A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 238 removed outlier: 4.190A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 Processing helix chain 'E' and resid 277 through 282 Processing helix chain 'E' and resid 287 through 296 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 324 through 338 Processing helix chain 'E' and resid 383 through 402 removed outlier: 3.783A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 437 Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.596A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG F 48 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 71 through 81 removed outlier: 3.807A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.567A pdb=" N GLU F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 161 Processing helix chain 'F' and resid 182 through 195 Processing helix chain 'F' and resid 196 through 198 No H-bonds generated for 'chain 'F' and resid 196 through 198' Processing helix chain 'F' and resid 205 through 216 removed outlier: 3.615A pdb=" N PHE F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 244 removed outlier: 4.037A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.675A pdb=" N ARG F 284 " --> pdb=" O GLN F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 297 Processing helix chain 'F' and resid 298 through 301 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 384 through 402 removed outlier: 3.613A pdb=" N PHE F 388 " --> pdb=" O ILE F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 411 Processing helix chain 'F' and resid 414 through 437 Processing helix chain 'G' and resid 10 through 29 Processing helix chain 'G' and resid 71 through 80 removed outlier: 4.543A pdb=" N ILE G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 85 removed outlier: 3.505A pdb=" N GLN G 85 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 Processing helix chain 'G' and resid 110 through 129 removed outlier: 3.856A pdb=" N ILE G 114 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 195 Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 223 through 238 removed outlier: 4.190A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 260 Processing helix chain 'G' and resid 277 through 282 Processing helix chain 'G' and resid 287 through 296 Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 324 through 338 Processing helix chain 'G' and resid 383 through 402 removed outlier: 3.784A pdb=" N ALA G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 Processing helix chain 'G' and resid 414 through 437 Processing helix chain 'H' and resid 10 through 29 removed outlier: 3.596A pdb=" N LYS H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG H 48 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 71 through 81 removed outlier: 3.807A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 102 through 107 Processing helix chain 'H' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU H 113 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 161 Processing helix chain 'H' and resid 182 through 195 Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 205 through 216 removed outlier: 3.614A pdb=" N PHE H 214 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 244 removed outlier: 4.038A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.675A pdb=" N ARG H 284 " --> pdb=" O GLN H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 297 Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 384 through 402 removed outlier: 3.612A pdb=" N PHE H 388 " --> pdb=" O ILE H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 411 Processing helix chain 'H' and resid 414 through 437 Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 71 through 80 removed outlier: 4.542A pdb=" N ILE I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.507A pdb=" N GLN I 85 " --> pdb=" O THR I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 Processing helix chain 'I' and resid 110 through 129 removed outlier: 3.856A pdb=" N ILE I 114 " --> pdb=" O ILE I 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 195 Processing helix chain 'I' and resid 205 through 216 Processing helix chain 'I' and resid 223 through 238 removed outlier: 4.190A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 260 Processing helix chain 'I' and resid 277 through 282 Processing helix chain 'I' and resid 287 through 296 Processing helix chain 'I' and resid 297 through 301 Processing helix chain 'I' and resid 324 through 338 Processing helix chain 'I' and resid 383 through 402 removed outlier: 3.783A pdb=" N ALA I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 410 Processing helix chain 'I' and resid 414 through 437 Processing helix chain 'J' and resid 10 through 29 removed outlier: 3.596A pdb=" N LYS J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU J 44 " --> pdb=" O SER J 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG J 48 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 71 through 81 removed outlier: 3.808A pdb=" N MET J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY J 81 " --> pdb=" O SER J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'J' and resid 102 through 107 Processing helix chain 'J' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU J 113 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 161 Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 196 through 198 No H-bonds generated for 'chain 'J' and resid 196 through 198' Processing helix chain 'J' and resid 205 through 216 removed outlier: 3.615A pdb=" N PHE J 214 " --> pdb=" O TYR J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 244 removed outlier: 4.037A pdb=" N CYS J 241 " --> pdb=" O GLY J 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU J 242 " --> pdb=" O VAL J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 279 through 284 removed outlier: 3.675A pdb=" N ARG J 284 " --> pdb=" O GLN J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 297 Processing helix chain 'J' and resid 298 through 301 Processing helix chain 'J' and resid 324 through 339 Processing helix chain 'J' and resid 384 through 402 removed outlier: 3.613A pdb=" N PHE J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 411 Processing helix chain 'J' and resid 414 through 437 Processing helix chain 'K' and resid 10 through 29 Processing helix chain 'K' and resid 71 through 80 removed outlier: 4.543A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN K 85 " --> pdb=" O THR K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 107 Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.857A pdb=" N ILE K 114 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 Processing helix chain 'K' and resid 205 through 216 Processing helix chain 'K' and resid 223 through 238 removed outlier: 4.191A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 260 Processing helix chain 'K' and resid 277 through 282 Processing helix chain 'K' and resid 287 through 296 Processing helix chain 'K' and resid 297 through 301 Processing helix chain 'K' and resid 324 through 338 Processing helix chain 'K' and resid 383 through 402 removed outlier: 3.784A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 414 through 437 Processing helix chain 'L' and resid 10 through 29 removed outlier: 3.595A pdb=" N LYS L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 48 removed outlier: 3.711A pdb=" N LEU L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG L 48 " --> pdb=" O LEU L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 71 through 81 removed outlier: 3.808A pdb=" N MET L 75 " --> pdb=" O GLU L 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY L 81 " --> pdb=" O SER L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'L' and resid 102 through 107 Processing helix chain 'L' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU L 113 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 161 Processing helix chain 'L' and resid 182 through 195 Processing helix chain 'L' and resid 196 through 198 No H-bonds generated for 'chain 'L' and resid 196 through 198' Processing helix chain 'L' and resid 205 through 216 removed outlier: 3.615A pdb=" N PHE L 214 " --> pdb=" O TYR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 244 removed outlier: 4.038A pdb=" N CYS L 241 " --> pdb=" O GLY L 237 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU L 242 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 279 through 284 removed outlier: 3.675A pdb=" N ARG L 284 " --> pdb=" O GLN L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 297 Processing helix chain 'L' and resid 298 through 301 Processing helix chain 'L' and resid 324 through 339 Processing helix chain 'L' and resid 384 through 402 removed outlier: 3.613A pdb=" N PHE L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 411 Processing helix chain 'L' and resid 414 through 437 Processing helix chain 'M' and resid 10 through 29 Processing helix chain 'M' and resid 71 through 80 removed outlier: 4.543A pdb=" N ILE M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN M 85 " --> pdb=" O THR M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 107 Processing helix chain 'M' and resid 110 through 129 removed outlier: 3.857A pdb=" N ILE M 114 " --> pdb=" O ILE M 110 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASP M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 195 Processing helix chain 'M' and resid 205 through 216 Processing helix chain 'M' and resid 223 through 238 removed outlier: 4.191A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 251 through 260 Processing helix chain 'M' and resid 277 through 282 Processing helix chain 'M' and resid 287 through 296 Processing helix chain 'M' and resid 297 through 301 Processing helix chain 'M' and resid 324 through 338 Processing helix chain 'M' and resid 383 through 402 removed outlier: 3.784A pdb=" N ALA M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 Processing helix chain 'M' and resid 414 through 437 Processing helix chain 'N' and resid 10 through 29 removed outlier: 3.595A pdb=" N LYS N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU N 44 " --> pdb=" O SER N 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG N 48 " --> pdb=" O LEU N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 71 through 81 removed outlier: 3.808A pdb=" N MET N 75 " --> pdb=" O GLU N 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY N 81 " --> pdb=" O SER N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 102 through 107 Processing helix chain 'N' and resid 109 through 129 removed outlier: 3.567A pdb=" N GLU N 113 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU N 114 " --> pdb=" O GLU N 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP N 116 " --> pdb=" O ALA N 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER N 117 " --> pdb=" O GLU N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 161 Processing helix chain 'N' and resid 182 through 195 Processing helix chain 'N' and resid 196 through 198 No H-bonds generated for 'chain 'N' and resid 196 through 198' Processing helix chain 'N' and resid 205 through 216 removed outlier: 3.615A pdb=" N PHE N 214 " --> pdb=" O TYR N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 244 removed outlier: 4.037A pdb=" N CYS N 241 " --> pdb=" O GLY N 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU N 242 " --> pdb=" O VAL N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 260 Processing helix chain 'N' and resid 279 through 284 removed outlier: 3.676A pdb=" N ARG N 284 " --> pdb=" O GLN N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 287 through 297 Processing helix chain 'N' and resid 298 through 301 Processing helix chain 'N' and resid 324 through 339 Processing helix chain 'N' and resid 384 through 402 removed outlier: 3.612A pdb=" N PHE N 388 " --> pdb=" O ILE N 384 " (cutoff:3.500A) Processing helix chain 'N' and resid 404 through 411 Processing helix chain 'N' and resid 414 through 437 Processing helix chain 'O' and resid 10 through 29 Processing helix chain 'O' and resid 71 through 80 removed outlier: 4.543A pdb=" N ILE O 75 " --> pdb=" O GLU O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN O 85 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 107 Processing helix chain 'O' and resid 110 through 129 removed outlier: 3.856A pdb=" N ILE O 114 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP O 116 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU O 117 " --> pdb=" O GLU O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 161 removed outlier: 3.537A pdb=" N ARG O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 195 Processing helix chain 'O' and resid 205 through 216 Processing helix chain 'O' and resid 223 through 238 removed outlier: 4.191A pdb=" N ARG O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 260 Processing helix chain 'O' and resid 277 through 282 Processing helix chain 'O' and resid 287 through 296 Processing helix chain 'O' and resid 297 through 301 Processing helix chain 'O' and resid 324 through 338 Processing helix chain 'O' and resid 383 through 402 removed outlier: 3.783A pdb=" N ALA O 387 " --> pdb=" O ALA O 383 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 410 Processing helix chain 'O' and resid 414 through 437 Processing helix chain 'P' and resid 10 through 29 removed outlier: 3.595A pdb=" N LYS P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU P 44 " --> pdb=" O SER P 40 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG P 48 " --> pdb=" O LEU P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 71 through 81 removed outlier: 3.807A pdb=" N MET P 75 " --> pdb=" O GLU P 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing helix chain 'P' and resid 102 through 107 Processing helix chain 'P' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU P 113 " --> pdb=" O THR P 109 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU P 114 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 161 Processing helix chain 'P' and resid 182 through 195 Processing helix chain 'P' and resid 196 through 198 No H-bonds generated for 'chain 'P' and resid 196 through 198' Processing helix chain 'P' and resid 205 through 216 removed outlier: 3.615A pdb=" N PHE P 214 " --> pdb=" O TYR P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 223 through 244 removed outlier: 4.038A pdb=" N CYS P 241 " --> pdb=" O GLY P 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU P 242 " --> pdb=" O VAL P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 251 through 260 Processing helix chain 'P' and resid 279 through 284 removed outlier: 3.676A pdb=" N ARG P 284 " --> pdb=" O GLN P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 297 Processing helix chain 'P' and resid 298 through 301 Processing helix chain 'P' and resid 324 through 339 Processing helix chain 'P' and resid 384 through 402 removed outlier: 3.612A pdb=" N PHE P 388 " --> pdb=" O ILE P 384 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 411 Processing helix chain 'P' and resid 414 through 437 Processing helix chain 'Q' and resid 10 through 29 Processing helix chain 'Q' and resid 71 through 80 removed outlier: 4.542A pdb=" N ILE Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 85 removed outlier: 3.506A pdb=" N GLN Q 85 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 107 Processing helix chain 'Q' and resid 110 through 129 removed outlier: 3.856A pdb=" N ILE Q 114 " --> pdb=" O ILE Q 110 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 147 through 161 removed outlier: 3.538A pdb=" N ARG Q 156 " --> pdb=" O LEU Q 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 195 Processing helix chain 'Q' and resid 205 through 216 Processing helix chain 'Q' and resid 223 through 238 removed outlier: 4.190A pdb=" N ARG Q 229 " --> pdb=" O THR Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 251 through 260 Processing helix chain 'Q' and resid 277 through 282 Processing helix chain 'Q' and resid 287 through 296 Processing helix chain 'Q' and resid 297 through 301 Processing helix chain 'Q' and resid 324 through 338 Processing helix chain 'Q' and resid 383 through 402 removed outlier: 3.783A pdb=" N ALA Q 387 " --> pdb=" O ALA Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 410 Processing helix chain 'Q' and resid 414 through 437 Processing helix chain 'R' and resid 10 through 29 removed outlier: 3.596A pdb=" N LYS R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 48 removed outlier: 3.712A pdb=" N LEU R 44 " --> pdb=" O SER R 40 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG R 48 " --> pdb=" O LEU R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 71 through 81 removed outlier: 3.808A pdb=" N MET R 75 " --> pdb=" O GLU R 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY R 81 " --> pdb=" O SER R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'R' and resid 102 through 107 Processing helix chain 'R' and resid 109 through 129 removed outlier: 3.566A pdb=" N GLU R 113 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER R 117 " --> pdb=" O GLU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 161 Processing helix chain 'R' and resid 182 through 195 Processing helix chain 'R' and resid 196 through 198 No H-bonds generated for 'chain 'R' and resid 196 through 198' Processing helix chain 'R' and resid 205 through 216 removed outlier: 3.615A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 244 removed outlier: 4.037A pdb=" N CYS R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 260 Processing helix chain 'R' and resid 279 through 284 removed outlier: 3.675A pdb=" N ARG R 284 " --> pdb=" O GLN R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 297 Processing helix chain 'R' and resid 298 through 301 Processing helix chain 'R' and resid 324 through 339 Processing helix chain 'R' and resid 384 through 402 removed outlier: 3.612A pdb=" N PHE R 388 " --> pdb=" O ILE R 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 411 Processing helix chain 'R' and resid 414 through 437 Processing sheet with id=A, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=C, first strand: chain 'A' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE A 355 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 321 " --> pdb=" O ASN A 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS B 356 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE B 319 " --> pdb=" O CYS B 356 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=F, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.865A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU C 3 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE C 135 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 5 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL C 137 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 7 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS C 139 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL C 9 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=H, first strand: chain 'C' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE C 355 " --> pdb=" O ALA C 247 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 321 " --> pdb=" O ASN C 356 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET D 166 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N TYR D 202 " --> pdb=" O MET D 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR D 168 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE D 204 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER D 170 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS D 356 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE D 319 " --> pdb=" O CYS D 356 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=K, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=M, first strand: chain 'E' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE E 355 " --> pdb=" O ALA E 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 321 " --> pdb=" O ASN E 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET F 166 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TYR F 202 " --> pdb=" O MET F 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR F 168 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE F 204 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER F 170 " --> pdb=" O ILE F 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS F 352 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL F 315 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA F 354 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA F 317 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS F 356 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE F 319 " --> pdb=" O CYS F 356 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain 'F' and resid 53 through 56 Processing sheet with id=P, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE G 67 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL G 137 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE G 7 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N GLN G 133 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N LEU G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE G 135 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE G 171 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS G 139 " --> pdb=" O ILE G 171 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain 'G' and resid 53 through 55 Processing sheet with id=R, first strand: chain 'G' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE G 355 " --> pdb=" O ALA G 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 321 " --> pdb=" O ASN G 356 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN G 380 " --> pdb=" O MET G 313 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS G 315 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU G 378 " --> pdb=" O CYS G 315 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU G 317 " --> pdb=" O CYS G 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS G 376 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR G 319 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ALA G 374 " --> pdb=" O TYR G 319 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET H 166 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TYR H 202 " --> pdb=" O MET H 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR H 168 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE H 204 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER H 170 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS H 352 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL H 315 " --> pdb=" O LYS H 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA H 354 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA H 317 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS H 356 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE H 319 " --> pdb=" O CYS H 356 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain 'H' and resid 53 through 56 Processing sheet with id=U, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL I 137 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE I 7 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN I 133 " --> pdb=" O SER I 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE I 135 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE I 171 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS I 139 " --> pdb=" O ILE I 171 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=W, first strand: chain 'I' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE I 355 " --> pdb=" O ALA I 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY I 321 " --> pdb=" O ASN I 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN I 380 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS I 315 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU I 378 " --> pdb=" O CYS I 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU I 317 " --> pdb=" O CYS I 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS I 376 " --> pdb=" O LEU I 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR I 319 " --> pdb=" O ALA I 374 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA I 374 " --> pdb=" O TYR I 319 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'J' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU J 67 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU J 3 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE J 135 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL J 5 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU J 137 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE J 7 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS J 139 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA J 9 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET J 166 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TYR J 202 " --> pdb=" O MET J 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR J 168 " --> pdb=" O TYR J 202 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N ILE J 204 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER J 170 " --> pdb=" O ILE J 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE J 267 " --> pdb=" O SER J 381 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N SER J 381 " --> pdb=" O PHE J 267 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LYS J 352 " --> pdb=" O LEU J 313 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL J 315 " --> pdb=" O LYS J 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA J 354 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA J 317 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS J 356 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE J 319 " --> pdb=" O CYS J 356 " (cutoff:3.500A) Processing sheet with id=Y, first strand: chain 'J' and resid 53 through 56 Processing sheet with id=Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU K 3 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE K 135 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE K 5 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL K 137 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE K 7 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS K 139 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL K 9 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN K 133 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU K 167 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N HIS K 139 " --> pdb=" O ILE K 171 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AB, first strand: chain 'K' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE K 355 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY K 321 " --> pdb=" O ASN K 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN K 380 " --> pdb=" O MET K 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS K 315 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU K 378 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU K 317 " --> pdb=" O CYS K 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS K 376 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR K 319 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA K 374 " --> pdb=" O TYR K 319 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'L' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU L 67 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU L 3 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N PHE L 135 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL L 5 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU L 137 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE L 7 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS L 139 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA L 9 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET L 166 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N TYR L 202 " --> pdb=" O MET L 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR L 168 " --> pdb=" O TYR L 202 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE L 204 " --> pdb=" O THR L 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER L 170 " --> pdb=" O ILE L 204 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE L 267 " --> pdb=" O SER L 381 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N SER L 381 " --> pdb=" O PHE L 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS L 352 " --> pdb=" O LEU L 313 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL L 315 " --> pdb=" O LYS L 352 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ALA L 354 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA L 317 " --> pdb=" O ALA L 354 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS L 356 " --> pdb=" O ALA L 317 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE L 319 " --> pdb=" O CYS L 356 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain 'L' and resid 53 through 56 Processing sheet with id=AE, first strand: chain 'M' and resid 92 through 94 removed outlier: 7.865A pdb=" N ILE M 93 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE M 67 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU M 3 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE M 135 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE M 5 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL M 137 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE M 7 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS M 139 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N VAL M 9 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN M 133 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU M 167 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE M 135 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE M 169 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL M 137 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE M 171 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS M 139 " --> pdb=" O ILE M 171 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'M' and resid 53 through 55 Processing sheet with id=AG, first strand: chain 'M' and resid 246 through 248 removed outlier: 6.452A pdb=" N ILE M 355 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY M 321 " --> pdb=" O ASN M 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN M 380 " --> pdb=" O MET M 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS M 315 " --> pdb=" O LEU M 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU M 378 " --> pdb=" O CYS M 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU M 317 " --> pdb=" O CYS M 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS M 376 " --> pdb=" O LEU M 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR M 319 " --> pdb=" O ALA M 374 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA M 374 " --> pdb=" O TYR M 319 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'N' and resid 92 through 94 removed outlier: 7.868A pdb=" N VAL N 93 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU N 67 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU N 3 " --> pdb=" O GLN N 133 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE N 135 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL N 5 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU N 137 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE N 7 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS N 139 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA N 9 " --> pdb=" O HIS N 139 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N MET N 166 " --> pdb=" O GLU N 200 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N TYR N 202 " --> pdb=" O MET N 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR N 168 " --> pdb=" O TYR N 202 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE N 204 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER N 170 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE N 267 " --> pdb=" O SER N 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER N 381 " --> pdb=" O PHE N 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS N 352 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL N 315 " --> pdb=" O LYS N 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA N 354 " --> pdb=" O VAL N 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA N 317 " --> pdb=" O ALA N 354 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS N 356 " --> pdb=" O ALA N 317 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE N 319 " --> pdb=" O CYS N 356 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'N' and resid 53 through 56 Processing sheet with id=AJ, first strand: chain 'O' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE O 93 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE O 67 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU O 3 " --> pdb=" O GLN O 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE O 135 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE O 5 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL O 137 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE O 7 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS O 139 " --> pdb=" O ILE O 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL O 9 " --> pdb=" O HIS O 139 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLN O 133 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N LEU O 167 " --> pdb=" O GLN O 133 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE O 135 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE O 169 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL O 137 " --> pdb=" O PHE O 169 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE O 171 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N HIS O 139 " --> pdb=" O ILE O 171 " (cutoff:3.500A) Processing sheet with id=AK, first strand: chain 'O' and resid 53 through 55 Processing sheet with id=AL, first strand: chain 'O' and resid 246 through 248 removed outlier: 6.453A pdb=" N ILE O 355 " --> pdb=" O ALA O 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY O 321 " --> pdb=" O ASN O 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN O 380 " --> pdb=" O MET O 313 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS O 315 " --> pdb=" O LEU O 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU O 378 " --> pdb=" O CYS O 315 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU O 317 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS O 376 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR O 319 " --> pdb=" O ALA O 374 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA O 374 " --> pdb=" O TYR O 319 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'P' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL P 93 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU P 67 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU P 3 " --> pdb=" O GLN P 133 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE P 135 " --> pdb=" O GLU P 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL P 5 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU P 137 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE P 7 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS P 139 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA P 9 " --> pdb=" O HIS P 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET P 166 " --> pdb=" O GLU P 200 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N TYR P 202 " --> pdb=" O MET P 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR P 168 " --> pdb=" O TYR P 202 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE P 204 " --> pdb=" O THR P 168 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER P 170 " --> pdb=" O ILE P 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE P 267 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER P 381 " --> pdb=" O PHE P 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS P 352 " --> pdb=" O LEU P 313 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL P 315 " --> pdb=" O LYS P 352 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA P 354 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA P 317 " --> pdb=" O ALA P 354 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS P 356 " --> pdb=" O ALA P 317 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N PHE P 319 " --> pdb=" O CYS P 356 " (cutoff:3.500A) Processing sheet with id=AN, first strand: chain 'P' and resid 53 through 56 Processing sheet with id=AO, first strand: chain 'Q' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE Q 93 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE Q 67 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU Q 3 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N PHE Q 135 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE Q 5 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N VAL Q 137 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE Q 7 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS Q 139 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL Q 9 " --> pdb=" O HIS Q 139 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLN Q 133 " --> pdb=" O SER Q 165 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU Q 167 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE Q 135 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N PHE Q 169 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL Q 137 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE Q 171 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N HIS Q 139 " --> pdb=" O ILE Q 171 " (cutoff:3.500A) Processing sheet with id=AP, first strand: chain 'Q' and resid 53 through 55 Processing sheet with id=AQ, first strand: chain 'Q' and resid 246 through 248 removed outlier: 6.453A pdb=" N ILE Q 355 " --> pdb=" O ALA Q 247 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY Q 321 " --> pdb=" O ASN Q 356 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN Q 380 " --> pdb=" O MET Q 313 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS Q 315 " --> pdb=" O LEU Q 378 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU Q 378 " --> pdb=" O CYS Q 315 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU Q 317 " --> pdb=" O CYS Q 376 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N CYS Q 376 " --> pdb=" O LEU Q 317 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR Q 319 " --> pdb=" O ALA Q 374 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA Q 374 " --> pdb=" O TYR Q 319 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'R' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL R 93 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU R 67 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU R 3 " --> pdb=" O GLN R 133 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N PHE R 135 " --> pdb=" O GLU R 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL R 5 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU R 137 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE R 7 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N HIS R 139 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA R 9 " --> pdb=" O HIS R 139 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N MET R 166 " --> pdb=" O GLU R 200 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N TYR R 202 " --> pdb=" O MET R 166 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR R 168 " --> pdb=" O TYR R 202 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE R 204 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER R 170 " --> pdb=" O ILE R 204 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N PHE R 267 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N SER R 381 " --> pdb=" O PHE R 267 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS R 352 " --> pdb=" O LEU R 313 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL R 315 " --> pdb=" O LYS R 352 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ALA R 354 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ALA R 317 " --> pdb=" O ALA R 354 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N CYS R 356 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N PHE R 319 " --> pdb=" O CYS R 356 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'R' and resid 53 through 56 3033 hydrogen bonds defined for protein. 8775 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: 25.03 Time building geometry restraints manager: 14.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16794 1.32 - 1.45: 17588 1.45 - 1.58: 27178 1.58 - 1.70: 54 1.70 - 1.83: 648 Bond restraints: 62262 Sorted by residual: bond pdb=" CA GLY Q 265 " pdb=" C GLY Q 265 " ideal model delta sigma weight residual 1.519 1.273 0.246 1.25e-02 6.40e+03 3.86e+02 bond pdb=" CA GLY M 265 " pdb=" C GLY M 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.85e+02 bond pdb=" CA GLY I 265 " pdb=" C GLY I 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.84e+02 bond pdb=" CA GLY E 265 " pdb=" C GLY E 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.84e+02 bond pdb=" CA GLY G 265 " pdb=" C GLY G 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.83e+02 ... (remaining 62257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 76802 4.38 - 8.76: 7035 8.76 - 13.15: 601 13.15 - 17.53: 117 17.53 - 21.91: 27 Bond angle restraints: 84582 Sorted by residual: angle pdb=" C ARG G 264 " pdb=" N GLY G 265 " pdb=" CA GLY G 265 " ideal model delta sigma weight residual 121.45 101.49 19.96 1.06e+00 8.90e-01 3.55e+02 angle pdb=" C ARG O 264 " pdb=" N GLY O 265 " pdb=" CA GLY O 265 " ideal model delta sigma weight residual 121.45 101.49 19.96 1.06e+00 8.90e-01 3.55e+02 angle pdb=" C ARG K 264 " pdb=" N GLY K 265 " pdb=" CA GLY K 265 " ideal model delta sigma weight residual 121.45 101.50 19.95 1.06e+00 8.90e-01 3.54e+02 angle pdb=" C ARG E 264 " pdb=" N GLY E 265 " pdb=" CA GLY E 265 " ideal model delta sigma weight residual 121.45 101.50 19.95 1.06e+00 8.90e-01 3.54e+02 angle pdb=" C ARG Q 264 " pdb=" N GLY Q 265 " pdb=" CA GLY Q 265 " ideal model delta sigma weight residual 121.45 101.50 19.95 1.06e+00 8.90e-01 3.54e+02 ... (remaining 84577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 36317 35.89 - 71.77: 577 71.77 - 107.66: 54 107.66 - 143.55: 18 143.55 - 179.43: 27 Dihedral angle restraints: 36993 sinusoidal: 14826 harmonic: 22167 Sorted by residual: dihedral pdb=" CA LEU L 248 " pdb=" C LEU L 248 " pdb=" N ASN L 249 " pdb=" CA ASN L 249 " ideal model delta harmonic sigma weight residual -180.00 -133.85 -46.15 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA LEU F 248 " pdb=" C LEU F 248 " pdb=" N ASN F 249 " pdb=" CA ASN F 249 " ideal model delta harmonic sigma weight residual 180.00 -133.86 -46.14 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA LEU B 248 " pdb=" C LEU B 248 " pdb=" N ASN B 249 " pdb=" CA ASN B 249 " ideal model delta harmonic sigma weight residual -180.00 -133.91 -46.09 0 5.00e+00 4.00e-02 8.50e+01 ... (remaining 36990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 6801 0.133 - 0.266: 1869 0.266 - 0.399: 384 0.399 - 0.532: 126 0.532 - 0.665: 36 Chirality restraints: 9216 Sorted by residual: chirality pdb=" CA HIS M 266 " pdb=" N HIS M 266 " pdb=" C HIS M 266 " pdb=" CB HIS M 266 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA HIS Q 266 " pdb=" N HIS Q 266 " pdb=" C HIS Q 266 " pdb=" CB HIS Q 266 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA HIS O 266 " pdb=" N HIS O 266 " pdb=" C HIS O 266 " pdb=" CB HIS O 266 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 9213 not shown) Planarity restraints: 11043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER Q 439 " 0.032 2.00e-02 2.50e+03 6.32e-02 4.00e+01 pdb=" C SER Q 439 " -0.109 2.00e-02 2.50e+03 pdb=" O SER Q 439 " 0.039 2.00e-02 2.50e+03 pdb=" OXT SER Q 439 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 439 " 0.032 2.00e-02 2.50e+03 6.31e-02 3.99e+01 pdb=" C SER M 439 " -0.109 2.00e-02 2.50e+03 pdb=" O SER M 439 " 0.039 2.00e-02 2.50e+03 pdb=" OXT SER M 439 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O 439 " 0.032 2.00e-02 2.50e+03 6.31e-02 3.98e+01 pdb=" C SER O 439 " -0.109 2.00e-02 2.50e+03 pdb=" O SER O 439 " 0.039 2.00e-02 2.50e+03 pdb=" OXT SER O 439 " 0.039 2.00e-02 2.50e+03 ... (remaining 11040 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 1523 2.59 - 3.17: 60141 3.17 - 3.75: 105722 3.75 - 4.32: 149308 4.32 - 4.90: 232275 Nonbonded interactions: 548969 Sorted by model distance: nonbonded pdb=" SG CYS N 241 " pdb=" SG CYS N 356 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS J 241 " pdb=" SG CYS J 356 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS P 241 " pdb=" SG CYS P 356 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS D 241 " pdb=" SG CYS D 356 " model vdw 2.017 3.760 nonbonded pdb=" SG CYS F 241 " pdb=" SG CYS F 356 " model vdw 2.017 3.760 ... (remaining 548964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } 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' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.080 Extract box with map and model: 1.720 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 97.220 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.290 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 0.021 0.257 62262 Z= 1.357 Angle : 2.641 21.911 84582 Z= 1.765 Chirality : 0.139 0.665 9216 Planarity : 0.008 0.063 11043 Dihedral : 14.012 179.431 22788 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.07 % Favored : 96.34 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.17 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 7632 helix: -0.74 (0.07), residues: 3564 sheet: 0.75 (0.14), residues: 1170 loop : -1.08 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP K 21 HIS 0.012 0.002 HIS Q 139 PHE 0.038 0.004 PHE K 49 TYR 0.077 0.010 TYR F 61 ARG 0.007 0.001 ARG N 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2868 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2859 time to evaluate : 5.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 ILE cc_start: 0.7973 (mt) cc_final: 0.7711 (mm) REVERT: A 21 TRP cc_start: 0.8672 (m100) cc_final: 0.8467 (m100) REVERT: A 26 LEU cc_start: 0.9097 (mt) cc_final: 0.8859 (mm) REVERT: A 33 ASP cc_start: 0.5831 (p0) cc_final: 0.5549 (t0) REVERT: A 53 PHE cc_start: 0.8519 (m-80) cc_final: 0.7259 (m-80) REVERT: A 66 VAL cc_start: 0.8854 (t) cc_final: 0.8064 (t) REVERT: A 122 ILE cc_start: 0.9175 (mt) cc_final: 0.8944 (mt) REVERT: A 171 ILE cc_start: 0.8487 (mm) cc_final: 0.8165 (mp) REVERT: A 188 ILE cc_start: 0.9289 (mm) cc_final: 0.8775 (tt) REVERT: A 209 ILE cc_start: 0.9406 (mt) cc_final: 0.8334 (mm) REVERT: A 227 LEU cc_start: 0.9209 (mt) cc_final: 0.8539 (mm) REVERT: A 230 LEU cc_start: 0.8941 (tp) cc_final: 0.8507 (tp) REVERT: A 242 LEU cc_start: 0.7333 (mt) cc_final: 0.6575 (mt) REVERT: A 248 LEU cc_start: 0.6718 (mt) cc_final: 0.5907 (mp) REVERT: A 302 MET cc_start: 0.7693 (mmm) cc_final: 0.7133 (tpt) REVERT: A 352 LYS cc_start: 0.8121 (tptt) cc_final: 0.7902 (tptp) REVERT: A 378 LEU cc_start: 0.8176 (mt) cc_final: 0.7560 (mt) REVERT: A 409 VAL cc_start: 0.8724 (t) cc_final: 0.8426 (p) REVERT: A 431 ASP cc_start: 0.8306 (m-30) cc_final: 0.7463 (m-30) REVERT: B 20 PHE cc_start: 0.8697 (t80) cc_final: 0.8295 (t80) REVERT: B 21 TRP cc_start: 0.8186 (m100) cc_final: 0.7661 (m100) REVERT: B 24 ILE cc_start: 0.9538 (mm) cc_final: 0.9141 (mm) REVERT: B 60 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8494 (mmtt) REVERT: B 66 ILE cc_start: 0.9074 (mt) cc_final: 0.8807 (mm) REVERT: B 67 LEU cc_start: 0.8450 (mt) cc_final: 0.8214 (mt) REVERT: B 70 LEU cc_start: 0.8233 (mt) cc_final: 0.7621 (mp) REVERT: B 91 ASN cc_start: 0.8668 (m-40) cc_final: 0.8294 (m110) REVERT: B 93 VAL cc_start: 0.9277 (t) cc_final: 0.8846 (t) REVERT: B 137 LEU cc_start: 0.7290 (mp) cc_final: 0.6831 (mt) REVERT: B 169 PHE cc_start: 0.6656 (m-80) cc_final: 0.5552 (m-10) REVERT: B 217 LEU cc_start: 0.8635 (mt) cc_final: 0.7847 (mt) REVERT: B 230 LEU cc_start: 0.8622 (mt) cc_final: 0.8267 (tt) REVERT: B 235 MET cc_start: 0.8477 (mtp) cc_final: 0.7956 (mtp) REVERT: B 239 THR cc_start: 0.9134 (p) cc_final: 0.8523 (t) REVERT: B 240 THR cc_start: 0.3590 (t) cc_final: 0.3056 (t) REVERT: B 267 PHE cc_start: 0.7821 (m-80) cc_final: 0.7540 (m-80) REVERT: B 378 ILE cc_start: 0.7809 (mt) cc_final: 0.7427 (mp) REVERT: B 398 MET cc_start: 0.7020 (mtm) cc_final: 0.6467 (mtm) REVERT: C 8 HIS cc_start: 0.5152 (m-70) cc_final: 0.4882 (m90) REVERT: C 60 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7326 (pttt) REVERT: C 75 ILE cc_start: 0.9108 (mm) cc_final: 0.8597 (tt) REVERT: C 153 LEU cc_start: 0.9162 (tp) cc_final: 0.8709 (tt) REVERT: C 157 LEU cc_start: 0.9090 (mt) cc_final: 0.8487 (mt) REVERT: C 188 ILE cc_start: 0.9298 (mm) cc_final: 0.8942 (tt) REVERT: C 227 LEU cc_start: 0.9370 (mt) cc_final: 0.9037 (mt) REVERT: C 290 GLU cc_start: 0.6188 (tp30) cc_final: 0.5911 (tp30) REVERT: C 347 CYS cc_start: 0.6338 (t) cc_final: 0.6114 (t) REVERT: C 378 LEU cc_start: 0.8406 (mt) cc_final: 0.7674 (mt) REVERT: D 60 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8075 (ttmt) REVERT: D 66 ILE cc_start: 0.8380 (mt) cc_final: 0.8112 (mm) REVERT: D 75 MET cc_start: 0.7484 (mmm) cc_final: 0.7103 (mmm) REVERT: D 137 LEU cc_start: 0.7610 (mp) cc_final: 0.7252 (mt) REVERT: D 157 ILE cc_start: 0.8650 (mt) cc_final: 0.8220 (mt) REVERT: D 163 ASP cc_start: 0.7382 (p0) cc_final: 0.7057 (p0) REVERT: D 169 PHE cc_start: 0.6373 (m-80) cc_final: 0.5611 (m-10) REVERT: D 239 THR cc_start: 0.9341 (p) cc_final: 0.9131 (t) REVERT: D 333 LEU cc_start: 0.8868 (tp) cc_final: 0.7604 (tt) REVERT: D 347 ILE cc_start: 0.9236 (mt) cc_final: 0.8963 (mp) REVERT: E 24 TYR cc_start: 0.7792 (m-80) cc_final: 0.6724 (m-80) REVERT: E 53 PHE cc_start: 0.8174 (m-80) cc_final: 0.7182 (m-80) REVERT: E 66 VAL cc_start: 0.8375 (t) cc_final: 0.8123 (p) REVERT: E 75 ILE cc_start: 0.8760 (mm) cc_final: 0.8387 (mm) REVERT: E 135 PHE cc_start: 0.7694 (p90) cc_final: 0.7491 (p90) REVERT: E 157 LEU cc_start: 0.8597 (mt) cc_final: 0.7973 (mt) REVERT: E 171 ILE cc_start: 0.8932 (mm) cc_final: 0.8503 (mp) REVERT: E 227 LEU cc_start: 0.9230 (mt) cc_final: 0.8408 (mm) REVERT: E 230 LEU cc_start: 0.8742 (tp) cc_final: 0.8329 (tp) REVERT: E 231 ILE cc_start: 0.9385 (mt) cc_final: 0.9020 (tt) REVERT: E 242 LEU cc_start: 0.7004 (mt) cc_final: 0.6506 (mt) REVERT: E 248 LEU cc_start: 0.6361 (mt) cc_final: 0.5924 (mt) REVERT: E 302 MET cc_start: 0.8624 (mmm) cc_final: 0.7696 (mmm) REVERT: E 318 LEU cc_start: 0.7384 (tp) cc_final: 0.6488 (tp) REVERT: E 335 ILE cc_start: 0.8650 (pt) cc_final: 0.8210 (mm) REVERT: E 352 LYS cc_start: 0.8843 (tptt) cc_final: 0.8603 (tptt) REVERT: E 363 VAL cc_start: 0.8313 (t) cc_final: 0.8010 (p) REVERT: E 378 LEU cc_start: 0.7777 (mt) cc_final: 0.6302 (mt) REVERT: E 428 LEU cc_start: 0.8711 (tp) cc_final: 0.8125 (tp) REVERT: F 24 ILE cc_start: 0.9544 (mm) cc_final: 0.9067 (mm) REVERT: F 67 LEU cc_start: 0.8474 (mt) cc_final: 0.7316 (mt) REVERT: F 157 ILE cc_start: 0.8767 (mt) cc_final: 0.8003 (mm) REVERT: F 163 ASP cc_start: 0.7229 (p0) cc_final: 0.6700 (p0) REVERT: F 179 ASP cc_start: 0.7809 (m-30) cc_final: 0.7384 (p0) REVERT: F 239 THR cc_start: 0.9177 (p) cc_final: 0.8608 (t) REVERT: F 252 LEU cc_start: 0.8680 (tp) cc_final: 0.8049 (tp) REVERT: F 259 MET cc_start: 0.7036 (mmm) cc_final: 0.6682 (mmm) REVERT: F 265 LEU cc_start: 0.9391 (mt) cc_final: 0.9029 (mp) REVERT: F 267 PHE cc_start: 0.7574 (m-80) cc_final: 0.6705 (m-80) REVERT: F 329 ASP cc_start: 0.7846 (m-30) cc_final: 0.7451 (m-30) REVERT: F 378 ILE cc_start: 0.6761 (mt) cc_final: 0.6368 (mp) REVERT: F 405 LEU cc_start: 0.8776 (mt) cc_final: 0.8348 (mt) REVERT: F 432 TYR cc_start: 0.8210 (m-80) cc_final: 0.7528 (m-80) REVERT: G 5 ILE cc_start: 0.8284 (mt) cc_final: 0.7764 (mm) REVERT: G 25 CYS cc_start: 0.7622 (m) cc_final: 0.7211 (m) REVERT: G 26 LEU cc_start: 0.9032 (mt) cc_final: 0.7654 (mt) REVERT: G 66 VAL cc_start: 0.8184 (t) cc_final: 0.7851 (p) REVERT: G 75 ILE cc_start: 0.9280 (mm) cc_final: 0.8596 (tt) REVERT: G 125 LEU cc_start: 0.9173 (mt) cc_final: 0.8958 (mm) REVERT: G 153 LEU cc_start: 0.8846 (tp) cc_final: 0.8535 (tt) REVERT: G 167 LEU cc_start: 0.7296 (mt) cc_final: 0.6351 (mt) REVERT: G 217 LEU cc_start: 0.8127 (mt) cc_final: 0.6473 (mt) REVERT: G 242 LEU cc_start: 0.7838 (mt) cc_final: 0.6419 (mt) REVERT: G 248 LEU cc_start: 0.8205 (mt) cc_final: 0.7931 (mm) REVERT: G 259 LEU cc_start: 0.6967 (mt) cc_final: 0.6715 (mt) REVERT: G 269 LEU cc_start: 0.8059 (mt) cc_final: 0.7855 (mt) REVERT: G 288 VAL cc_start: 0.8810 (t) cc_final: 0.8193 (t) REVERT: G 317 LEU cc_start: 0.8867 (mt) cc_final: 0.8568 (mm) REVERT: G 318 LEU cc_start: 0.7448 (tp) cc_final: 0.7224 (tp) REVERT: G 376 CYS cc_start: 0.7891 (t) cc_final: 0.6942 (t) REVERT: G 378 LEU cc_start: 0.7358 (mt) cc_final: 0.6897 (mt) REVERT: G 388 TRP cc_start: 0.6777 (m100) cc_final: 0.5889 (m100) REVERT: G 409 VAL cc_start: 0.8631 (t) cc_final: 0.8340 (p) REVERT: H 20 PHE cc_start: 0.8395 (t80) cc_final: 0.7949 (t80) REVERT: H 24 ILE cc_start: 0.9233 (mm) cc_final: 0.8994 (mm) REVERT: H 28 HIS cc_start: 0.7885 (m-70) cc_final: 0.7275 (m90) REVERT: H 60 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7271 (ptmt) REVERT: H 212 ILE cc_start: 0.9071 (mt) cc_final: 0.8207 (mt) REVERT: H 230 LEU cc_start: 0.8563 (mt) cc_final: 0.8335 (mm) REVERT: H 232 SER cc_start: 0.8001 (p) cc_final: 0.7700 (p) REVERT: H 351 VAL cc_start: 0.9353 (t) cc_final: 0.9111 (p) REVERT: I 25 CYS cc_start: 0.7518 (m) cc_final: 0.7270 (m) REVERT: I 26 LEU cc_start: 0.9154 (mt) cc_final: 0.8947 (mm) REVERT: I 53 PHE cc_start: 0.7475 (m-80) cc_final: 0.6620 (m-80) REVERT: I 66 VAL cc_start: 0.8267 (t) cc_final: 0.7548 (p) REVERT: I 74 VAL cc_start: 0.8678 (t) cc_final: 0.8054 (t) REVERT: I 122 ILE cc_start: 0.8887 (mt) cc_final: 0.8392 (mt) REVERT: I 138 PHE cc_start: 0.6805 (m-80) cc_final: 0.6180 (m-80) REVERT: I 171 ILE cc_start: 0.8548 (mm) cc_final: 0.8298 (mm) REVERT: I 205 ASP cc_start: 0.8587 (t0) cc_final: 0.8322 (t0) REVERT: I 209 ILE cc_start: 0.9423 (mt) cc_final: 0.9069 (mm) REVERT: I 217 LEU cc_start: 0.7933 (mt) cc_final: 0.6312 (mt) REVERT: I 227 LEU cc_start: 0.9332 (mt) cc_final: 0.8863 (mt) REVERT: I 230 LEU cc_start: 0.8553 (tp) cc_final: 0.8323 (tp) REVERT: I 234 ILE cc_start: 0.8985 (mt) cc_final: 0.8686 (mt) REVERT: I 238 ILE cc_start: 0.8438 (mt) cc_final: 0.7715 (tp) REVERT: I 248 LEU cc_start: 0.8678 (mt) cc_final: 0.7863 (mp) REVERT: I 258 ASN cc_start: 0.6870 (m-40) cc_final: 0.5909 (m-40) REVERT: I 262 TYR cc_start: 0.7193 (m-80) cc_final: 0.6760 (m-80) REVERT: I 288 VAL cc_start: 0.8854 (t) cc_final: 0.8503 (m) REVERT: I 317 LEU cc_start: 0.8951 (mt) cc_final: 0.8292 (mt) REVERT: I 318 LEU cc_start: 0.7823 (tp) cc_final: 0.7063 (tp) REVERT: I 335 ILE cc_start: 0.8563 (pt) cc_final: 0.8208 (tp) REVERT: I 376 CYS cc_start: 0.7976 (t) cc_final: 0.7604 (t) REVERT: I 378 LEU cc_start: 0.8382 (mt) cc_final: 0.7960 (mt) REVERT: J 6 HIS cc_start: 0.7206 (t70) cc_final: 0.6969 (t-90) REVERT: J 24 ILE cc_start: 0.9199 (mm) cc_final: 0.8223 (mm) REVERT: J 87 PHE cc_start: 0.8354 (m-80) cc_final: 0.7862 (m-80) REVERT: J 141 LEU cc_start: 0.7394 (mt) cc_final: 0.6697 (mt) REVERT: J 216 THR cc_start: 0.7787 (p) cc_final: 0.6515 (p) REVERT: J 351 VAL cc_start: 0.9360 (t) cc_final: 0.9049 (p) REVERT: J 352 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8009 (tmtt) REVERT: J 388 PHE cc_start: 0.6057 (m-10) cc_final: 0.4680 (m-80) REVERT: J 435 TYR cc_start: 0.7833 (m-80) cc_final: 0.7372 (m-80) REVERT: K 7 ILE cc_start: 0.9281 (mt) cc_final: 0.8968 (mp) REVERT: K 25 CYS cc_start: 0.8262 (m) cc_final: 0.7618 (m) REVERT: K 33 ASP cc_start: 0.6178 (p0) cc_final: 0.5698 (t0) REVERT: K 122 ILE cc_start: 0.8714 (mt) cc_final: 0.7555 (mt) REVERT: K 125 LEU cc_start: 0.8432 (mt) cc_final: 0.7792 (mm) REVERT: K 129 CYS cc_start: 0.8142 (m) cc_final: 0.7892 (m) REVERT: K 167 LEU cc_start: 0.7888 (mt) cc_final: 0.7629 (mt) REVERT: K 205 ASP cc_start: 0.8530 (t0) cc_final: 0.7876 (t0) REVERT: K 217 LEU cc_start: 0.8236 (mt) cc_final: 0.7117 (mt) REVERT: K 242 LEU cc_start: 0.7331 (mt) cc_final: 0.6376 (mp) REVERT: K 248 LEU cc_start: 0.8843 (mt) cc_final: 0.8560 (mp) REVERT: K 252 LEU cc_start: 0.7157 (mt) cc_final: 0.6955 (mt) REVERT: K 262 TYR cc_start: 0.6900 (m-80) cc_final: 0.6500 (m-80) REVERT: K 288 VAL cc_start: 0.9276 (t) cc_final: 0.8336 (m) REVERT: K 292 THR cc_start: 0.8856 (p) cc_final: 0.8647 (p) REVERT: K 325 PRO cc_start: 0.7591 (Cg_exo) cc_final: 0.6990 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8668 (pt) cc_final: 0.8006 (tp) REVERT: K 347 CYS cc_start: 0.5514 (t) cc_final: 0.4669 (t) REVERT: K 355 ILE cc_start: 0.9146 (mt) cc_final: 0.8686 (tp) REVERT: K 431 ASP cc_start: 0.6654 (m-30) cc_final: 0.6223 (m-30) REVERT: L 24 ILE cc_start: 0.9116 (mm) cc_final: 0.8673 (mm) REVERT: L 288 VAL cc_start: 0.8466 (t) cc_final: 0.8012 (t) REVERT: L 291 LEU cc_start: 0.9167 (mt) cc_final: 0.7927 (mt) REVERT: L 329 ASP cc_start: 0.7481 (m-30) cc_final: 0.7194 (m-30) REVERT: L 352 LYS cc_start: 0.9373 (mmtt) cc_final: 0.8221 (tmtt) REVERT: L 355 VAL cc_start: 0.6607 (t) cc_final: 0.6380 (m) REVERT: L 395 PHE cc_start: 0.7978 (t80) cc_final: 0.7342 (t80) REVERT: M 5 ILE cc_start: 0.8422 (mt) cc_final: 0.7660 (mm) REVERT: M 53 PHE cc_start: 0.6912 (m-80) cc_final: 0.6413 (m-80) REVERT: M 74 VAL cc_start: 0.8986 (t) cc_final: 0.8078 (t) REVERT: M 75 ILE cc_start: 0.8866 (mm) cc_final: 0.8547 (tt) REVERT: M 137 VAL cc_start: 0.8711 (t) cc_final: 0.8448 (p) REVERT: M 171 ILE cc_start: 0.8027 (mm) cc_final: 0.7724 (mp) REVERT: M 227 LEU cc_start: 0.9291 (mt) cc_final: 0.8801 (mm) REVERT: M 230 LEU cc_start: 0.8440 (tp) cc_final: 0.8139 (tp) REVERT: M 231 ILE cc_start: 0.9194 (mt) cc_final: 0.8789 (mm) REVERT: M 238 ILE cc_start: 0.8463 (mt) cc_final: 0.8073 (tt) REVERT: M 275 VAL cc_start: 0.8692 (t) cc_final: 0.8386 (t) REVERT: M 322 ASP cc_start: 0.7014 (t0) cc_final: 0.6597 (t70) REVERT: M 335 ILE cc_start: 0.8329 (pt) cc_final: 0.7844 (tp) REVERT: M 428 LEU cc_start: 0.8509 (tp) cc_final: 0.8302 (tp) REVERT: N 7 ILE cc_start: 0.8880 (mt) cc_final: 0.8174 (mm) REVERT: N 8 GLN cc_start: 0.6748 (mt0) cc_final: 0.6044 (mt0) REVERT: N 21 TRP cc_start: 0.8281 (m100) cc_final: 0.7816 (m100) REVERT: N 42 LEU cc_start: 0.8843 (mt) cc_final: 0.8333 (mt) REVERT: N 90 ASP cc_start: 0.6848 (m-30) cc_final: 0.6619 (m-30) REVERT: N 92 PHE cc_start: 0.8367 (m-80) cc_final: 0.8035 (m-80) REVERT: N 115 VAL cc_start: 0.8914 (t) cc_final: 0.8675 (p) REVERT: N 230 LEU cc_start: 0.8794 (mt) cc_final: 0.8555 (mt) REVERT: N 235 MET cc_start: 0.7968 (mtp) cc_final: 0.7551 (ttm) REVERT: N 252 LEU cc_start: 0.7895 (tp) cc_final: 0.7585 (tp) REVERT: N 255 LEU cc_start: 0.6940 (tp) cc_final: 0.6376 (tp) REVERT: N 266 HIS cc_start: 0.7700 (p90) cc_final: 0.7462 (p-80) REVERT: N 288 VAL cc_start: 0.9417 (t) cc_final: 0.9160 (t) REVERT: N 297 ASP cc_start: 0.7855 (t0) cc_final: 0.7543 (t0) REVERT: N 314 THR cc_start: 0.6986 (p) cc_final: 0.6262 (p) REVERT: N 315 VAL cc_start: 0.7574 (t) cc_final: 0.7130 (t) REVERT: N 333 LEU cc_start: 0.8786 (tp) cc_final: 0.8178 (tt) REVERT: N 378 ILE cc_start: 0.7480 (mt) cc_final: 0.7266 (mp) REVERT: O 21 TRP cc_start: 0.8323 (m100) cc_final: 0.7899 (m100) REVERT: O 53 PHE cc_start: 0.7240 (m-80) cc_final: 0.6648 (m-80) REVERT: O 74 VAL cc_start: 0.8757 (t) cc_final: 0.7430 (t) REVERT: O 118 VAL cc_start: 0.8905 (t) cc_final: 0.8541 (t) REVERT: O 152 LEU cc_start: 0.8475 (tp) cc_final: 0.8199 (tp) REVERT: O 171 ILE cc_start: 0.7971 (mm) cc_final: 0.7732 (mm) REVERT: O 230 LEU cc_start: 0.8078 (tp) cc_final: 0.7644 (tp) REVERT: O 231 ILE cc_start: 0.9225 (mt) cc_final: 0.8546 (tt) REVERT: O 242 LEU cc_start: 0.6201 (mt) cc_final: 0.5301 (mt) REVERT: O 275 VAL cc_start: 0.8784 (t) cc_final: 0.8226 (t) REVERT: O 286 LEU cc_start: 0.8250 (mt) cc_final: 0.7103 (mt) REVERT: O 378 LEU cc_start: 0.8802 (mt) cc_final: 0.8568 (mt) REVERT: O 398 MET cc_start: 0.6906 (mtp) cc_final: 0.6684 (mmm) REVERT: P 7 ILE cc_start: 0.9139 (mt) cc_final: 0.8919 (mm) REVERT: P 24 ILE cc_start: 0.9449 (mm) cc_final: 0.9149 (mm) REVERT: P 86 ILE cc_start: 0.9006 (tt) cc_final: 0.8577 (tt) REVERT: P 108 TYR cc_start: 0.7462 (t80) cc_final: 0.6669 (t80) REVERT: P 154 ILE cc_start: 0.8310 (mt) cc_final: 0.7971 (mt) REVERT: P 201 THR cc_start: 0.7704 (t) cc_final: 0.7013 (p) REVERT: P 221 THR cc_start: 0.8350 (p) cc_final: 0.8128 (p) REVERT: P 259 MET cc_start: 0.7460 (mmm) cc_final: 0.7008 (mmt) REVERT: P 333 LEU cc_start: 0.9021 (tp) cc_final: 0.8029 (tt) REVERT: P 378 ILE cc_start: 0.8158 (mt) cc_final: 0.7631 (mp) REVERT: P 384 ILE cc_start: 0.8076 (mt) cc_final: 0.7755 (mm) REVERT: P 428 LEU cc_start: 0.8559 (mt) cc_final: 0.7768 (mt) REVERT: Q 53 PHE cc_start: 0.6806 (m-80) cc_final: 0.6509 (m-80) REVERT: Q 66 VAL cc_start: 0.8368 (t) cc_final: 0.7914 (t) REVERT: Q 171 ILE cc_start: 0.7949 (mm) cc_final: 0.7491 (mm) REVERT: Q 231 ILE cc_start: 0.9388 (mt) cc_final: 0.9041 (tt) REVERT: Q 286 LEU cc_start: 0.8272 (mt) cc_final: 0.7579 (mt) REVERT: Q 315 CYS cc_start: 0.7397 (t) cc_final: 0.5389 (t) REVERT: Q 317 LEU cc_start: 0.6841 (mt) cc_final: 0.5959 (mm) REVERT: Q 378 LEU cc_start: 0.7791 (mt) cc_final: 0.6884 (mt) REVERT: Q 398 MET cc_start: 0.7109 (mtp) cc_final: 0.6731 (mmm) REVERT: Q 407 TRP cc_start: 0.7900 (m100) cc_final: 0.7467 (m100) REVERT: Q 431 ASP cc_start: 0.6681 (m-30) cc_final: 0.6328 (m-30) REVERT: R 7 ILE cc_start: 0.8953 (mt) cc_final: 0.8663 (mm) REVERT: R 67 LEU cc_start: 0.8266 (mt) cc_final: 0.7167 (mm) REVERT: R 92 PHE cc_start: 0.7476 (m-80) cc_final: 0.7123 (m-80) REVERT: R 108 TYR cc_start: 0.7360 (t80) cc_final: 0.6781 (t80) REVERT: R 171 VAL cc_start: 0.8784 (t) cc_final: 0.8424 (t) REVERT: R 230 LEU cc_start: 0.8928 (mt) cc_final: 0.8682 (mm) REVERT: R 235 MET cc_start: 0.7932 (mtp) cc_final: 0.7729 (ttm) REVERT: R 248 LEU cc_start: 0.8007 (mt) cc_final: 0.7801 (mt) REVERT: R 254 LYS cc_start: 0.7625 (tttt) cc_final: 0.7127 (ttmt) REVERT: R 259 MET cc_start: 0.7927 (mmm) cc_final: 0.7250 (mmt) REVERT: R 260 VAL cc_start: 0.9275 (t) cc_final: 0.9022 (t) REVERT: R 275 LEU cc_start: 0.9578 (tp) cc_final: 0.9359 (tp) REVERT: R 378 ILE cc_start: 0.7369 (mt) cc_final: 0.6973 (mp) outliers start: 9 outliers final: 0 residues processed: 2859 average time/residue: 0.6292 time to fit residues: 2932.8432 Evaluate side-chains 1481 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1481 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 30.0000 chunk 573 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 195 optimal weight: 9.9990 chunk 386 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 592 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 360 optimal weight: 40.0000 chunk 441 optimal weight: 8.9990 chunk 686 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS C 61 HIS C 91 GLN D 37 HIS D 193 GLN D 309 HIS ** E 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS F 37 HIS F 96 GLN F 193 GLN F 309 HIS G 61 HIS G 133 GLN G 197 HIS ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 37 HIS H 133 GLN H 139 HIS H 193 GLN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 HIS ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN J 193 GLN ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN K 258 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN L 15 GLN L 193 GLN ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS N 96 GLN ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS O 226 ASN ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN P 193 GLN ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN P 433 GLN Q 293 ASN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 96 GLN R 107 HIS R 136 GLN ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 349 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 62262 Z= 0.277 Angle : 0.766 9.366 84582 Z= 0.411 Chirality : 0.048 0.191 9216 Planarity : 0.006 0.128 11043 Dihedral : 12.716 178.746 8595 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 7632 helix: 0.45 (0.08), residues: 3564 sheet: 1.09 (0.16), residues: 1017 loop : -0.07 (0.12), residues: 3051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 21 HIS 0.013 0.002 HIS I 266 PHE 0.028 0.002 PHE M 255 TYR 0.028 0.002 TYR M 24 ARG 0.014 0.001 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2018 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2010 time to evaluate : 5.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8548 (m100) cc_final: 0.8297 (m100) REVERT: A 53 PHE cc_start: 0.8043 (m-80) cc_final: 0.6800 (m-80) REVERT: A 157 LEU cc_start: 0.8910 (mt) cc_final: 0.8597 (mt) REVERT: A 291 ILE cc_start: 0.9029 (mt) cc_final: 0.7943 (tp) REVERT: B 20 PHE cc_start: 0.8506 (t80) cc_final: 0.7886 (t80) REVERT: B 66 ILE cc_start: 0.9383 (mt) cc_final: 0.9087 (mm) REVERT: B 76 ASP cc_start: 0.3803 (m-30) cc_final: 0.3037 (m-30) REVERT: B 120 ASP cc_start: 0.7532 (t70) cc_final: 0.6435 (t0) REVERT: B 124 LYS cc_start: 0.9042 (pptt) cc_final: 0.8163 (pttm) REVERT: B 139 HIS cc_start: 0.8339 (p90) cc_final: 0.7625 (p90) REVERT: B 165 ILE cc_start: 0.8662 (mt) cc_final: 0.7813 (tp) REVERT: B 221 THR cc_start: 0.8495 (p) cc_final: 0.8153 (p) REVERT: B 268 PHE cc_start: 0.5886 (m-80) cc_final: 0.5473 (m-80) REVERT: B 297 ASP cc_start: 0.6577 (t0) cc_final: 0.6341 (t70) REVERT: B 422 GLU cc_start: 0.8884 (pt0) cc_final: 0.8672 (pp20) REVERT: C 16 ILE cc_start: 0.9021 (pt) cc_final: 0.8683 (pt) REVERT: C 21 TRP cc_start: 0.7347 (m100) cc_final: 0.6632 (m100) REVERT: C 60 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7797 (tttt) REVERT: C 75 ILE cc_start: 0.9131 (mm) cc_final: 0.7892 (tt) REVERT: C 78 VAL cc_start: 0.9361 (t) cc_final: 0.9055 (t) REVERT: C 125 LEU cc_start: 0.8419 (mt) cc_final: 0.7991 (tp) REVERT: C 135 PHE cc_start: 0.6601 (p90) cc_final: 0.6225 (p90) REVERT: C 154 MET cc_start: 0.6836 (tpt) cc_final: 0.6490 (tpp) REVERT: C 157 LEU cc_start: 0.9184 (mt) cc_final: 0.8902 (pp) REVERT: C 200 CYS cc_start: 0.6513 (t) cc_final: 0.4777 (t) REVERT: C 300 ASN cc_start: 0.8650 (m-40) cc_final: 0.8309 (m-40) REVERT: C 318 LEU cc_start: 0.7509 (tp) cc_final: 0.6469 (tp) REVERT: D 75 MET cc_start: 0.7501 (mmm) cc_final: 0.7052 (mmt) REVERT: D 132 LEU cc_start: 0.8875 (mm) cc_final: 0.8670 (mm) REVERT: D 139 HIS cc_start: 0.7996 (p90) cc_final: 0.7535 (p90) REVERT: D 154 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8466 (mp) REVERT: D 165 ILE cc_start: 0.9071 (mt) cc_final: 0.8475 (mt) REVERT: D 260 VAL cc_start: 0.8653 (t) cc_final: 0.8317 (t) REVERT: D 265 LEU cc_start: 0.9357 (mt) cc_final: 0.9043 (mp) REVERT: D 302 MET cc_start: 0.7132 (mtm) cc_final: 0.6899 (mtt) REVERT: D 333 LEU cc_start: 0.7301 (tp) cc_final: 0.7013 (tt) REVERT: D 356 CYS cc_start: 0.7291 (m) cc_final: 0.6762 (m) REVERT: D 380 ASN cc_start: 0.8175 (t0) cc_final: 0.7924 (t0) REVERT: D 405 LEU cc_start: 0.8834 (mt) cc_final: 0.8548 (mt) REVERT: D 435 TYR cc_start: 0.6132 (m-80) cc_final: 0.5602 (m-80) REVERT: E 14 VAL cc_start: 0.9197 (t) cc_final: 0.8977 (p) REVERT: E 25 CYS cc_start: 0.7631 (m) cc_final: 0.7272 (m) REVERT: E 33 ASP cc_start: 0.7281 (p0) cc_final: 0.6882 (p0) REVERT: E 53 PHE cc_start: 0.7075 (m-80) cc_final: 0.6440 (m-80) REVERT: E 152 LEU cc_start: 0.8255 (tp) cc_final: 0.7998 (tp) REVERT: E 228 ASN cc_start: 0.8723 (m-40) cc_final: 0.8424 (p0) REVERT: E 291 ILE cc_start: 0.9083 (mt) cc_final: 0.8027 (tp) REVERT: E 335 ILE cc_start: 0.8932 (pt) cc_final: 0.8324 (tp) REVERT: E 349 THR cc_start: 0.6759 (p) cc_final: 0.6495 (p) REVERT: E 352 LYS cc_start: 0.8968 (tptt) cc_final: 0.8756 (tptp) REVERT: F 90 ASP cc_start: 0.7087 (m-30) cc_final: 0.6766 (m-30) REVERT: F 120 ASP cc_start: 0.7436 (m-30) cc_final: 0.7034 (m-30) REVERT: F 139 HIS cc_start: 0.8292 (p90) cc_final: 0.7629 (p90) REVERT: F 163 ASP cc_start: 0.6770 (p0) cc_final: 0.6270 (p0) REVERT: F 180 THR cc_start: 0.5987 (t) cc_final: 0.5649 (t) REVERT: F 248 LEU cc_start: 0.7513 (mt) cc_final: 0.7146 (mm) REVERT: F 286 LEU cc_start: 0.8187 (mt) cc_final: 0.7741 (mt) REVERT: F 302 MET cc_start: 0.8457 (mmm) cc_final: 0.8211 (mmm) REVERT: F 327 GLU cc_start: 0.7957 (tp30) cc_final: 0.7347 (tm-30) REVERT: F 329 ASP cc_start: 0.7508 (m-30) cc_final: 0.7269 (m-30) REVERT: F 332 MET cc_start: 0.6561 (tmm) cc_final: 0.6274 (tmm) REVERT: F 398 MET cc_start: 0.7442 (mtp) cc_final: 0.6323 (ptm) REVERT: F 405 LEU cc_start: 0.8449 (mt) cc_final: 0.8147 (mt) REVERT: G 5 ILE cc_start: 0.8215 (mt) cc_final: 0.7751 (mm) REVERT: G 16 ILE cc_start: 0.8118 (pt) cc_final: 0.7900 (pt) REVERT: G 25 CYS cc_start: 0.7616 (m) cc_final: 0.6003 (m) REVERT: G 33 ASP cc_start: 0.6829 (p0) cc_final: 0.5483 (t0) REVERT: G 75 ILE cc_start: 0.9189 (mm) cc_final: 0.8705 (mt) REVERT: G 209 ILE cc_start: 0.9195 (mm) cc_final: 0.8400 (mm) REVERT: G 217 LEU cc_start: 0.7675 (mt) cc_final: 0.7390 (mt) REVERT: G 258 ASN cc_start: 0.6184 (m110) cc_final: 0.5708 (m-40) REVERT: G 262 TYR cc_start: 0.5362 (m-80) cc_final: 0.5025 (m-80) REVERT: G 376 CYS cc_start: 0.6754 (t) cc_final: 0.5971 (t) REVERT: G 378 LEU cc_start: 0.8253 (mt) cc_final: 0.6399 (mt) REVERT: H 5 VAL cc_start: 0.8573 (t) cc_final: 0.8263 (t) REVERT: H 19 LYS cc_start: 0.8679 (mmmt) cc_final: 0.8474 (mmmt) REVERT: H 20 PHE cc_start: 0.8214 (t80) cc_final: 0.7983 (t80) REVERT: H 24 ILE cc_start: 0.9013 (mm) cc_final: 0.8559 (tp) REVERT: H 28 HIS cc_start: 0.6935 (m-70) cc_final: 0.5985 (m-70) REVERT: H 132 LEU cc_start: 0.8961 (tp) cc_final: 0.8245 (tp) REVERT: H 154 ILE cc_start: 0.8226 (mt) cc_final: 0.7926 (mt) REVERT: H 213 CYS cc_start: 0.6742 (p) cc_final: 0.6114 (p) REVERT: H 275 LEU cc_start: 0.8153 (pt) cc_final: 0.7845 (pp) REVERT: H 292 THR cc_start: 0.8912 (p) cc_final: 0.7632 (p) REVERT: H 388 PHE cc_start: 0.6871 (m-10) cc_final: 0.6320 (m-80) REVERT: H 432 TYR cc_start: 0.7018 (m-80) cc_final: 0.6251 (m-80) REVERT: I 53 PHE cc_start: 0.6813 (m-80) cc_final: 0.6215 (m-80) REVERT: I 83 TYR cc_start: 0.6243 (m-10) cc_final: 0.6009 (m-10) REVERT: I 155 GLU cc_start: 0.7131 (tp30) cc_final: 0.6929 (tp30) REVERT: I 172 TYR cc_start: 0.6411 (t80) cc_final: 0.5612 (t80) REVERT: I 227 LEU cc_start: 0.9256 (mt) cc_final: 0.8899 (mp) REVERT: I 238 ILE cc_start: 0.9042 (mt) cc_final: 0.8607 (tp) REVERT: I 335 ILE cc_start: 0.8622 (pt) cc_final: 0.8000 (tp) REVERT: I 377 MET cc_start: 0.7351 (tmm) cc_final: 0.6478 (tmm) REVERT: J 21 TRP cc_start: 0.7839 (m100) cc_final: 0.7469 (m100) REVERT: J 24 ILE cc_start: 0.8949 (mm) cc_final: 0.8287 (tp) REVERT: J 67 LEU cc_start: 0.8234 (mt) cc_final: 0.6874 (mt) REVERT: J 122 VAL cc_start: 0.9246 (t) cc_final: 0.8796 (t) REVERT: J 124 LYS cc_start: 0.8087 (pttp) cc_final: 0.7650 (pttt) REVERT: J 132 LEU cc_start: 0.7837 (mm) cc_final: 0.7498 (mm) REVERT: J 181 VAL cc_start: 0.6606 (t) cc_final: 0.6252 (t) REVERT: J 205 ASP cc_start: 0.8434 (t0) cc_final: 0.8040 (t0) REVERT: J 216 THR cc_start: 0.8243 (p) cc_final: 0.7231 (p) REVERT: J 291 LEU cc_start: 0.8734 (mt) cc_final: 0.7815 (mp) REVERT: J 333 LEU cc_start: 0.7596 (mt) cc_final: 0.7184 (mt) REVERT: J 351 VAL cc_start: 0.9636 (t) cc_final: 0.9268 (p) REVERT: J 435 TYR cc_start: 0.7552 (m-80) cc_final: 0.5976 (m-80) REVERT: K 16 ILE cc_start: 0.8760 (pt) cc_final: 0.8525 (pt) REVERT: K 33 ASP cc_start: 0.6521 (p0) cc_final: 0.5875 (t0) REVERT: K 75 ILE cc_start: 0.8542 (mt) cc_final: 0.8312 (mt) REVERT: K 86 LEU cc_start: 0.8515 (tp) cc_final: 0.8286 (tp) REVERT: K 122 ILE cc_start: 0.8220 (mt) cc_final: 0.7473 (mt) REVERT: K 167 LEU cc_start: 0.7722 (mt) cc_final: 0.6850 (mt) REVERT: K 191 THR cc_start: 0.8441 (m) cc_final: 0.8065 (m) REVERT: K 205 ASP cc_start: 0.7558 (t0) cc_final: 0.7170 (t0) REVERT: K 258 ASN cc_start: 0.7717 (m110) cc_final: 0.7204 (t0) REVERT: K 262 TYR cc_start: 0.6819 (m-80) cc_final: 0.6215 (m-80) REVERT: K 280 LYS cc_start: 0.7461 (mtmt) cc_final: 0.6646 (mmmt) REVERT: K 288 VAL cc_start: 0.8952 (t) cc_final: 0.8552 (m) REVERT: K 325 PRO cc_start: 0.7887 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8637 (pt) cc_final: 0.8132 (tp) REVERT: K 352 LYS cc_start: 0.7501 (tptt) cc_final: 0.6815 (tptt) REVERT: K 355 ILE cc_start: 0.8903 (mt) cc_final: 0.8635 (pt) REVERT: L 21 TRP cc_start: 0.7302 (m100) cc_final: 0.7035 (m100) REVERT: L 24 ILE cc_start: 0.8797 (mm) cc_final: 0.8212 (tp) REVERT: L 86 ILE cc_start: 0.9014 (mt) cc_final: 0.8373 (mt) REVERT: L 138 THR cc_start: 0.5219 (p) cc_final: 0.4667 (p) REVERT: L 154 ILE cc_start: 0.8692 (mt) cc_final: 0.8109 (pt) REVERT: L 181 VAL cc_start: 0.6520 (t) cc_final: 0.6250 (t) REVERT: L 239 THR cc_start: 0.9060 (t) cc_final: 0.8282 (t) REVERT: L 242 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.7451 (mt) REVERT: L 291 LEU cc_start: 0.8638 (mt) cc_final: 0.7891 (mt) REVERT: L 327 GLU cc_start: 0.6459 (tm-30) cc_final: 0.5569 (tm-30) REVERT: L 333 LEU cc_start: 0.8479 (mt) cc_final: 0.7319 (mt) REVERT: M 16 ILE cc_start: 0.8699 (mt) cc_final: 0.8443 (mt) REVERT: M 21 TRP cc_start: 0.7886 (m100) cc_final: 0.7606 (m100) REVERT: M 23 LEU cc_start: 0.8632 (tp) cc_final: 0.7801 (tp) REVERT: M 24 TYR cc_start: 0.7317 (m-80) cc_final: 0.7103 (m-80) REVERT: M 53 PHE cc_start: 0.6027 (m-80) cc_final: 0.5480 (m-80) REVERT: M 122 ILE cc_start: 0.8769 (mt) cc_final: 0.8510 (mt) REVERT: M 172 TYR cc_start: 0.5205 (t80) cc_final: 0.4976 (t80) REVERT: M 175 PRO cc_start: 0.6470 (Cg_endo) cc_final: 0.5208 (Cg_exo) REVERT: M 230 LEU cc_start: 0.8454 (tp) cc_final: 0.7811 (tp) REVERT: M 269 LEU cc_start: 0.8060 (mt) cc_final: 0.7769 (mt) REVERT: M 315 CYS cc_start: 0.8087 (t) cc_final: 0.7841 (t) REVERT: M 317 LEU cc_start: 0.6592 (mt) cc_final: 0.6180 (mp) REVERT: M 335 ILE cc_start: 0.7977 (pt) cc_final: 0.7408 (tp) REVERT: M 413 MET cc_start: 0.8032 (mmm) cc_final: 0.7745 (mmm) REVERT: M 428 LEU cc_start: 0.8549 (tp) cc_final: 0.8225 (tp) REVERT: N 62 VAL cc_start: 0.8646 (t) cc_final: 0.8049 (p) REVERT: N 154 ILE cc_start: 0.9271 (mt) cc_final: 0.8946 (mt) REVERT: N 193 GLN cc_start: 0.7523 (mm110) cc_final: 0.6576 (tt0) REVERT: N 266 HIS cc_start: 0.7936 (p90) cc_final: 0.7671 (p-80) REVERT: N 292 THR cc_start: 0.7433 (p) cc_final: 0.6831 (t) REVERT: N 355 VAL cc_start: 0.5948 (t) cc_final: 0.5721 (t) REVERT: N 378 ILE cc_start: 0.7620 (mt) cc_final: 0.7248 (mp) REVERT: N 384 ILE cc_start: 0.8150 (mp) cc_final: 0.7926 (mp) REVERT: N 425 MET cc_start: 0.8630 (tpp) cc_final: 0.8351 (tpp) REVERT: O 21 TRP cc_start: 0.8542 (m100) cc_final: 0.7451 (m100) REVERT: O 76 ASP cc_start: 0.8514 (m-30) cc_final: 0.8112 (m-30) REVERT: O 127 ASP cc_start: 0.7494 (t0) cc_final: 0.7255 (t70) REVERT: O 171 ILE cc_start: 0.7724 (mm) cc_final: 0.7506 (mm) REVERT: O 230 LEU cc_start: 0.8137 (tp) cc_final: 0.7248 (tp) REVERT: O 269 LEU cc_start: 0.8459 (mt) cc_final: 0.8109 (mt) REVERT: O 306 ASP cc_start: 0.6969 (t0) cc_final: 0.6580 (t70) REVERT: O 353 VAL cc_start: 0.8558 (t) cc_final: 0.7903 (p) REVERT: O 377 MET cc_start: 0.5810 (ttm) cc_final: 0.5120 (mtt) REVERT: O 398 MET cc_start: 0.6957 (mtp) cc_final: 0.6484 (mmt) REVERT: P 14 ASN cc_start: 0.8121 (m-40) cc_final: 0.7865 (m-40) REVERT: P 49 ILE cc_start: 0.8016 (tp) cc_final: 0.7610 (tp) REVERT: P 86 ILE cc_start: 0.9147 (tt) cc_final: 0.8599 (tt) REVERT: P 118 VAL cc_start: 0.8894 (t) cc_final: 0.8486 (t) REVERT: P 124 LYS cc_start: 0.8749 (ttpp) cc_final: 0.8395 (ptmt) REVERT: P 163 ASP cc_start: 0.8265 (p0) cc_final: 0.7611 (p0) REVERT: P 201 THR cc_start: 0.7411 (t) cc_final: 0.6857 (p) REVERT: P 217 LEU cc_start: 0.7293 (tp) cc_final: 0.6834 (tp) REVERT: P 259 MET cc_start: 0.7515 (mmm) cc_final: 0.7161 (mmt) REVERT: P 268 PHE cc_start: 0.7149 (m-80) cc_final: 0.6934 (m-10) REVERT: P 314 THR cc_start: 0.7519 (p) cc_final: 0.7051 (p) REVERT: P 326 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7356 (ttmt) REVERT: P 384 ILE cc_start: 0.8726 (mt) cc_final: 0.8296 (mt) REVERT: P 425 MET cc_start: 0.8738 (tpp) cc_final: 0.8481 (tpp) REVERT: Q 16 ILE cc_start: 0.9046 (pt) cc_final: 0.8801 (pt) REVERT: Q 214 ARG cc_start: 0.5778 (ptp-170) cc_final: 0.5462 (ptp-110) REVERT: Q 227 LEU cc_start: 0.8915 (mt) cc_final: 0.8710 (mp) REVERT: Q 230 LEU cc_start: 0.8493 (tp) cc_final: 0.7999 (tp) REVERT: Q 234 ILE cc_start: 0.9127 (mt) cc_final: 0.8662 (tt) REVERT: R 22 GLU cc_start: 0.6707 (tm-30) cc_final: 0.6137 (tm-30) REVERT: R 115 VAL cc_start: 0.9096 (p) cc_final: 0.8717 (p) REVERT: R 118 VAL cc_start: 0.8680 (t) cc_final: 0.8469 (t) REVERT: R 119 LEU cc_start: 0.8764 (tp) cc_final: 0.8482 (tt) REVERT: R 132 LEU cc_start: 0.7914 (mm) cc_final: 0.7550 (mt) REVERT: R 139 HIS cc_start: 0.6993 (p90) cc_final: 0.6760 (p90) REVERT: R 165 ILE cc_start: 0.8786 (mt) cc_final: 0.8252 (mt) REVERT: R 194 LEU cc_start: 0.8538 (tt) cc_final: 0.7732 (tp) REVERT: R 259 MET cc_start: 0.8267 (mmm) cc_final: 0.7631 (mmt) REVERT: R 268 PHE cc_start: 0.6868 (m-80) cc_final: 0.5162 (m-80) REVERT: R 425 MET cc_start: 0.8639 (tpp) cc_final: 0.8241 (tpp) outliers start: 8 outliers final: 2 residues processed: 2016 average time/residue: 0.6141 time to fit residues: 2074.9662 Evaluate side-chains 1344 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1340 time to evaluate : 5.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 50.0000 chunk 213 optimal weight: 0.9980 chunk 571 optimal weight: 40.0000 chunk 467 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 687 optimal weight: 5.9990 chunk 742 optimal weight: 40.0000 chunk 612 optimal weight: 30.0000 chunk 682 optimal weight: 30.0000 chunk 234 optimal weight: 0.1980 chunk 551 optimal weight: 50.0000 overall best weight: 7.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 101 ASN A 139 HIS ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 309 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS C 91 GLN C 293 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 96 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS J 133 GLN ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 300 ASN J 349 ASN ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 334 ASN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS M 258 ASN M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 GLN N 229 HIS ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 HIS ** N 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 283 HIS O 309 HIS P 37 HIS P 249 ASN Q 35 GLN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS Q 233 GLN Q 301 GLN Q 380 ASN R 14 ASN ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.6172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62262 Z= 0.226 Angle : 0.679 10.163 84582 Z= 0.359 Chirality : 0.046 0.298 9216 Planarity : 0.006 0.113 11043 Dihedral : 11.845 177.428 8595 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 7632 helix: 0.52 (0.08), residues: 3600 sheet: 1.11 (0.15), residues: 1143 loop : 0.11 (0.13), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 21 HIS 0.011 0.001 HIS A 8 PHE 0.035 0.002 PHE N 268 TYR 0.022 0.002 TYR E 83 ARG 0.018 0.001 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1817 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1808 time to evaluate : 5.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8494 (m100) cc_final: 0.7988 (m100) REVERT: A 53 PHE cc_start: 0.7824 (m-80) cc_final: 0.6575 (m-80) REVERT: A 75 ILE cc_start: 0.9129 (mm) cc_final: 0.8906 (tt) REVERT: A 78 VAL cc_start: 0.9142 (t) cc_final: 0.8861 (t) REVERT: A 125 LEU cc_start: 0.9299 (mp) cc_final: 0.8586 (tp) REVERT: A 193 THR cc_start: 0.8599 (p) cc_final: 0.8031 (t) REVERT: A 218 ASP cc_start: 0.7393 (m-30) cc_final: 0.6904 (m-30) REVERT: A 227 LEU cc_start: 0.9130 (mt) cc_final: 0.8800 (mt) REVERT: A 258 ASN cc_start: 0.6260 (t0) cc_final: 0.5509 (t0) REVERT: A 291 ILE cc_start: 0.9093 (mt) cc_final: 0.8218 (tp) REVERT: A 296 PHE cc_start: 0.7835 (m-80) cc_final: 0.7478 (m-10) REVERT: A 317 LEU cc_start: 0.7749 (mt) cc_final: 0.7330 (mt) REVERT: A 335 ILE cc_start: 0.8445 (tp) cc_final: 0.8000 (tp) REVERT: A 347 CYS cc_start: 0.8183 (p) cc_final: 0.7899 (p) REVERT: A 352 LYS cc_start: 0.8754 (tptt) cc_final: 0.8254 (tptp) REVERT: A 408 TYR cc_start: 0.5207 (m-80) cc_final: 0.4474 (m-80) REVERT: A 415 GLU cc_start: 0.8541 (mp0) cc_final: 0.7993 (mp0) REVERT: A 431 ASP cc_start: 0.8098 (m-30) cc_final: 0.7722 (m-30) REVERT: B 20 PHE cc_start: 0.8217 (t80) cc_final: 0.7516 (t80) REVERT: B 21 TRP cc_start: 0.7824 (m100) cc_final: 0.7618 (m100) REVERT: B 66 ILE cc_start: 0.9063 (mt) cc_final: 0.8539 (mm) REVERT: B 67 LEU cc_start: 0.8793 (mm) cc_final: 0.8359 (mm) REVERT: B 136 GLN cc_start: 0.7062 (pt0) cc_final: 0.6628 (pt0) REVERT: B 139 HIS cc_start: 0.8254 (p90) cc_final: 0.7356 (p90) REVERT: B 165 ILE cc_start: 0.8722 (mt) cc_final: 0.8297 (mt) REVERT: B 217 LEU cc_start: 0.8914 (mm) cc_final: 0.8515 (mm) REVERT: B 283 TYR cc_start: 0.6372 (m-80) cc_final: 0.5721 (m-10) REVERT: B 297 ASP cc_start: 0.7891 (t0) cc_final: 0.7299 (t0) REVERT: B 422 GLU cc_start: 0.8832 (pt0) cc_final: 0.8589 (pp20) REVERT: C 21 TRP cc_start: 0.7616 (m100) cc_final: 0.7216 (m100) REVERT: C 36 MET cc_start: 0.3130 (ptt) cc_final: 0.1431 (ptt) REVERT: C 60 LYS cc_start: 0.7871 (mmtt) cc_final: 0.7583 (tttt) REVERT: C 75 ILE cc_start: 0.9176 (mm) cc_final: 0.8039 (tt) REVERT: C 120 ASP cc_start: 0.6770 (t0) cc_final: 0.6438 (t70) REVERT: C 203 MET cc_start: 0.7586 (pmm) cc_final: 0.7205 (pmm) REVERT: C 209 ILE cc_start: 0.8969 (mm) cc_final: 0.8398 (mm) REVERT: C 230 LEU cc_start: 0.8617 (tp) cc_final: 0.8236 (tp) REVERT: C 292 THR cc_start: 0.8880 (t) cc_final: 0.8412 (p) REVERT: C 353 VAL cc_start: 0.7705 (t) cc_final: 0.6977 (m) REVERT: C 435 VAL cc_start: 0.9245 (t) cc_final: 0.8759 (t) REVERT: D 75 MET cc_start: 0.7360 (mmm) cc_final: 0.7076 (mmt) REVERT: D 137 LEU cc_start: 0.7476 (mp) cc_final: 0.7085 (mp) REVERT: D 139 HIS cc_start: 0.7942 (p90) cc_final: 0.7331 (p90) REVERT: D 398 MET cc_start: 0.6677 (ptp) cc_final: 0.6417 (ptp) REVERT: D 405 LEU cc_start: 0.8882 (mt) cc_final: 0.8545 (mt) REVERT: D 420 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6599 (pp20) REVERT: D 435 TYR cc_start: 0.6193 (m-80) cc_final: 0.5868 (m-80) REVERT: E 21 TRP cc_start: 0.8550 (m100) cc_final: 0.7820 (m100) REVERT: E 33 ASP cc_start: 0.7190 (p0) cc_final: 0.6083 (p0) REVERT: E 53 PHE cc_start: 0.7817 (m-80) cc_final: 0.7176 (m-80) REVERT: E 75 ILE cc_start: 0.8939 (mm) cc_final: 0.8676 (tt) REVERT: E 78 VAL cc_start: 0.9329 (t) cc_final: 0.9126 (t) REVERT: E 125 LEU cc_start: 0.8424 (mt) cc_final: 0.7962 (mt) REVERT: E 132 LEU cc_start: 0.8366 (tp) cc_final: 0.8128 (tp) REVERT: E 135 PHE cc_start: 0.5720 (p90) cc_final: 0.5503 (p90) REVERT: E 193 THR cc_start: 0.8979 (p) cc_final: 0.8148 (t) REVERT: E 228 ASN cc_start: 0.8424 (m-40) cc_final: 0.7546 (p0) REVERT: E 288 VAL cc_start: 0.7978 (m) cc_final: 0.7727 (m) REVERT: E 335 ILE cc_start: 0.8584 (pt) cc_final: 0.8253 (tp) REVERT: E 347 CYS cc_start: 0.8174 (p) cc_final: 0.7532 (p) REVERT: E 352 LYS cc_start: 0.9208 (tptt) cc_final: 0.8966 (tptp) REVERT: F 21 TRP cc_start: 0.8004 (m100) cc_final: 0.7717 (m100) REVERT: F 22 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6474 (mt-10) REVERT: F 66 ILE cc_start: 0.8868 (mm) cc_final: 0.8536 (mm) REVERT: F 139 HIS cc_start: 0.8227 (p90) cc_final: 0.7152 (p90) REVERT: F 163 ASP cc_start: 0.7251 (p0) cc_final: 0.6309 (p0) REVERT: F 267 PHE cc_start: 0.6724 (m-80) cc_final: 0.6478 (m-80) REVERT: F 269 MET cc_start: 0.6636 (mtp) cc_final: 0.6407 (mtp) REVERT: F 286 LEU cc_start: 0.8088 (mt) cc_final: 0.7707 (mt) REVERT: F 302 MET cc_start: 0.8480 (mmm) cc_final: 0.8280 (mmm) REVERT: F 329 ASP cc_start: 0.7551 (m-30) cc_final: 0.7146 (m-30) REVERT: F 356 CYS cc_start: 0.8533 (t) cc_final: 0.8226 (t) REVERT: F 398 MET cc_start: 0.7266 (mtp) cc_final: 0.6485 (ptm) REVERT: F 425 MET cc_start: 0.8199 (tpp) cc_final: 0.7406 (tpp) REVERT: G 5 ILE cc_start: 0.8348 (mt) cc_final: 0.8009 (mm) REVERT: G 25 CYS cc_start: 0.7866 (m) cc_final: 0.6145 (m) REVERT: G 33 ASP cc_start: 0.5736 (p0) cc_final: 0.4632 (t0) REVERT: G 75 ILE cc_start: 0.8943 (mm) cc_final: 0.8104 (tt) REVERT: G 209 ILE cc_start: 0.8850 (mm) cc_final: 0.8334 (mm) REVERT: G 212 ILE cc_start: 0.9240 (mt) cc_final: 0.8831 (mt) REVERT: G 280 LYS cc_start: 0.6888 (mtmt) cc_final: 0.6660 (mmmt) REVERT: G 376 CYS cc_start: 0.6940 (t) cc_final: 0.6299 (t) REVERT: H 19 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8383 (mmmt) REVERT: H 21 TRP cc_start: 0.7379 (m100) cc_final: 0.6270 (m100) REVERT: H 51 VAL cc_start: 0.8731 (t) cc_final: 0.8416 (t) REVERT: H 53 TYR cc_start: 0.5075 (m-10) cc_final: 0.4208 (m-80) REVERT: H 132 LEU cc_start: 0.8907 (tp) cc_final: 0.8149 (tp) REVERT: H 176 LYS cc_start: 0.7152 (mmmt) cc_final: 0.5566 (tmtt) REVERT: H 213 CYS cc_start: 0.6100 (p) cc_final: 0.5570 (p) REVERT: H 292 THR cc_start: 0.8491 (p) cc_final: 0.7408 (p) REVERT: I 20 CYS cc_start: 0.9327 (p) cc_final: 0.8804 (p) REVERT: I 53 PHE cc_start: 0.6923 (m-80) cc_final: 0.5969 (m-80) REVERT: I 73 THR cc_start: 0.8084 (m) cc_final: 0.7522 (p) REVERT: I 83 TYR cc_start: 0.5994 (m-10) cc_final: 0.5644 (m-10) REVERT: I 92 LEU cc_start: 0.9142 (mt) cc_final: 0.8808 (mt) REVERT: I 120 ASP cc_start: 0.7767 (t70) cc_final: 0.7493 (t70) REVERT: I 127 ASP cc_start: 0.6642 (m-30) cc_final: 0.6086 (m-30) REVERT: I 209 ILE cc_start: 0.9039 (mm) cc_final: 0.8774 (mm) REVERT: I 212 ILE cc_start: 0.8956 (mt) cc_final: 0.8731 (mt) REVERT: I 227 LEU cc_start: 0.9078 (mt) cc_final: 0.8626 (mp) REVERT: I 238 ILE cc_start: 0.8881 (mt) cc_final: 0.8679 (tp) REVERT: I 257 THR cc_start: 0.7990 (p) cc_final: 0.7684 (p) REVERT: I 335 ILE cc_start: 0.8619 (pt) cc_final: 0.8231 (tp) REVERT: I 377 MET cc_start: 0.7702 (tmm) cc_final: 0.7420 (tmm) REVERT: I 386 GLU cc_start: 0.8072 (mp0) cc_final: 0.7722 (mp0) REVERT: J 21 TRP cc_start: 0.7780 (m100) cc_final: 0.7575 (m100) REVERT: J 24 ILE cc_start: 0.9054 (mm) cc_final: 0.8611 (tp) REVERT: J 55 GLU cc_start: 0.5064 (mm-30) cc_final: 0.4397 (pm20) REVERT: J 92 PHE cc_start: 0.7677 (m-10) cc_final: 0.7444 (m-80) REVERT: J 138 THR cc_start: 0.8272 (p) cc_final: 0.7389 (p) REVERT: J 205 ASP cc_start: 0.8624 (t0) cc_final: 0.8219 (t0) REVERT: J 257 VAL cc_start: 0.9118 (t) cc_final: 0.8833 (p) REVERT: J 435 TYR cc_start: 0.6985 (m-80) cc_final: 0.6591 (m-80) REVERT: K 16 ILE cc_start: 0.8382 (pt) cc_final: 0.8072 (pt) REVERT: K 23 LEU cc_start: 0.8557 (tp) cc_final: 0.8325 (tp) REVERT: K 33 ASP cc_start: 0.6259 (p0) cc_final: 0.5809 (t0) REVERT: K 116 ASP cc_start: 0.7664 (m-30) cc_final: 0.7250 (m-30) REVERT: K 120 ASP cc_start: 0.7706 (m-30) cc_final: 0.5162 (t70) REVERT: K 205 ASP cc_start: 0.7443 (t0) cc_final: 0.7165 (t0) REVERT: K 260 VAL cc_start: 0.8168 (t) cc_final: 0.7935 (t) REVERT: K 279 GLU cc_start: 0.8082 (mp0) cc_final: 0.7351 (mp0) REVERT: K 280 LYS cc_start: 0.6935 (mtmt) cc_final: 0.6515 (mmmt) REVERT: K 335 ILE cc_start: 0.8592 (pt) cc_final: 0.8017 (tp) REVERT: K 352 LYS cc_start: 0.7558 (tptt) cc_final: 0.6923 (tptt) REVERT: K 413 MET cc_start: 0.7941 (mmp) cc_final: 0.7686 (mmp) REVERT: L 21 TRP cc_start: 0.7630 (m100) cc_final: 0.7018 (m100) REVERT: L 132 LEU cc_start: 0.8022 (tp) cc_final: 0.7717 (tp) REVERT: L 181 VAL cc_start: 0.6348 (t) cc_final: 0.5953 (t) REVERT: L 239 THR cc_start: 0.8842 (t) cc_final: 0.8200 (t) REVERT: L 291 LEU cc_start: 0.8836 (mt) cc_final: 0.8074 (mt) REVERT: L 333 LEU cc_start: 0.8524 (mt) cc_final: 0.8258 (mt) REVERT: M 21 TRP cc_start: 0.7835 (m100) cc_final: 0.7147 (m100) REVERT: M 23 LEU cc_start: 0.8455 (tp) cc_final: 0.7604 (tp) REVERT: M 118 VAL cc_start: 0.9192 (t) cc_final: 0.8964 (t) REVERT: M 175 PRO cc_start: 0.6536 (Cg_endo) cc_final: 0.5606 (Cg_exo) REVERT: M 196 GLU cc_start: 0.6499 (pp20) cc_final: 0.6118 (pm20) REVERT: M 275 VAL cc_start: 0.8189 (m) cc_final: 0.7407 (m) REVERT: M 291 ILE cc_start: 0.8225 (mt) cc_final: 0.7675 (mt) REVERT: M 315 CYS cc_start: 0.8209 (t) cc_final: 0.7937 (t) REVERT: M 335 ILE cc_start: 0.8043 (pt) cc_final: 0.7577 (tp) REVERT: M 378 LEU cc_start: 0.7951 (mm) cc_final: 0.7584 (mm) REVERT: M 428 LEU cc_start: 0.8482 (tp) cc_final: 0.8257 (tp) REVERT: M 430 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7445 (mmmt) REVERT: N 19 LYS cc_start: 0.8542 (tptp) cc_final: 0.7626 (tptp) REVERT: N 132 LEU cc_start: 0.7859 (mm) cc_final: 0.7590 (mt) REVERT: N 292 THR cc_start: 0.7959 (p) cc_final: 0.7663 (t) REVERT: N 384 ILE cc_start: 0.8294 (mp) cc_final: 0.7922 (mp) REVERT: N 413 MET cc_start: 0.5766 (mmm) cc_final: 0.5383 (mmt) REVERT: N 425 MET cc_start: 0.8808 (tpp) cc_final: 0.8346 (tpp) REVERT: O 16 ILE cc_start: 0.8556 (mt) cc_final: 0.8331 (mt) REVERT: O 21 TRP cc_start: 0.8451 (m100) cc_final: 0.7819 (m100) REVERT: O 23 LEU cc_start: 0.7809 (tp) cc_final: 0.7283 (tp) REVERT: O 293 ASN cc_start: 0.7180 (t0) cc_final: 0.6708 (t0) REVERT: O 315 CYS cc_start: 0.6665 (m) cc_final: 0.6393 (m) REVERT: O 353 VAL cc_start: 0.8203 (t) cc_final: 0.7718 (p) REVERT: O 398 MET cc_start: 0.7237 (mtp) cc_final: 0.6544 (mmt) REVERT: P 14 ASN cc_start: 0.8190 (m-40) cc_final: 0.7970 (m110) REVERT: P 21 TRP cc_start: 0.8046 (m100) cc_final: 0.7724 (m100) REVERT: P 49 ILE cc_start: 0.7677 (tp) cc_final: 0.7268 (tp) REVERT: P 86 ILE cc_start: 0.9209 (tt) cc_final: 0.8827 (tt) REVERT: P 163 ASP cc_start: 0.8139 (p0) cc_final: 0.7601 (p0) REVERT: P 194 LEU cc_start: 0.8977 (tt) cc_final: 0.8699 (tt) REVERT: P 201 THR cc_start: 0.7687 (t) cc_final: 0.7229 (p) REVERT: P 259 MET cc_start: 0.7550 (mmm) cc_final: 0.7222 (mmt) REVERT: P 268 PHE cc_start: 0.7234 (m-80) cc_final: 0.6771 (m-10) REVERT: P 288 VAL cc_start: 0.8938 (t) cc_final: 0.8682 (t) REVERT: P 314 THR cc_start: 0.7577 (p) cc_final: 0.7067 (p) REVERT: P 326 LYS cc_start: 0.7696 (ttmt) cc_final: 0.6962 (ttmt) REVERT: P 335 VAL cc_start: 0.7923 (t) cc_final: 0.6260 (t) REVERT: P 355 VAL cc_start: 0.7287 (t) cc_final: 0.7064 (t) REVERT: P 380 ASN cc_start: 0.8493 (t0) cc_final: 0.8231 (t0) REVERT: P 420 GLU cc_start: 0.5911 (mt-10) cc_final: 0.5683 (mt-10) REVERT: P 425 MET cc_start: 0.8303 (tpp) cc_final: 0.7770 (tpp) REVERT: Q 23 LEU cc_start: 0.8381 (tp) cc_final: 0.7887 (tp) REVERT: Q 52 PHE cc_start: 0.6882 (m-10) cc_final: 0.6587 (m-10) REVERT: R 115 VAL cc_start: 0.9022 (p) cc_final: 0.8590 (p) REVERT: R 154 ILE cc_start: 0.8582 (mt) cc_final: 0.8352 (mt) REVERT: R 166 MET cc_start: 0.6550 (mmp) cc_final: 0.5923 (mmm) REVERT: R 171 VAL cc_start: 0.8484 (t) cc_final: 0.8280 (t) REVERT: R 259 MET cc_start: 0.7994 (mmm) cc_final: 0.7324 (mmt) REVERT: R 268 PHE cc_start: 0.6530 (m-80) cc_final: 0.3990 (m-80) REVERT: R 302 MET cc_start: 0.8394 (mmm) cc_final: 0.7922 (mpp) outliers start: 9 outliers final: 4 residues processed: 1810 average time/residue: 0.6534 time to fit residues: 2001.7450 Evaluate side-chains 1293 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1289 time to evaluate : 5.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 4.9990 chunk 517 optimal weight: 8.9990 chunk 356 optimal weight: 0.3980 chunk 76 optimal weight: 40.0000 chunk 328 optimal weight: 40.0000 chunk 461 optimal weight: 8.9990 chunk 690 optimal weight: 10.0000 chunk 730 optimal weight: 50.0000 chunk 360 optimal weight: 9.9990 chunk 654 optimal weight: 4.9990 chunk 196 optimal weight: 30.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 HIS ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 300 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN J 294 GLN ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 394 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 GLN O 309 HIS ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 339 ASN P 349 ASN ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62262 Z= 0.199 Angle : 0.647 12.190 84582 Z= 0.339 Chirality : 0.046 0.231 9216 Planarity : 0.005 0.088 11043 Dihedral : 11.478 174.676 8595 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.08 % Allowed : 2.60 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 7632 helix: 0.51 (0.08), residues: 3627 sheet: 1.14 (0.16), residues: 1116 loop : 0.23 (0.13), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 21 HIS 0.013 0.001 HIS A 8 PHE 0.035 0.002 PHE D 262 TYR 0.034 0.002 TYR N 161 ARG 0.012 0.001 ARG N 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1709 time to evaluate : 5.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8510 (m100) cc_final: 0.8139 (m100) REVERT: A 53 PHE cc_start: 0.7973 (m-80) cc_final: 0.6705 (m-80) REVERT: A 75 ILE cc_start: 0.9088 (mm) cc_final: 0.8771 (tt) REVERT: A 193 THR cc_start: 0.8652 (p) cc_final: 0.8098 (t) REVERT: A 217 LEU cc_start: 0.8829 (mm) cc_final: 0.8483 (mm) REVERT: A 258 ASN cc_start: 0.6276 (t160) cc_final: 0.5307 (t0) REVERT: A 291 ILE cc_start: 0.9212 (mt) cc_final: 0.8406 (tp) REVERT: A 296 PHE cc_start: 0.7748 (m-80) cc_final: 0.7334 (m-10) REVERT: A 300 ASN cc_start: 0.8373 (p0) cc_final: 0.8025 (t0) REVERT: A 317 LEU cc_start: 0.7695 (mt) cc_final: 0.7258 (mt) REVERT: A 335 ILE cc_start: 0.8429 (tp) cc_final: 0.8094 (tp) REVERT: A 352 LYS cc_start: 0.8774 (tptt) cc_final: 0.8436 (tptp) REVERT: A 408 TYR cc_start: 0.5185 (m-80) cc_final: 0.4778 (m-80) REVERT: A 415 GLU cc_start: 0.8667 (mp0) cc_final: 0.7999 (pm20) REVERT: B 66 ILE cc_start: 0.9051 (mt) cc_final: 0.8581 (mm) REVERT: B 67 LEU cc_start: 0.8793 (mm) cc_final: 0.8524 (mm) REVERT: B 120 ASP cc_start: 0.8022 (t0) cc_final: 0.7609 (t0) REVERT: B 136 GLN cc_start: 0.6891 (pt0) cc_final: 0.6300 (pt0) REVERT: B 139 HIS cc_start: 0.8236 (p90) cc_final: 0.7377 (p90) REVERT: B 215 ARG cc_start: 0.7731 (tmm160) cc_final: 0.6849 (ttp80) REVERT: B 217 LEU cc_start: 0.8850 (mm) cc_final: 0.8306 (mm) REVERT: B 221 THR cc_start: 0.9011 (p) cc_final: 0.8789 (p) REVERT: B 268 PHE cc_start: 0.5978 (m-80) cc_final: 0.5495 (m-80) REVERT: B 283 TYR cc_start: 0.6471 (m-80) cc_final: 0.6130 (m-10) REVERT: B 422 GLU cc_start: 0.8792 (pt0) cc_final: 0.8457 (pp20) REVERT: B 425 MET cc_start: 0.8726 (ttt) cc_final: 0.8466 (ttt) REVERT: B 432 TYR cc_start: 0.6469 (m-10) cc_final: 0.5624 (m-80) REVERT: B 435 TYR cc_start: 0.6827 (m-80) cc_final: 0.6331 (m-80) REVERT: C 21 TRP cc_start: 0.7596 (m100) cc_final: 0.6672 (m100) REVERT: C 60 LYS cc_start: 0.8397 (mmtt) cc_final: 0.7587 (tttt) REVERT: C 75 ILE cc_start: 0.9040 (mm) cc_final: 0.7907 (tt) REVERT: C 167 LEU cc_start: 0.6759 (mt) cc_final: 0.6408 (mt) REVERT: C 292 THR cc_start: 0.9037 (t) cc_final: 0.8345 (p) REVERT: C 300 ASN cc_start: 0.8555 (m-40) cc_final: 0.8273 (m110) REVERT: C 315 CYS cc_start: 0.7380 (t) cc_final: 0.6968 (m) REVERT: C 316 CYS cc_start: 0.6823 (t) cc_final: 0.5020 (t) REVERT: C 353 VAL cc_start: 0.7881 (t) cc_final: 0.7678 (m) REVERT: C 435 VAL cc_start: 0.9157 (t) cc_final: 0.8840 (t) REVERT: D 53 TYR cc_start: 0.4606 (m-80) cc_final: 0.4378 (m-80) REVERT: D 137 LEU cc_start: 0.7391 (mp) cc_final: 0.7097 (mp) REVERT: D 139 HIS cc_start: 0.7700 (p90) cc_final: 0.7040 (p90) REVERT: D 154 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8785 (mp) REVERT: D 259 MET cc_start: 0.8130 (mmm) cc_final: 0.7212 (mmp) REVERT: D 292 THR cc_start: 0.8217 (t) cc_final: 0.6555 (t) REVERT: D 302 MET cc_start: 0.6593 (mtt) cc_final: 0.6294 (mtp) REVERT: D 398 MET cc_start: 0.7017 (ptp) cc_final: 0.6720 (ptp) REVERT: D 413 MET cc_start: 0.5444 (mmm) cc_final: 0.5234 (mmm) REVERT: E 21 TRP cc_start: 0.8505 (m100) cc_final: 0.7866 (m100) REVERT: E 23 LEU cc_start: 0.8286 (tp) cc_final: 0.7951 (tp) REVERT: E 33 ASP cc_start: 0.7041 (p0) cc_final: 0.6326 (p0) REVERT: E 53 PHE cc_start: 0.7603 (m-80) cc_final: 0.7078 (m-80) REVERT: E 75 ILE cc_start: 0.8923 (mm) cc_final: 0.8461 (tt) REVERT: E 169 PHE cc_start: 0.3999 (m-10) cc_final: 0.3749 (m-10) REVERT: E 193 THR cc_start: 0.8614 (p) cc_final: 0.8380 (p) REVERT: E 228 ASN cc_start: 0.8292 (m-40) cc_final: 0.7312 (p0) REVERT: E 291 ILE cc_start: 0.9036 (mt) cc_final: 0.8003 (tt) REVERT: E 335 ILE cc_start: 0.8581 (pt) cc_final: 0.8216 (tp) REVERT: E 347 CYS cc_start: 0.8042 (p) cc_final: 0.7116 (p) REVERT: E 352 LYS cc_start: 0.9180 (tptt) cc_final: 0.8891 (tptp) REVERT: E 355 ILE cc_start: 0.8611 (mm) cc_final: 0.8345 (tp) REVERT: F 21 TRP cc_start: 0.7921 (m100) cc_final: 0.7450 (m100) REVERT: F 66 ILE cc_start: 0.8934 (mm) cc_final: 0.8684 (mm) REVERT: F 116 ASP cc_start: 0.7721 (m-30) cc_final: 0.7159 (m-30) REVERT: F 139 HIS cc_start: 0.7931 (p90) cc_final: 0.7082 (p90) REVERT: F 153 LEU cc_start: 0.8680 (mt) cc_final: 0.8294 (mt) REVERT: F 163 ASP cc_start: 0.7427 (p0) cc_final: 0.6806 (p0) REVERT: F 166 MET cc_start: 0.7540 (mmp) cc_final: 0.7230 (mmm) REVERT: F 325 MET cc_start: 0.8059 (mpp) cc_final: 0.7656 (mpp) REVERT: F 326 LYS cc_start: 0.6741 (tptt) cc_final: 0.6370 (tptp) REVERT: F 333 LEU cc_start: 0.8560 (tp) cc_final: 0.8351 (tp) REVERT: F 356 CYS cc_start: 0.8146 (t) cc_final: 0.7600 (t) REVERT: F 398 MET cc_start: 0.7606 (mtp) cc_final: 0.6631 (ptm) REVERT: G 5 ILE cc_start: 0.8270 (mt) cc_final: 0.7902 (mm) REVERT: G 25 CYS cc_start: 0.7457 (m) cc_final: 0.5408 (m) REVERT: G 199 ASP cc_start: 0.7467 (m-30) cc_final: 0.7224 (m-30) REVERT: G 209 ILE cc_start: 0.8781 (mm) cc_final: 0.8420 (mm) REVERT: G 269 LEU cc_start: 0.6883 (mt) cc_final: 0.6384 (mt) REVERT: G 291 ILE cc_start: 0.8057 (mt) cc_final: 0.7219 (mt) REVERT: G 292 THR cc_start: 0.8353 (p) cc_final: 0.8076 (p) REVERT: G 379 SER cc_start: 0.7798 (p) cc_final: 0.7371 (t) REVERT: H 21 TRP cc_start: 0.7600 (m100) cc_final: 0.6527 (m100) REVERT: H 60 LYS cc_start: 0.1427 (pttt) cc_final: 0.0625 (pttp) REVERT: H 66 ILE cc_start: 0.8589 (mm) cc_final: 0.8292 (mm) REVERT: H 262 PHE cc_start: 0.7417 (t80) cc_final: 0.7196 (t80) REVERT: H 413 MET cc_start: 0.5666 (mtt) cc_final: 0.5342 (mtt) REVERT: I 20 CYS cc_start: 0.9352 (p) cc_final: 0.8678 (p) REVERT: I 25 CYS cc_start: 0.6952 (m) cc_final: 0.6421 (m) REVERT: I 53 PHE cc_start: 0.7189 (m-80) cc_final: 0.6210 (m-80) REVERT: I 83 TYR cc_start: 0.5855 (m-10) cc_final: 0.5472 (m-10) REVERT: I 127 ASP cc_start: 0.6214 (m-30) cc_final: 0.5872 (m-30) REVERT: I 158 SER cc_start: 0.8813 (p) cc_final: 0.8323 (t) REVERT: I 212 ILE cc_start: 0.8870 (mt) cc_final: 0.8378 (pt) REVERT: I 238 ILE cc_start: 0.8987 (mt) cc_final: 0.8751 (tp) REVERT: I 335 ILE cc_start: 0.8597 (pt) cc_final: 0.8194 (tp) REVERT: I 376 CYS cc_start: 0.7255 (t) cc_final: 0.6803 (t) REVERT: I 386 GLU cc_start: 0.7660 (mp0) cc_final: 0.7327 (mp0) REVERT: J 55 GLU cc_start: 0.4900 (mm-30) cc_final: 0.4431 (pm20) REVERT: J 138 THR cc_start: 0.7990 (p) cc_final: 0.7354 (p) REVERT: J 165 ILE cc_start: 0.8145 (pt) cc_final: 0.7837 (pt) REVERT: J 205 ASP cc_start: 0.8216 (t0) cc_final: 0.7434 (t0) REVERT: J 257 VAL cc_start: 0.9066 (t) cc_final: 0.8843 (p) REVERT: J 291 LEU cc_start: 0.8666 (mt) cc_final: 0.7899 (mt) REVERT: J 428 LEU cc_start: 0.8668 (tp) cc_final: 0.7974 (mm) REVERT: J 432 TYR cc_start: 0.5803 (m-10) cc_final: 0.5488 (m-10) REVERT: K 23 LEU cc_start: 0.8419 (tp) cc_final: 0.8210 (tp) REVERT: K 33 ASP cc_start: 0.5508 (p0) cc_final: 0.5134 (t0) REVERT: K 78 VAL cc_start: 0.8966 (t) cc_final: 0.8606 (t) REVERT: K 116 ASP cc_start: 0.7937 (m-30) cc_final: 0.7645 (p0) REVERT: K 120 ASP cc_start: 0.8019 (m-30) cc_final: 0.5041 (t70) REVERT: K 121 ARG cc_start: 0.7589 (mmp80) cc_final: 0.7049 (mmp80) REVERT: K 205 ASP cc_start: 0.7576 (t0) cc_final: 0.7286 (t0) REVERT: K 212 ILE cc_start: 0.8345 (mt) cc_final: 0.8078 (pt) REVERT: K 260 VAL cc_start: 0.7942 (t) cc_final: 0.7734 (t) REVERT: K 279 GLU cc_start: 0.7720 (mp0) cc_final: 0.7377 (mp0) REVERT: K 280 LYS cc_start: 0.7295 (mtpt) cc_final: 0.7008 (mmmt) REVERT: K 288 VAL cc_start: 0.9089 (m) cc_final: 0.8796 (p) REVERT: K 335 ILE cc_start: 0.8788 (pt) cc_final: 0.8159 (tp) REVERT: K 352 LYS cc_start: 0.7821 (tptt) cc_final: 0.7294 (tptm) REVERT: L 21 TRP cc_start: 0.7621 (m100) cc_final: 0.6944 (m100) REVERT: L 138 THR cc_start: 0.4960 (p) cc_final: 0.3754 (p) REVERT: L 205 ASP cc_start: 0.8477 (t0) cc_final: 0.8165 (t0) REVERT: L 228 ASN cc_start: 0.7282 (m-40) cc_final: 0.6933 (m-40) REVERT: L 291 LEU cc_start: 0.8898 (mt) cc_final: 0.7911 (mt) REVERT: L 333 LEU cc_start: 0.8240 (mt) cc_final: 0.7821 (mt) REVERT: L 334 ASN cc_start: 0.7689 (m110) cc_final: 0.6196 (m110) REVERT: L 355 VAL cc_start: 0.7356 (t) cc_final: 0.6937 (t) REVERT: M 21 TRP cc_start: 0.7806 (m100) cc_final: 0.7491 (m100) REVERT: M 23 LEU cc_start: 0.8515 (tp) cc_final: 0.8048 (tp) REVERT: M 123 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7395 (mmm-85) REVERT: M 196 GLU cc_start: 0.6426 (pp20) cc_final: 0.6146 (pm20) REVERT: M 275 VAL cc_start: 0.8299 (m) cc_final: 0.7883 (m) REVERT: M 285 GLN cc_start: 0.7662 (pm20) cc_final: 0.7398 (pm20) REVERT: M 316 CYS cc_start: 0.4777 (p) cc_final: 0.3570 (p) REVERT: M 317 LEU cc_start: 0.7194 (mt) cc_final: 0.6831 (mt) REVERT: N 132 LEU cc_start: 0.8103 (mm) cc_final: 0.7721 (mt) REVERT: N 161 TYR cc_start: 0.7364 (m-80) cc_final: 0.6872 (m-10) REVERT: N 227 LEU cc_start: 0.8338 (mt) cc_final: 0.7835 (mt) REVERT: N 292 THR cc_start: 0.7471 (p) cc_final: 0.6984 (t) REVERT: N 332 MET cc_start: 0.6010 (tmm) cc_final: 0.5809 (tmm) REVERT: N 384 ILE cc_start: 0.8017 (mp) cc_final: 0.7271 (mp) REVERT: N 391 ILE cc_start: 0.8917 (mm) cc_final: 0.8683 (mm) REVERT: N 425 MET cc_start: 0.8228 (ttt) cc_final: 0.7775 (tpp) REVERT: O 21 TRP cc_start: 0.8594 (m100) cc_final: 0.8076 (m100) REVERT: O 23 LEU cc_start: 0.7975 (tp) cc_final: 0.7389 (tp) REVERT: O 51 THR cc_start: 0.6450 (p) cc_final: 0.6221 (p) REVERT: O 74 VAL cc_start: 0.8408 (t) cc_final: 0.7368 (t) REVERT: O 76 ASP cc_start: 0.7823 (m-30) cc_final: 0.7475 (t70) REVERT: O 125 LEU cc_start: 0.8578 (mm) cc_final: 0.8367 (mm) REVERT: O 203 MET cc_start: 0.6358 (pmm) cc_final: 0.5997 (pmm) REVERT: O 398 MET cc_start: 0.7362 (mtp) cc_final: 0.6768 (mmt) REVERT: P 14 ASN cc_start: 0.8281 (m-40) cc_final: 0.7864 (m-40) REVERT: P 21 TRP cc_start: 0.8258 (m100) cc_final: 0.7888 (m100) REVERT: P 86 ILE cc_start: 0.9183 (tt) cc_final: 0.8805 (tt) REVERT: P 163 ASP cc_start: 0.8299 (p0) cc_final: 0.7754 (p0) REVERT: P 201 THR cc_start: 0.7016 (t) cc_final: 0.6736 (p) REVERT: P 259 MET cc_start: 0.7468 (mmm) cc_final: 0.6812 (mmt) REVERT: P 268 PHE cc_start: 0.7230 (m-80) cc_final: 0.6726 (m-10) REVERT: P 384 ILE cc_start: 0.8159 (mt) cc_final: 0.7941 (mt) REVERT: P 398 MET cc_start: 0.8182 (ptm) cc_final: 0.7823 (ptm) REVERT: P 425 MET cc_start: 0.8356 (tpp) cc_final: 0.7857 (tpp) REVERT: Q 66 VAL cc_start: 0.8448 (t) cc_final: 0.8226 (t) REVERT: Q 86 LEU cc_start: 0.8675 (tp) cc_final: 0.8464 (tp) REVERT: Q 154 MET cc_start: 0.7461 (tmm) cc_final: 0.7113 (tmm) REVERT: Q 182 VAL cc_start: 0.8453 (m) cc_final: 0.8112 (m) REVERT: Q 290 GLU cc_start: 0.8092 (pp20) cc_final: 0.7560 (pp20) REVERT: Q 429 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6476 (mm-30) REVERT: R 115 VAL cc_start: 0.9060 (p) cc_final: 0.8718 (p) REVERT: R 154 ILE cc_start: 0.8658 (mt) cc_final: 0.8388 (mt) REVERT: R 166 MET cc_start: 0.6144 (mmp) cc_final: 0.5704 (mmm) REVERT: R 259 MET cc_start: 0.7709 (mmm) cc_final: 0.7375 (mmt) REVERT: R 315 VAL cc_start: 0.7786 (t) cc_final: 0.7439 (t) REVERT: R 325 MET cc_start: 0.7242 (tpp) cc_final: 0.6917 (tpp) REVERT: R 332 MET cc_start: 0.5952 (tmm) cc_final: 0.5159 (tmm) REVERT: R 398 MET cc_start: 0.7464 (ptm) cc_final: 0.6305 (ptm) outliers start: 5 outliers final: 1 residues processed: 1713 average time/residue: 0.5751 time to fit residues: 1662.7125 Evaluate side-chains 1257 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1255 time to evaluate : 5.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 40.0000 chunk 414 optimal weight: 50.0000 chunk 10 optimal weight: 9.9990 chunk 544 optimal weight: 30.0000 chunk 301 optimal weight: 40.0000 chunk 623 optimal weight: 30.0000 chunk 505 optimal weight: 8.9990 chunk 0 optimal weight: 80.0000 chunk 373 optimal weight: 8.9990 chunk 655 optimal weight: 0.0980 chunk 184 optimal weight: 0.0970 overall best weight: 5.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 309 HIS B 394 GLN C 8 HIS C 176 GLN C 258 ASN D 37 HIS D 193 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 136 GLN F 249 ASN ** F 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN I 101 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 349 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN M 176 GLN M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 300 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS R 136 GLN ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 349 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.7301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 62262 Z= 0.194 Angle : 0.639 11.753 84582 Z= 0.335 Chirality : 0.046 0.215 9216 Planarity : 0.005 0.088 11043 Dihedral : 11.248 171.455 8595 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.12 % Allowed : 2.31 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.10), residues: 7632 helix: 0.70 (0.08), residues: 3582 sheet: 1.16 (0.16), residues: 1116 loop : 0.21 (0.13), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP R 21 HIS 0.012 0.001 HIS C 8 PHE 0.025 0.002 PHE D 296 TYR 0.030 0.002 TYR N 161 ARG 0.010 0.001 ARG N 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1655 time to evaluate : 5.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.8381 (m100) cc_final: 0.8148 (m100) REVERT: A 53 PHE cc_start: 0.7847 (m-80) cc_final: 0.6849 (m-80) REVERT: A 75 ILE cc_start: 0.9106 (mm) cc_final: 0.8782 (tt) REVERT: A 193 THR cc_start: 0.8786 (p) cc_final: 0.7710 (t) REVERT: A 217 LEU cc_start: 0.8891 (mm) cc_final: 0.8415 (mm) REVERT: A 218 ASP cc_start: 0.6901 (m-30) cc_final: 0.6595 (m-30) REVERT: A 291 ILE cc_start: 0.9231 (mt) cc_final: 0.8279 (tp) REVERT: A 300 ASN cc_start: 0.8278 (p0) cc_final: 0.7892 (t0) REVERT: A 317 LEU cc_start: 0.7744 (mt) cc_final: 0.7333 (mt) REVERT: A 335 ILE cc_start: 0.8291 (tp) cc_final: 0.7913 (tp) REVERT: A 352 LYS cc_start: 0.8526 (tptt) cc_final: 0.8258 (tptp) REVERT: A 395 PHE cc_start: 0.7369 (t80) cc_final: 0.7101 (t80) REVERT: A 408 TYR cc_start: 0.5197 (m-80) cc_final: 0.4199 (m-80) REVERT: A 415 GLU cc_start: 0.8603 (mp0) cc_final: 0.8167 (pm20) REVERT: A 417 GLU cc_start: 0.7275 (mp0) cc_final: 0.7067 (mp0) REVERT: A 431 ASP cc_start: 0.8182 (m-30) cc_final: 0.7926 (m-30) REVERT: B 21 TRP cc_start: 0.7787 (m100) cc_final: 0.7379 (m100) REVERT: B 66 ILE cc_start: 0.9146 (mt) cc_final: 0.8799 (mm) REVERT: B 75 MET cc_start: 0.7688 (ttp) cc_final: 0.7018 (tmm) REVERT: B 139 HIS cc_start: 0.7757 (p90) cc_final: 0.7228 (p-80) REVERT: B 165 ILE cc_start: 0.8931 (mt) cc_final: 0.8725 (mt) REVERT: B 215 ARG cc_start: 0.7883 (tmm160) cc_final: 0.6961 (ttp80) REVERT: B 217 LEU cc_start: 0.8445 (mm) cc_final: 0.8021 (mm) REVERT: B 268 PHE cc_start: 0.5946 (m-80) cc_final: 0.5089 (m-80) REVERT: B 269 MET cc_start: 0.7110 (ttm) cc_final: 0.6661 (ttm) REVERT: B 422 GLU cc_start: 0.8723 (pt0) cc_final: 0.8484 (pp20) REVERT: B 432 TYR cc_start: 0.5978 (m-10) cc_final: 0.5502 (m-80) REVERT: C 33 ASP cc_start: 0.6895 (p0) cc_final: 0.6288 (t70) REVERT: C 60 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7564 (tttt) REVERT: C 75 ILE cc_start: 0.8705 (mm) cc_final: 0.7455 (tt) REVERT: C 227 LEU cc_start: 0.8896 (mt) cc_final: 0.8683 (mp) REVERT: C 435 VAL cc_start: 0.9113 (t) cc_final: 0.8837 (t) REVERT: D 53 TYR cc_start: 0.4714 (m-80) cc_final: 0.4069 (m-80) REVERT: D 165 ILE cc_start: 0.8651 (mt) cc_final: 0.8018 (mt) REVERT: D 259 MET cc_start: 0.8069 (mmm) cc_final: 0.7211 (mmp) REVERT: D 292 THR cc_start: 0.7991 (t) cc_final: 0.6740 (t) REVERT: D 398 MET cc_start: 0.7181 (ptp) cc_final: 0.6829 (ptp) REVERT: E 21 TRP cc_start: 0.8465 (m100) cc_final: 0.7782 (m100) REVERT: E 23 LEU cc_start: 0.8360 (tp) cc_final: 0.8001 (tp) REVERT: E 24 TYR cc_start: 0.7323 (m-80) cc_final: 0.5973 (m-80) REVERT: E 33 ASP cc_start: 0.7141 (p0) cc_final: 0.6481 (p0) REVERT: E 53 PHE cc_start: 0.7571 (m-80) cc_final: 0.6897 (m-80) REVERT: E 193 THR cc_start: 0.8667 (p) cc_final: 0.8294 (p) REVERT: E 260 VAL cc_start: 0.7570 (t) cc_final: 0.6860 (t) REVERT: E 269 LEU cc_start: 0.7955 (mp) cc_final: 0.7751 (mp) REVERT: E 291 ILE cc_start: 0.9151 (mt) cc_final: 0.7964 (tt) REVERT: E 335 ILE cc_start: 0.8542 (pt) cc_final: 0.8327 (tp) REVERT: E 344 VAL cc_start: 0.7477 (t) cc_final: 0.6767 (p) REVERT: E 352 LYS cc_start: 0.9145 (tptt) cc_final: 0.8860 (tptp) REVERT: E 355 ILE cc_start: 0.8727 (mm) cc_final: 0.8330 (tp) REVERT: F 21 TRP cc_start: 0.8184 (m100) cc_final: 0.7564 (m100) REVERT: F 66 ILE cc_start: 0.8943 (mm) cc_final: 0.8718 (mm) REVERT: F 116 ASP cc_start: 0.7518 (m-30) cc_final: 0.6766 (m-30) REVERT: F 139 HIS cc_start: 0.7856 (p90) cc_final: 0.7004 (p-80) REVERT: F 163 ASP cc_start: 0.7556 (p0) cc_final: 0.6894 (p0) REVERT: F 166 MET cc_start: 0.7615 (mmp) cc_final: 0.7246 (mmm) REVERT: F 194 LEU cc_start: 0.8604 (mp) cc_final: 0.8344 (mp) REVERT: F 356 CYS cc_start: 0.7657 (t) cc_final: 0.7165 (t) REVERT: F 398 MET cc_start: 0.7591 (mtp) cc_final: 0.6562 (ptp) REVERT: G 5 ILE cc_start: 0.8440 (mt) cc_final: 0.8068 (mm) REVERT: G 25 CYS cc_start: 0.7555 (m) cc_final: 0.7306 (m) REVERT: G 209 ILE cc_start: 0.8600 (mm) cc_final: 0.8139 (mm) REVERT: G 269 LEU cc_start: 0.6544 (mt) cc_final: 0.5920 (mt) REVERT: G 271 THR cc_start: 0.6343 (p) cc_final: 0.5973 (t) REVERT: G 295 CYS cc_start: 0.8285 (m) cc_final: 0.7892 (m) REVERT: G 379 SER cc_start: 0.6913 (p) cc_final: 0.6479 (t) REVERT: G 395 PHE cc_start: 0.7146 (t80) cc_final: 0.6813 (t80) REVERT: H 21 TRP cc_start: 0.7781 (m100) cc_final: 0.6456 (m100) REVERT: H 51 VAL cc_start: 0.9057 (t) cc_final: 0.8809 (t) REVERT: H 60 LYS cc_start: 0.1478 (pttt) cc_final: 0.1244 (pttm) REVERT: H 67 LEU cc_start: 0.7259 (mt) cc_final: 0.6906 (mt) REVERT: H 132 LEU cc_start: 0.8851 (tp) cc_final: 0.8070 (tp) REVERT: H 138 THR cc_start: 0.6698 (p) cc_final: 0.6429 (p) REVERT: H 275 LEU cc_start: 0.8200 (pt) cc_final: 0.7904 (pt) REVERT: H 288 VAL cc_start: 0.9043 (t) cc_final: 0.8772 (t) REVERT: H 325 MET cc_start: 0.6876 (ptp) cc_final: 0.6564 (ptp) REVERT: H 413 MET cc_start: 0.5907 (mtt) cc_final: 0.5432 (mtt) REVERT: I 23 LEU cc_start: 0.8246 (tt) cc_final: 0.7766 (tt) REVERT: I 53 PHE cc_start: 0.7371 (m-80) cc_final: 0.6508 (m-80) REVERT: I 83 TYR cc_start: 0.6054 (m-10) cc_final: 0.5605 (m-10) REVERT: I 92 LEU cc_start: 0.9276 (mt) cc_final: 0.8933 (mt) REVERT: I 158 SER cc_start: 0.8792 (p) cc_final: 0.8425 (t) REVERT: I 238 ILE cc_start: 0.8993 (mt) cc_final: 0.8738 (tp) REVERT: I 288 VAL cc_start: 0.8393 (m) cc_final: 0.8120 (t) REVERT: I 291 ILE cc_start: 0.8116 (mt) cc_final: 0.7808 (mt) REVERT: I 376 CYS cc_start: 0.7373 (t) cc_final: 0.6747 (t) REVERT: I 377 MET cc_start: 0.7875 (tmm) cc_final: 0.7490 (tmm) REVERT: I 386 GLU cc_start: 0.7721 (mp0) cc_final: 0.7452 (mp0) REVERT: J 21 TRP cc_start: 0.7446 (m100) cc_final: 0.6256 (m100) REVERT: J 55 GLU cc_start: 0.5076 (mm-30) cc_final: 0.4053 (pm20) REVERT: J 138 THR cc_start: 0.7918 (p) cc_final: 0.7437 (p) REVERT: J 165 ILE cc_start: 0.8596 (pt) cc_final: 0.8259 (pt) REVERT: J 205 ASP cc_start: 0.8083 (t0) cc_final: 0.7714 (t0) REVERT: J 216 THR cc_start: 0.8034 (p) cc_final: 0.7737 (p) REVERT: J 248 LEU cc_start: 0.7003 (mm) cc_final: 0.6504 (mt) REVERT: J 257 VAL cc_start: 0.9079 (t) cc_final: 0.8716 (p) REVERT: J 269 MET cc_start: 0.6219 (ttm) cc_final: 0.5891 (ttm) REVERT: J 291 LEU cc_start: 0.8497 (mt) cc_final: 0.8126 (mm) REVERT: J 351 VAL cc_start: 0.9508 (m) cc_final: 0.9156 (p) REVERT: J 420 GLU cc_start: 0.6681 (tp30) cc_final: 0.6284 (tt0) REVERT: J 428 LEU cc_start: 0.8634 (tp) cc_final: 0.8011 (mm) REVERT: K 33 ASP cc_start: 0.5195 (p0) cc_final: 0.4537 (t70) REVERT: K 116 ASP cc_start: 0.7918 (m-30) cc_final: 0.7570 (p0) REVERT: K 120 ASP cc_start: 0.7958 (m-30) cc_final: 0.7090 (t70) REVERT: K 260 VAL cc_start: 0.7937 (t) cc_final: 0.7655 (t) REVERT: K 279 GLU cc_start: 0.8257 (mp0) cc_final: 0.7639 (mp0) REVERT: K 280 LYS cc_start: 0.7058 (mtpt) cc_final: 0.6810 (mmmt) REVERT: K 335 ILE cc_start: 0.8782 (pt) cc_final: 0.8006 (tp) REVERT: K 352 LYS cc_start: 0.8018 (tptt) cc_final: 0.7345 (tptm) REVERT: L 21 TRP cc_start: 0.7811 (m100) cc_final: 0.6898 (m100) REVERT: L 53 TYR cc_start: 0.5099 (m-80) cc_final: 0.4048 (m-80) REVERT: L 205 ASP cc_start: 0.8456 (t0) cc_final: 0.8138 (t0) REVERT: L 286 LEU cc_start: 0.7988 (mt) cc_final: 0.7509 (mt) REVERT: L 288 VAL cc_start: 0.8125 (t) cc_final: 0.7732 (t) REVERT: L 291 LEU cc_start: 0.8772 (mt) cc_final: 0.7776 (mt) REVERT: M 21 TRP cc_start: 0.7999 (m100) cc_final: 0.7399 (m100) REVERT: M 23 LEU cc_start: 0.8537 (tp) cc_final: 0.7306 (tp) REVERT: M 269 LEU cc_start: 0.7515 (pp) cc_final: 0.7101 (pp) REVERT: M 291 ILE cc_start: 0.7937 (mt) cc_final: 0.7499 (mt) REVERT: M 316 CYS cc_start: 0.4912 (p) cc_final: 0.3451 (p) REVERT: N 132 LEU cc_start: 0.7989 (mm) cc_final: 0.7605 (mt) REVERT: N 227 LEU cc_start: 0.8182 (mt) cc_final: 0.7814 (mt) REVERT: N 292 THR cc_start: 0.7553 (p) cc_final: 0.7081 (t) REVERT: N 384 ILE cc_start: 0.8116 (mp) cc_final: 0.7040 (mp) REVERT: N 413 MET cc_start: 0.4267 (mmt) cc_final: 0.3884 (mmp) REVERT: N 425 MET cc_start: 0.8275 (ttt) cc_final: 0.7943 (tpp) REVERT: O 16 ILE cc_start: 0.8428 (mt) cc_final: 0.8227 (mt) REVERT: O 21 TRP cc_start: 0.8572 (m100) cc_final: 0.8118 (m100) REVERT: O 23 LEU cc_start: 0.7978 (tp) cc_final: 0.7479 (tp) REVERT: O 66 VAL cc_start: 0.8293 (t) cc_final: 0.8080 (t) REVERT: O 74 VAL cc_start: 0.8452 (t) cc_final: 0.6737 (t) REVERT: O 76 ASP cc_start: 0.7932 (m-30) cc_final: 0.7663 (t70) REVERT: O 207 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6982 (mt-10) REVERT: O 318 LEU cc_start: 0.6552 (tp) cc_final: 0.5997 (tp) REVERT: O 376 CYS cc_start: 0.7766 (p) cc_final: 0.7344 (p) REVERT: O 398 MET cc_start: 0.7597 (mtp) cc_final: 0.6885 (mmt) REVERT: P 14 ASN cc_start: 0.8112 (m-40) cc_final: 0.7874 (m110) REVERT: P 21 TRP cc_start: 0.8359 (m100) cc_final: 0.7934 (m100) REVERT: P 51 VAL cc_start: 0.8717 (t) cc_final: 0.8469 (t) REVERT: P 62 VAL cc_start: 0.8539 (m) cc_final: 0.8305 (m) REVERT: P 86 ILE cc_start: 0.9120 (tt) cc_final: 0.8801 (tt) REVERT: P 115 VAL cc_start: 0.9256 (t) cc_final: 0.8872 (t) REVERT: P 124 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7743 (ptmt) REVERT: P 163 ASP cc_start: 0.8402 (p0) cc_final: 0.8092 (p0) REVERT: P 259 MET cc_start: 0.7369 (mmm) cc_final: 0.6166 (mmt) REVERT: P 268 PHE cc_start: 0.6850 (m-80) cc_final: 0.5740 (m-80) REVERT: P 283 TYR cc_start: 0.8020 (m-80) cc_final: 0.7449 (m-80) REVERT: P 292 THR cc_start: 0.8203 (p) cc_final: 0.7325 (p) REVERT: P 425 MET cc_start: 0.8438 (tpp) cc_final: 0.7776 (tpp) REVERT: Q 23 LEU cc_start: 0.8403 (tp) cc_final: 0.8191 (tp) REVERT: Q 86 LEU cc_start: 0.8640 (tp) cc_final: 0.8413 (tp) REVERT: Q 398 MET cc_start: 0.6941 (ptm) cc_final: 0.6471 (ttp) REVERT: Q 431 ASP cc_start: 0.5728 (m-30) cc_final: 0.5142 (m-30) REVERT: R 66 ILE cc_start: 0.8678 (mm) cc_final: 0.8451 (mm) REVERT: R 115 VAL cc_start: 0.9058 (p) cc_final: 0.8717 (p) REVERT: R 120 ASP cc_start: 0.8298 (m-30) cc_final: 0.7837 (m-30) REVERT: R 154 ILE cc_start: 0.8694 (mt) cc_final: 0.8351 (mt) REVERT: R 166 MET cc_start: 0.6038 (mmp) cc_final: 0.5733 (mmm) REVERT: R 259 MET cc_start: 0.7787 (mmm) cc_final: 0.6043 (mmm) REVERT: R 268 PHE cc_start: 0.6648 (m-80) cc_final: 0.3325 (m-80) REVERT: R 269 MET cc_start: 0.4801 (tpt) cc_final: 0.4424 (tpt) REVERT: R 315 VAL cc_start: 0.7928 (t) cc_final: 0.7691 (t) REVERT: R 332 MET cc_start: 0.5797 (tmm) cc_final: 0.4984 (tmm) REVERT: R 384 ILE cc_start: 0.7633 (mp) cc_final: 0.7328 (mp) REVERT: R 398 MET cc_start: 0.7350 (ptm) cc_final: 0.6490 (ptm) REVERT: R 425 MET cc_start: 0.8486 (tpp) cc_final: 0.8055 (tpt) outliers start: 8 outliers final: 1 residues processed: 1660 average time/residue: 0.5733 time to fit residues: 1608.1062 Evaluate side-chains 1208 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1207 time to evaluate : 5.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 0.7980 chunk 658 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 8.9990 chunk 731 optimal weight: 50.0000 chunk 607 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 384 optimal weight: 40.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 35 GLN C 300 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 193 GLN D 249 ASN D 309 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 197 ASN F 249 ASN F 309 HIS G 176 GLN G 216 ASN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 349 ASN K 197 HIS ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 283 HIS O 285 GLN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 GLN ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 GLN ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62262 Z= 0.201 Angle : 0.641 10.012 84582 Z= 0.335 Chirality : 0.046 0.268 9216 Planarity : 0.005 0.080 11043 Dihedral : 11.227 176.671 8595 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.14 % Allowed : 1.65 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 7632 helix: 0.70 (0.08), residues: 3600 sheet: 1.19 (0.15), residues: 1098 loop : 0.20 (0.13), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP R 21 HIS 0.010 0.001 HIS E 8 PHE 0.028 0.002 PHE D 92 TYR 0.041 0.002 TYR P 161 ARG 0.009 0.001 ARG I 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1599 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.8094 (m-80) cc_final: 0.7030 (m-80) REVERT: A 75 ILE cc_start: 0.9171 (mm) cc_final: 0.8704 (tt) REVERT: A 167 LEU cc_start: 0.8192 (mm) cc_final: 0.7370 (mt) REVERT: A 193 THR cc_start: 0.8500 (p) cc_final: 0.8166 (t) REVERT: A 202 PHE cc_start: 0.7120 (m-80) cc_final: 0.6898 (m-10) REVERT: A 218 ASP cc_start: 0.6709 (m-30) cc_final: 0.6425 (m-30) REVERT: A 291 ILE cc_start: 0.9306 (mt) cc_final: 0.8210 (tp) REVERT: A 317 LEU cc_start: 0.7741 (mt) cc_final: 0.7306 (mt) REVERT: A 347 CYS cc_start: 0.8250 (p) cc_final: 0.7872 (p) REVERT: A 352 LYS cc_start: 0.8338 (tptt) cc_final: 0.7739 (tptp) REVERT: A 408 TYR cc_start: 0.5692 (m-80) cc_final: 0.5268 (m-80) REVERT: A 415 GLU cc_start: 0.8617 (mp0) cc_final: 0.8116 (pm20) REVERT: A 432 TYR cc_start: 0.6589 (m-10) cc_final: 0.6248 (m-10) REVERT: B 21 TRP cc_start: 0.7725 (m100) cc_final: 0.7472 (m100) REVERT: B 22 GLU cc_start: 0.6695 (tp30) cc_final: 0.5991 (tp30) REVERT: B 75 MET cc_start: 0.7941 (ttp) cc_final: 0.7342 (tmm) REVERT: B 119 LEU cc_start: 0.9023 (tt) cc_final: 0.8377 (mt) REVERT: B 136 GLN cc_start: 0.6756 (pt0) cc_final: 0.5757 (pm20) REVERT: B 137 LEU cc_start: 0.6870 (mp) cc_final: 0.6258 (mt) REVERT: B 139 HIS cc_start: 0.7767 (p90) cc_final: 0.7236 (p90) REVERT: B 165 ILE cc_start: 0.9001 (mt) cc_final: 0.8640 (mp) REVERT: B 215 ARG cc_start: 0.7804 (tmm160) cc_final: 0.6815 (ttp80) REVERT: B 217 LEU cc_start: 0.8497 (mm) cc_final: 0.8119 (mm) REVERT: B 268 PHE cc_start: 0.5992 (m-80) cc_final: 0.5599 (m-80) REVERT: B 302 MET cc_start: 0.7353 (mpp) cc_final: 0.6930 (mpp) REVERT: B 422 GLU cc_start: 0.8777 (pt0) cc_final: 0.8394 (pp20) REVERT: B 432 TYR cc_start: 0.6625 (m-10) cc_final: 0.6299 (m-80) REVERT: C 7 ILE cc_start: 0.8956 (mm) cc_final: 0.8729 (mm) REVERT: C 75 ILE cc_start: 0.8546 (mm) cc_final: 0.7299 (tt) REVERT: C 152 LEU cc_start: 0.8721 (tp) cc_final: 0.8403 (tp) REVERT: C 217 LEU cc_start: 0.8413 (mm) cc_final: 0.8172 (mm) REVERT: C 230 LEU cc_start: 0.8388 (tp) cc_final: 0.8122 (tp) REVERT: C 295 CYS cc_start: 0.9154 (t) cc_final: 0.8893 (t) REVERT: C 300 ASN cc_start: 0.8532 (m-40) cc_final: 0.7901 (m110) REVERT: C 435 VAL cc_start: 0.9004 (t) cc_final: 0.8784 (t) REVERT: D 7 ILE cc_start: 0.7870 (mm) cc_final: 0.7128 (mm) REVERT: D 53 TYR cc_start: 0.4516 (m-80) cc_final: 0.4129 (m-80) REVERT: D 83 PHE cc_start: 0.6826 (m-10) cc_final: 0.6593 (m-10) REVERT: D 86 ILE cc_start: 0.9248 (pt) cc_final: 0.8896 (mp) REVERT: D 119 LEU cc_start: 0.8687 (mt) cc_final: 0.8010 (mt) REVERT: D 137 LEU cc_start: 0.7593 (tt) cc_final: 0.6911 (mp) REVERT: D 139 HIS cc_start: 0.8042 (p90) cc_final: 0.7429 (p-80) REVERT: D 163 ASP cc_start: 0.7517 (p0) cc_final: 0.7170 (p0) REVERT: D 165 ILE cc_start: 0.8837 (mt) cc_final: 0.8408 (mt) REVERT: D 173 PRO cc_start: 0.8582 (Cg_exo) cc_final: 0.8328 (Cg_endo) REVERT: D 259 MET cc_start: 0.8109 (mmm) cc_final: 0.7026 (mmp) REVERT: D 264 ARG cc_start: 0.5680 (mtt180) cc_final: 0.5215 (mtt180) REVERT: D 283 TYR cc_start: 0.6893 (m-10) cc_final: 0.6384 (m-10) REVERT: D 398 MET cc_start: 0.7179 (ptp) cc_final: 0.6664 (ptp) REVERT: E 14 VAL cc_start: 0.9163 (m) cc_final: 0.8709 (p) REVERT: E 21 TRP cc_start: 0.8490 (m100) cc_final: 0.7862 (m100) REVERT: E 53 PHE cc_start: 0.7449 (m-80) cc_final: 0.6771 (m-80) REVERT: E 193 THR cc_start: 0.8806 (p) cc_final: 0.8382 (p) REVERT: E 217 LEU cc_start: 0.8423 (mm) cc_final: 0.8191 (mm) REVERT: E 228 ASN cc_start: 0.8534 (m110) cc_final: 0.7907 (p0) REVERT: E 291 ILE cc_start: 0.9174 (mt) cc_final: 0.8074 (tt) REVERT: E 335 ILE cc_start: 0.8897 (pt) cc_final: 0.8630 (tp) REVERT: E 344 VAL cc_start: 0.7405 (t) cc_final: 0.6553 (t) REVERT: E 352 LYS cc_start: 0.9149 (tptt) cc_final: 0.8860 (tptp) REVERT: E 398 MET cc_start: 0.6899 (ptt) cc_final: 0.6643 (ptt) REVERT: F 66 ILE cc_start: 0.9091 (mm) cc_final: 0.8791 (mm) REVERT: F 116 ASP cc_start: 0.7575 (m-30) cc_final: 0.6638 (m-30) REVERT: F 139 HIS cc_start: 0.8001 (p90) cc_final: 0.7154 (p90) REVERT: F 163 ASP cc_start: 0.7767 (p0) cc_final: 0.7215 (p0) REVERT: F 217 LEU cc_start: 0.8275 (mm) cc_final: 0.7635 (mm) REVERT: F 356 CYS cc_start: 0.6586 (t) cc_final: 0.6023 (t) REVERT: F 389 LYS cc_start: 0.8891 (ptpt) cc_final: 0.8647 (ptpp) REVERT: F 398 MET cc_start: 0.7594 (mtp) cc_final: 0.6600 (ptp) REVERT: F 432 TYR cc_start: 0.5774 (m-80) cc_final: 0.5336 (m-80) REVERT: G 25 CYS cc_start: 0.7054 (m) cc_final: 0.6559 (m) REVERT: G 269 LEU cc_start: 0.6345 (mt) cc_final: 0.5955 (mt) REVERT: G 271 THR cc_start: 0.6405 (p) cc_final: 0.4782 (m) REVERT: G 395 PHE cc_start: 0.6804 (t80) cc_final: 0.6530 (t80) REVERT: H 21 TRP cc_start: 0.7883 (m100) cc_final: 0.6596 (m100) REVERT: H 60 LYS cc_start: 0.1522 (pttt) cc_final: 0.0402 (pttp) REVERT: H 66 ILE cc_start: 0.8673 (mm) cc_final: 0.8407 (mm) REVERT: H 132 LEU cc_start: 0.8838 (tp) cc_final: 0.7801 (tp) REVERT: H 153 LEU cc_start: 0.9156 (mt) cc_final: 0.8852 (mt) REVERT: H 239 THR cc_start: 0.9063 (t) cc_final: 0.8813 (t) REVERT: H 372 LYS cc_start: 0.7353 (mmmt) cc_final: 0.6481 (mmmt) REVERT: I 36 MET cc_start: 0.4611 (ttm) cc_final: 0.4045 (tpp) REVERT: I 53 PHE cc_start: 0.7690 (m-80) cc_final: 0.7008 (m-80) REVERT: I 83 TYR cc_start: 0.6218 (m-10) cc_final: 0.5970 (m-10) REVERT: I 86 LEU cc_start: 0.8836 (tp) cc_final: 0.8404 (tp) REVERT: I 92 LEU cc_start: 0.9306 (mt) cc_final: 0.9029 (mt) REVERT: I 158 SER cc_start: 0.8864 (p) cc_final: 0.8510 (t) REVERT: I 211 ASP cc_start: 0.5887 (t0) cc_final: 0.5522 (t0) REVERT: I 212 ILE cc_start: 0.9048 (pt) cc_final: 0.8796 (pt) REVERT: I 217 LEU cc_start: 0.7772 (mt) cc_final: 0.7543 (mt) REVERT: I 238 ILE cc_start: 0.8952 (mt) cc_final: 0.8704 (tp) REVERT: I 300 ASN cc_start: 0.7340 (m-40) cc_final: 0.6848 (m-40) REVERT: I 376 CYS cc_start: 0.7250 (t) cc_final: 0.6390 (t) REVERT: I 377 MET cc_start: 0.7712 (tmm) cc_final: 0.7401 (tmm) REVERT: I 386 GLU cc_start: 0.7688 (mp0) cc_final: 0.7425 (mp0) REVERT: J 75 MET cc_start: 0.6482 (tpt) cc_final: 0.5273 (tpt) REVERT: J 76 ASP cc_start: 0.5817 (m-30) cc_final: 0.4594 (m-30) REVERT: J 138 THR cc_start: 0.8028 (p) cc_final: 0.7368 (p) REVERT: J 165 ILE cc_start: 0.8572 (pt) cc_final: 0.8207 (pt) REVERT: J 205 ASP cc_start: 0.8136 (t0) cc_final: 0.7816 (t0) REVERT: J 216 THR cc_start: 0.8179 (p) cc_final: 0.7744 (p) REVERT: J 248 LEU cc_start: 0.7467 (mm) cc_final: 0.7099 (mt) REVERT: J 257 VAL cc_start: 0.9030 (t) cc_final: 0.8670 (p) REVERT: J 269 MET cc_start: 0.5515 (ttm) cc_final: 0.4852 (ttm) REVERT: J 291 LEU cc_start: 0.8590 (mt) cc_final: 0.8277 (mm) REVERT: J 327 GLU cc_start: 0.7819 (pt0) cc_final: 0.7061 (pt0) REVERT: K 16 ILE cc_start: 0.8173 (pt) cc_final: 0.7837 (pt) REVERT: K 33 ASP cc_start: 0.5270 (p0) cc_final: 0.4403 (t70) REVERT: K 78 VAL cc_start: 0.8430 (t) cc_final: 0.7894 (t) REVERT: K 116 ASP cc_start: 0.7428 (m-30) cc_final: 0.7119 (p0) REVERT: K 120 ASP cc_start: 0.7427 (m-30) cc_final: 0.5045 (t70) REVERT: K 121 ARG cc_start: 0.7308 (mmp80) cc_final: 0.6625 (mmp80) REVERT: K 122 ILE cc_start: 0.7911 (mt) cc_final: 0.7655 (mt) REVERT: K 149 PHE cc_start: 0.7000 (t80) cc_final: 0.6357 (t80) REVERT: K 279 GLU cc_start: 0.8353 (mp0) cc_final: 0.7722 (mp0) REVERT: K 280 LYS cc_start: 0.7174 (mtpt) cc_final: 0.6866 (mmmt) REVERT: K 288 VAL cc_start: 0.8970 (m) cc_final: 0.8527 (p) REVERT: K 335 ILE cc_start: 0.8772 (pt) cc_final: 0.7899 (tp) REVERT: K 352 LYS cc_start: 0.7793 (tptt) cc_final: 0.7184 (tptm) REVERT: L 21 TRP cc_start: 0.7854 (m100) cc_final: 0.6863 (m100) REVERT: L 239 THR cc_start: 0.8330 (t) cc_final: 0.7886 (t) REVERT: L 333 LEU cc_start: 0.8271 (mt) cc_final: 0.7823 (mt) REVERT: M 21 TRP cc_start: 0.8342 (m100) cc_final: 0.7655 (m100) REVERT: M 23 LEU cc_start: 0.7871 (tp) cc_final: 0.7570 (tp) REVERT: M 269 LEU cc_start: 0.7284 (pp) cc_final: 0.6983 (pp) REVERT: M 291 ILE cc_start: 0.8280 (mt) cc_final: 0.7514 (mt) REVERT: M 316 CYS cc_start: 0.5168 (p) cc_final: 0.3644 (p) REVERT: M 398 MET cc_start: 0.6446 (ptt) cc_final: 0.6222 (ptt) REVERT: N 103 TRP cc_start: 0.6744 (t-100) cc_final: 0.6513 (t-100) REVERT: N 149 MET cc_start: 0.4747 (ptp) cc_final: 0.4267 (ptp) REVERT: N 213 CYS cc_start: 0.6998 (p) cc_final: 0.6775 (p) REVERT: N 269 MET cc_start: 0.6200 (tpt) cc_final: 0.5870 (tpt) REVERT: N 292 THR cc_start: 0.7688 (p) cc_final: 0.7250 (t) REVERT: N 332 MET cc_start: 0.6088 (tmm) cc_final: 0.5877 (tmm) REVERT: N 384 ILE cc_start: 0.8016 (mp) cc_final: 0.7130 (mp) REVERT: N 413 MET cc_start: 0.4896 (mmt) cc_final: 0.4302 (mmt) REVERT: N 425 MET cc_start: 0.8616 (ttt) cc_final: 0.8387 (tpp) REVERT: O 21 TRP cc_start: 0.8333 (m100) cc_final: 0.7672 (m100) REVERT: O 23 LEU cc_start: 0.8116 (tp) cc_final: 0.7843 (tp) REVERT: O 152 LEU cc_start: 0.8960 (tp) cc_final: 0.8599 (tp) REVERT: O 376 CYS cc_start: 0.7703 (p) cc_final: 0.7206 (p) REVERT: O 398 MET cc_start: 0.7645 (mtp) cc_final: 0.6695 (mmt) REVERT: P 14 ASN cc_start: 0.8059 (m-40) cc_final: 0.7688 (m110) REVERT: P 115 VAL cc_start: 0.9276 (t) cc_final: 0.9054 (t) REVERT: P 124 LYS cc_start: 0.7865 (ptmt) cc_final: 0.7573 (ptmt) REVERT: P 259 MET cc_start: 0.7096 (mmm) cc_final: 0.5952 (mmt) REVERT: P 268 PHE cc_start: 0.6943 (m-80) cc_final: 0.5442 (m-80) REVERT: P 283 TYR cc_start: 0.8060 (m-80) cc_final: 0.7425 (m-80) REVERT: P 292 THR cc_start: 0.7972 (p) cc_final: 0.7374 (p) REVERT: P 389 LYS cc_start: 0.8894 (ptpp) cc_final: 0.8633 (pttp) REVERT: P 425 MET cc_start: 0.8443 (tpp) cc_final: 0.7613 (tpp) REVERT: Q 76 ASP cc_start: 0.7710 (m-30) cc_final: 0.7216 (t0) REVERT: Q 154 MET cc_start: 0.7534 (tmm) cc_final: 0.7101 (tmm) REVERT: R 66 ILE cc_start: 0.8658 (mm) cc_final: 0.8405 (mm) REVERT: R 115 VAL cc_start: 0.9093 (p) cc_final: 0.8716 (p) REVERT: R 154 ILE cc_start: 0.8813 (mt) cc_final: 0.8593 (mt) REVERT: R 166 MET cc_start: 0.5996 (mmp) cc_final: 0.5714 (mmm) REVERT: R 259 MET cc_start: 0.7613 (mmm) cc_final: 0.6614 (mmt) REVERT: R 268 PHE cc_start: 0.6402 (m-80) cc_final: 0.3339 (m-80) REVERT: R 269 MET cc_start: 0.5203 (tpt) cc_final: 0.4825 (tpt) REVERT: R 332 MET cc_start: 0.6054 (tmm) cc_final: 0.5564 (tmm) REVERT: R 398 MET cc_start: 0.7383 (ptm) cc_final: 0.6455 (ptm) REVERT: R 425 MET cc_start: 0.8483 (tpp) cc_final: 0.8099 (tpt) outliers start: 9 outliers final: 3 residues processed: 1604 average time/residue: 0.5809 time to fit residues: 1572.9930 Evaluate side-chains 1189 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1186 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 50.0000 chunk 82 optimal weight: 7.9990 chunk 416 optimal weight: 8.9990 chunk 534 optimal weight: 40.0000 chunk 413 optimal weight: 3.9990 chunk 615 optimal weight: 30.0000 chunk 408 optimal weight: 0.9980 chunk 728 optimal weight: 50.0000 chunk 456 optimal weight: 10.0000 chunk 444 optimal weight: 40.0000 chunk 336 optimal weight: 50.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 HIS B 249 ASN C 133 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 249 ASN D 309 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 136 GLN F 249 ASN F 309 HIS F 394 GLN ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN J 349 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** M 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 249 ASN N 300 ASN N 334 ASN ** O 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 283 HIS ** O 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 249 ASN ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 GLN R 249 ASN R 282 GLN ** R 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.8081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 62262 Z= 0.196 Angle : 0.640 9.746 84582 Z= 0.335 Chirality : 0.046 0.296 9216 Planarity : 0.005 0.078 11043 Dihedral : 11.142 178.667 8595 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.14 % Allowed : 1.27 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.10), residues: 7632 helix: 0.71 (0.08), residues: 3600 sheet: 1.01 (0.15), residues: 1206 loop : 0.19 (0.13), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP R 21 HIS 0.018 0.001 HIS O 28 PHE 0.022 0.002 PHE L 267 TYR 0.020 0.002 TYR E 83 ARG 0.011 0.001 ARG N 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1594 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1585 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.8638 (mm) cc_final: 0.8412 (mm) REVERT: A 21 TRP cc_start: 0.7283 (m100) cc_final: 0.6955 (m100) REVERT: A 53 PHE cc_start: 0.7878 (m-80) cc_final: 0.7003 (m-80) REVERT: A 75 ILE cc_start: 0.9126 (mm) cc_final: 0.8425 (tt) REVERT: A 122 ILE cc_start: 0.8938 (mt) cc_final: 0.8706 (mt) REVERT: A 193 THR cc_start: 0.8815 (p) cc_final: 0.8103 (t) REVERT: A 291 ILE cc_start: 0.9272 (mt) cc_final: 0.8180 (tp) REVERT: A 317 LEU cc_start: 0.7503 (mt) cc_final: 0.7180 (mt) REVERT: A 347 CYS cc_start: 0.8315 (p) cc_final: 0.7911 (p) REVERT: A 352 LYS cc_start: 0.7969 (tptt) cc_final: 0.7504 (tptp) REVERT: A 357 TYR cc_start: 0.7788 (m-80) cc_final: 0.7550 (m-80) REVERT: A 408 TYR cc_start: 0.5672 (m-80) cc_final: 0.5163 (m-80) REVERT: A 415 GLU cc_start: 0.8238 (mp0) cc_final: 0.7938 (pm20) REVERT: B 14 ASN cc_start: 0.7671 (m110) cc_final: 0.7405 (m110) REVERT: B 21 TRP cc_start: 0.7934 (m100) cc_final: 0.7622 (m100) REVERT: B 22 GLU cc_start: 0.6617 (tp30) cc_final: 0.6073 (tp30) REVERT: B 75 MET cc_start: 0.7544 (ttp) cc_final: 0.7333 (tmm) REVERT: B 136 GLN cc_start: 0.6043 (pt0) cc_final: 0.5795 (pm20) REVERT: B 137 LEU cc_start: 0.6187 (mp) cc_final: 0.5971 (mt) REVERT: B 139 HIS cc_start: 0.7733 (p90) cc_final: 0.7375 (p90) REVERT: B 165 ILE cc_start: 0.9060 (mt) cc_final: 0.8042 (mp) REVERT: B 185 TYR cc_start: 0.5750 (m-10) cc_final: 0.4748 (m-80) REVERT: B 199 ASP cc_start: 0.8399 (m-30) cc_final: 0.7639 (m-30) REVERT: B 215 ARG cc_start: 0.7746 (tmm160) cc_final: 0.6712 (ttp80) REVERT: B 235 MET cc_start: 0.8747 (mmp) cc_final: 0.8413 (mmp) REVERT: B 275 LEU cc_start: 0.8894 (mt) cc_final: 0.8676 (mt) REVERT: B 302 MET cc_start: 0.7575 (mpp) cc_final: 0.6952 (mpp) REVERT: B 398 MET cc_start: 0.7288 (ptm) cc_final: 0.5775 (ptm) REVERT: B 399 PHE cc_start: 0.7079 (t80) cc_final: 0.6849 (t80) REVERT: B 405 LEU cc_start: 0.8679 (mm) cc_final: 0.8221 (tt) REVERT: B 422 GLU cc_start: 0.8831 (pt0) cc_final: 0.8260 (pp20) REVERT: C 33 ASP cc_start: 0.7326 (p0) cc_final: 0.7049 (p0) REVERT: C 66 VAL cc_start: 0.8844 (p) cc_final: 0.8613 (m) REVERT: C 75 ILE cc_start: 0.8616 (mm) cc_final: 0.7364 (tt) REVERT: C 123 ARG cc_start: 0.7087 (tpp-160) cc_final: 0.6395 (tpp80) REVERT: C 217 LEU cc_start: 0.8380 (mm) cc_final: 0.7983 (mm) REVERT: C 230 LEU cc_start: 0.8413 (tp) cc_final: 0.8106 (tp) REVERT: C 295 CYS cc_start: 0.9228 (t) cc_final: 0.8962 (t) REVERT: C 300 ASN cc_start: 0.8720 (m-40) cc_final: 0.8005 (m-40) REVERT: C 316 CYS cc_start: 0.6679 (t) cc_final: 0.6339 (t) REVERT: C 435 VAL cc_start: 0.9012 (t) cc_final: 0.8696 (t) REVERT: D 53 TYR cc_start: 0.4383 (m-80) cc_final: 0.4121 (m-80) REVERT: D 83 PHE cc_start: 0.6755 (m-10) cc_final: 0.6290 (m-10) REVERT: D 86 ILE cc_start: 0.9192 (pt) cc_final: 0.8460 (tt) REVERT: D 119 LEU cc_start: 0.8588 (mt) cc_final: 0.8004 (mt) REVERT: D 139 HIS cc_start: 0.7743 (p90) cc_final: 0.7280 (p90) REVERT: D 163 ASP cc_start: 0.7617 (p0) cc_final: 0.7363 (p0) REVERT: D 165 ILE cc_start: 0.8662 (mt) cc_final: 0.8280 (mt) REVERT: D 207 GLU cc_start: 0.8375 (mp0) cc_final: 0.8138 (mp0) REVERT: D 220 THR cc_start: 0.7629 (p) cc_final: 0.7397 (p) REVERT: D 239 THR cc_start: 0.8553 (t) cc_final: 0.7767 (t) REVERT: D 240 THR cc_start: 0.8095 (t) cc_final: 0.7488 (p) REVERT: D 259 MET cc_start: 0.8182 (mmm) cc_final: 0.7375 (mmp) REVERT: D 264 ARG cc_start: 0.6371 (mtt180) cc_final: 0.5871 (mtt180) REVERT: D 432 TYR cc_start: 0.6449 (m-10) cc_final: 0.5990 (m-10) REVERT: E 21 TRP cc_start: 0.8418 (m100) cc_final: 0.7827 (m100) REVERT: E 23 LEU cc_start: 0.8519 (tp) cc_final: 0.7740 (tp) REVERT: E 53 PHE cc_start: 0.7452 (m-80) cc_final: 0.6813 (m-80) REVERT: E 167 LEU cc_start: 0.7301 (mm) cc_final: 0.7019 (mt) REVERT: E 193 THR cc_start: 0.8525 (p) cc_final: 0.8051 (p) REVERT: E 217 LEU cc_start: 0.8580 (mm) cc_final: 0.8249 (mm) REVERT: E 228 ASN cc_start: 0.8494 (m110) cc_final: 0.7979 (p0) REVERT: E 257 THR cc_start: 0.8789 (p) cc_final: 0.8559 (p) REVERT: E 260 VAL cc_start: 0.7542 (t) cc_final: 0.7143 (t) REVERT: E 291 ILE cc_start: 0.9210 (mt) cc_final: 0.8228 (tt) REVERT: E 335 ILE cc_start: 0.8903 (pt) cc_final: 0.8659 (tp) REVERT: E 344 VAL cc_start: 0.7426 (t) cc_final: 0.6475 (t) REVERT: E 398 MET cc_start: 0.6278 (ptt) cc_final: 0.5729 (ptt) REVERT: F 26 ASP cc_start: 0.8243 (t0) cc_final: 0.7961 (t0) REVERT: F 66 ILE cc_start: 0.9305 (mm) cc_final: 0.9025 (mm) REVERT: F 116 ASP cc_start: 0.7720 (m-30) cc_final: 0.7012 (m-30) REVERT: F 139 HIS cc_start: 0.7694 (p90) cc_final: 0.6936 (p90) REVERT: F 163 ASP cc_start: 0.7759 (p0) cc_final: 0.7163 (p0) REVERT: F 166 MET cc_start: 0.7707 (mmp) cc_final: 0.7241 (mmm) REVERT: F 217 LEU cc_start: 0.8168 (mm) cc_final: 0.7614 (mm) REVERT: F 356 CYS cc_start: 0.5486 (t) cc_final: 0.4871 (t) REVERT: F 425 MET cc_start: 0.8160 (tpp) cc_final: 0.7504 (tpp) REVERT: F 432 TYR cc_start: 0.5840 (m-80) cc_final: 0.5118 (m-80) REVERT: G 5 ILE cc_start: 0.8057 (mp) cc_final: 0.7674 (mm) REVERT: G 217 LEU cc_start: 0.7632 (mt) cc_final: 0.7430 (mt) REVERT: G 292 THR cc_start: 0.8590 (p) cc_final: 0.8381 (p) REVERT: H 5 VAL cc_start: 0.8194 (t) cc_final: 0.7917 (t) REVERT: H 21 TRP cc_start: 0.7624 (m100) cc_final: 0.6337 (m100) REVERT: H 132 LEU cc_start: 0.8896 (tp) cc_final: 0.8010 (tp) REVERT: H 153 LEU cc_start: 0.9183 (mt) cc_final: 0.8860 (mt) REVERT: H 269 MET cc_start: 0.4935 (ptt) cc_final: 0.4588 (ptt) REVERT: H 388 PHE cc_start: 0.6410 (m-80) cc_final: 0.5612 (m-10) REVERT: I 53 PHE cc_start: 0.7566 (m-80) cc_final: 0.6766 (m-80) REVERT: I 73 THR cc_start: 0.8532 (p) cc_final: 0.7443 (t) REVERT: I 83 TYR cc_start: 0.6429 (m-10) cc_final: 0.5886 (m-10) REVERT: I 92 LEU cc_start: 0.9237 (mt) cc_final: 0.8861 (tp) REVERT: I 155 GLU cc_start: 0.6923 (tp30) cc_final: 0.6643 (tp30) REVERT: I 212 ILE cc_start: 0.9148 (pt) cc_final: 0.8945 (pt) REVERT: I 217 LEU cc_start: 0.8103 (mt) cc_final: 0.7408 (mt) REVERT: I 227 LEU cc_start: 0.8747 (mp) cc_final: 0.8492 (mp) REVERT: I 238 ILE cc_start: 0.9019 (mt) cc_final: 0.8718 (tp) REVERT: I 286 LEU cc_start: 0.7945 (tp) cc_final: 0.7721 (tp) REVERT: I 300 ASN cc_start: 0.7196 (m-40) cc_final: 0.6761 (m-40) REVERT: I 376 CYS cc_start: 0.7559 (t) cc_final: 0.6778 (t) REVERT: I 377 MET cc_start: 0.7741 (tmm) cc_final: 0.7320 (tmm) REVERT: I 386 GLU cc_start: 0.7769 (mp0) cc_final: 0.7440 (mp0) REVERT: J 21 TRP cc_start: 0.7746 (m100) cc_final: 0.6828 (m100) REVERT: J 120 ASP cc_start: 0.8094 (t70) cc_final: 0.7716 (t70) REVERT: J 123 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7143 (ttp80) REVERT: J 132 LEU cc_start: 0.8522 (mm) cc_final: 0.8237 (mm) REVERT: J 165 ILE cc_start: 0.8613 (pt) cc_final: 0.8149 (pt) REVERT: J 205 ASP cc_start: 0.8174 (t0) cc_final: 0.7884 (t0) REVERT: J 216 THR cc_start: 0.8070 (p) cc_final: 0.7793 (p) REVERT: J 257 VAL cc_start: 0.9069 (t) cc_final: 0.8776 (p) REVERT: J 266 HIS cc_start: 0.8019 (p90) cc_final: 0.7580 (p-80) REVERT: J 291 LEU cc_start: 0.8404 (mt) cc_final: 0.7798 (mm) REVERT: J 327 GLU cc_start: 0.7607 (pt0) cc_final: 0.6654 (pt0) REVERT: J 349 ASN cc_start: 0.9092 (m-40) cc_final: 0.8864 (t0) REVERT: J 355 VAL cc_start: 0.6604 (t) cc_final: 0.6191 (t) REVERT: K 16 ILE cc_start: 0.7881 (pt) cc_final: 0.7653 (pt) REVERT: K 23 LEU cc_start: 0.8119 (tp) cc_final: 0.7770 (tp) REVERT: K 78 VAL cc_start: 0.8575 (t) cc_final: 0.7958 (t) REVERT: K 116 ASP cc_start: 0.7438 (m-30) cc_final: 0.7179 (p0) REVERT: K 120 ASP cc_start: 0.7374 (m-30) cc_final: 0.4894 (t70) REVERT: K 121 ARG cc_start: 0.7152 (mmp80) cc_final: 0.6396 (mmp80) REVERT: K 149 PHE cc_start: 0.7049 (t80) cc_final: 0.6226 (t80) REVERT: K 166 LYS cc_start: 0.6149 (mppt) cc_final: 0.5944 (mptt) REVERT: K 279 GLU cc_start: 0.8371 (mp0) cc_final: 0.7790 (mp0) REVERT: K 302 MET cc_start: 0.6339 (mpp) cc_final: 0.4476 (mpp) REVERT: K 335 ILE cc_start: 0.8581 (pt) cc_final: 0.7951 (tp) REVERT: K 352 LYS cc_start: 0.8099 (tptt) cc_final: 0.7017 (tptm) REVERT: L 21 TRP cc_start: 0.7870 (m100) cc_final: 0.6910 (m100) REVERT: L 138 THR cc_start: 0.4912 (p) cc_final: 0.4624 (p) REVERT: L 163 ASP cc_start: 0.6684 (p0) cc_final: 0.6276 (m-30) REVERT: L 291 LEU cc_start: 0.8578 (mt) cc_final: 0.7425 (mt) REVERT: L 356 CYS cc_start: 0.5962 (t) cc_final: 0.4689 (t) REVERT: M 3 GLU cc_start: 0.6364 (mp0) cc_final: 0.6144 (mp0) REVERT: M 21 TRP cc_start: 0.8236 (m100) cc_final: 0.7869 (m100) REVERT: M 23 LEU cc_start: 0.7840 (tp) cc_final: 0.7457 (tp) REVERT: M 269 LEU cc_start: 0.7322 (pp) cc_final: 0.6869 (pp) REVERT: M 291 ILE cc_start: 0.8220 (mt) cc_final: 0.7591 (mt) REVERT: M 316 CYS cc_start: 0.5380 (p) cc_final: 0.4487 (p) REVERT: N 149 MET cc_start: 0.4622 (ptp) cc_final: 0.4404 (ptp) REVERT: N 166 MET cc_start: 0.3921 (ptt) cc_final: 0.3474 (ptt) REVERT: N 227 LEU cc_start: 0.8227 (mt) cc_final: 0.7515 (mt) REVERT: N 292 THR cc_start: 0.7315 (p) cc_final: 0.6972 (t) REVERT: N 384 ILE cc_start: 0.7894 (mp) cc_final: 0.7043 (mp) REVERT: N 413 MET cc_start: 0.5308 (mmt) cc_final: 0.4785 (mmt) REVERT: O 21 TRP cc_start: 0.8440 (m100) cc_final: 0.7840 (m100) REVERT: O 23 LEU cc_start: 0.7873 (tp) cc_final: 0.6981 (tp) REVERT: O 36 MET cc_start: 0.2689 (ttp) cc_final: 0.1749 (ttp) REVERT: O 53 PHE cc_start: 0.7030 (m-80) cc_final: 0.6618 (m-80) REVERT: O 62 VAL cc_start: 0.7456 (p) cc_final: 0.7132 (p) REVERT: O 74 VAL cc_start: 0.8811 (t) cc_final: 0.7266 (t) REVERT: O 152 LEU cc_start: 0.9107 (tp) cc_final: 0.8742 (tp) REVERT: O 275 VAL cc_start: 0.9079 (m) cc_final: 0.8617 (m) REVERT: O 398 MET cc_start: 0.7638 (mtp) cc_final: 0.6675 (mmt) REVERT: P 14 ASN cc_start: 0.8113 (m-40) cc_final: 0.7604 (m110) REVERT: P 115 VAL cc_start: 0.9307 (t) cc_final: 0.9036 (t) REVERT: P 154 ILE cc_start: 0.8713 (mt) cc_final: 0.8504 (mt) REVERT: P 259 MET cc_start: 0.7412 (mmm) cc_final: 0.6255 (mmp) REVERT: P 268 PHE cc_start: 0.6854 (m-80) cc_final: 0.5350 (m-80) REVERT: P 292 THR cc_start: 0.7792 (p) cc_final: 0.6978 (p) REVERT: P 315 VAL cc_start: 0.8273 (t) cc_final: 0.7927 (t) REVERT: P 325 MET cc_start: 0.7858 (ptp) cc_final: 0.7440 (ptp) REVERT: P 384 ILE cc_start: 0.8038 (mt) cc_final: 0.7819 (mt) REVERT: P 425 MET cc_start: 0.8449 (tpp) cc_final: 0.7768 (tpp) REVERT: Q 66 VAL cc_start: 0.8207 (t) cc_final: 0.7976 (t) REVERT: Q 76 ASP cc_start: 0.7787 (m-30) cc_final: 0.7406 (t0) REVERT: Q 86 LEU cc_start: 0.8750 (tp) cc_final: 0.8521 (tp) REVERT: Q 154 MET cc_start: 0.7631 (tmm) cc_final: 0.7033 (tmm) REVERT: Q 160 ASP cc_start: 0.7268 (m-30) cc_final: 0.7009 (m-30) REVERT: Q 391 LEU cc_start: 0.8934 (mm) cc_final: 0.8687 (tp) REVERT: Q 398 MET cc_start: 0.7295 (ptm) cc_final: 0.6977 (ttp) REVERT: R 115 VAL cc_start: 0.9103 (p) cc_final: 0.8649 (p) REVERT: R 139 HIS cc_start: 0.7133 (p90) cc_final: 0.6659 (p-80) REVERT: R 154 ILE cc_start: 0.8790 (mt) cc_final: 0.8520 (mt) REVERT: R 259 MET cc_start: 0.7631 (mmm) cc_final: 0.6542 (mmt) REVERT: R 268 PHE cc_start: 0.6966 (m-80) cc_final: 0.4564 (m-80) REVERT: R 269 MET cc_start: 0.5074 (tpt) cc_final: 0.4828 (tpt) REVERT: R 332 MET cc_start: 0.5808 (tmm) cc_final: 0.5282 (tmm) REVERT: R 398 MET cc_start: 0.7384 (ptm) cc_final: 0.6476 (ptm) outliers start: 9 outliers final: 2 residues processed: 1587 average time/residue: 0.5787 time to fit residues: 1547.5627 Evaluate side-chains 1186 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1184 time to evaluate : 5.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 chunk 219 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 463 optimal weight: 40.0000 chunk 496 optimal weight: 0.7980 chunk 360 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 572 optimal weight: 20.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN C 380 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 249 ASN D 309 HIS E 133 GLN E 197 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 249 ASN F 309 HIS ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 294 GLN H 349 ASN I 380 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 300 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** M 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 GLN ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 GLN R 249 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.8401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 62262 Z= 0.186 Angle : 0.648 10.444 84582 Z= 0.337 Chirality : 0.046 0.248 9216 Planarity : 0.005 0.074 11043 Dihedral : 11.011 178.952 8595 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.09 % Allowed : 0.95 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.10), residues: 7632 helix: 0.80 (0.09), residues: 3555 sheet: 0.75 (0.14), residues: 1269 loop : 0.15 (0.13), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP R 21 HIS 0.014 0.001 HIS O 8 PHE 0.021 0.001 PHE J 262 TYR 0.039 0.002 TYR K 24 ARG 0.010 0.001 ARG L 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1565 time to evaluate : 5.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TRP cc_start: 0.7626 (m100) cc_final: 0.7259 (m100) REVERT: A 53 PHE cc_start: 0.7660 (m-80) cc_final: 0.7082 (m-80) REVERT: A 75 ILE cc_start: 0.9179 (mm) cc_final: 0.8178 (tt) REVERT: A 152 LEU cc_start: 0.8432 (tp) cc_final: 0.8130 (tp) REVERT: A 176 GLN cc_start: 0.6947 (mp10) cc_final: 0.6724 (mp10) REVERT: A 193 THR cc_start: 0.8935 (p) cc_final: 0.8255 (t) REVERT: A 291 ILE cc_start: 0.9319 (mt) cc_final: 0.8138 (tp) REVERT: A 317 LEU cc_start: 0.7439 (mt) cc_final: 0.7131 (mt) REVERT: A 347 CYS cc_start: 0.8381 (p) cc_final: 0.7927 (p) REVERT: A 352 LYS cc_start: 0.8034 (tptt) cc_final: 0.7580 (tptp) REVERT: A 353 VAL cc_start: 0.9289 (t) cc_final: 0.9063 (m) REVERT: A 408 TYR cc_start: 0.5770 (m-80) cc_final: 0.5389 (m-80) REVERT: A 415 GLU cc_start: 0.8312 (mp0) cc_final: 0.7887 (pm20) REVERT: B 14 ASN cc_start: 0.7795 (m110) cc_final: 0.7439 (m110) REVERT: B 21 TRP cc_start: 0.7855 (m100) cc_final: 0.7645 (m100) REVERT: B 139 HIS cc_start: 0.7774 (p90) cc_final: 0.7451 (p90) REVERT: B 185 TYR cc_start: 0.5387 (m-10) cc_final: 0.4505 (m-80) REVERT: B 215 ARG cc_start: 0.7618 (tmm160) cc_final: 0.6414 (ttp80) REVERT: B 217 LEU cc_start: 0.8571 (mm) cc_final: 0.8024 (mm) REVERT: B 235 MET cc_start: 0.8759 (mmp) cc_final: 0.8454 (mmp) REVERT: B 302 MET cc_start: 0.7613 (mpp) cc_final: 0.6768 (mpp) REVERT: B 398 MET cc_start: 0.7216 (ptm) cc_final: 0.5504 (ptm) REVERT: B 405 LEU cc_start: 0.8700 (mm) cc_final: 0.8261 (tt) REVERT: B 422 GLU cc_start: 0.8808 (pt0) cc_final: 0.8538 (pp20) REVERT: C 7 ILE cc_start: 0.8916 (mp) cc_final: 0.8645 (mm) REVERT: C 36 MET cc_start: 0.7759 (mmp) cc_final: 0.7384 (mmm) REVERT: C 66 VAL cc_start: 0.8952 (p) cc_final: 0.8667 (m) REVERT: C 75 ILE cc_start: 0.8587 (mm) cc_final: 0.7240 (tt) REVERT: C 196 GLU cc_start: 0.7896 (pm20) cc_final: 0.7561 (mp0) REVERT: C 217 LEU cc_start: 0.8343 (mm) cc_final: 0.7955 (mm) REVERT: C 221 ARG cc_start: 0.7871 (mpp-170) cc_final: 0.7364 (mmm-85) REVERT: C 295 CYS cc_start: 0.9300 (t) cc_final: 0.9092 (t) REVERT: C 300 ASN cc_start: 0.8602 (m-40) cc_final: 0.7851 (m-40) REVERT: C 316 CYS cc_start: 0.6732 (t) cc_final: 0.6024 (t) REVERT: C 327 ASP cc_start: 0.7329 (m-30) cc_final: 0.7107 (m-30) REVERT: C 435 VAL cc_start: 0.8948 (t) cc_final: 0.8668 (t) REVERT: D 86 ILE cc_start: 0.9171 (pt) cc_final: 0.8389 (tt) REVERT: D 119 LEU cc_start: 0.8589 (mt) cc_final: 0.8079 (mt) REVERT: D 139 HIS cc_start: 0.7780 (p90) cc_final: 0.7139 (p90) REVERT: D 163 ASP cc_start: 0.7583 (p0) cc_final: 0.7376 (p0) REVERT: D 165 ILE cc_start: 0.8700 (mt) cc_final: 0.8267 (mt) REVERT: D 207 GLU cc_start: 0.8331 (mp0) cc_final: 0.8026 (mp0) REVERT: D 259 MET cc_start: 0.8406 (mmm) cc_final: 0.8118 (mmm) REVERT: D 260 VAL cc_start: 0.9044 (t) cc_final: 0.8828 (t) REVERT: D 264 ARG cc_start: 0.6223 (mtt180) cc_final: 0.5502 (mtt180) REVERT: D 395 PHE cc_start: 0.7497 (t80) cc_final: 0.7269 (t80) REVERT: E 14 VAL cc_start: 0.9046 (m) cc_final: 0.8628 (p) REVERT: E 21 TRP cc_start: 0.8309 (m100) cc_final: 0.7721 (m100) REVERT: E 75 ILE cc_start: 0.9016 (mm) cc_final: 0.8636 (mm) REVERT: E 167 LEU cc_start: 0.7220 (mm) cc_final: 0.6704 (mt) REVERT: E 193 THR cc_start: 0.8557 (p) cc_final: 0.8131 (p) REVERT: E 217 LEU cc_start: 0.8623 (mm) cc_final: 0.8312 (mm) REVERT: E 228 ASN cc_start: 0.8371 (m110) cc_final: 0.7932 (p0) REVERT: E 235 VAL cc_start: 0.8457 (t) cc_final: 0.8219 (t) REVERT: E 291 ILE cc_start: 0.9179 (mt) cc_final: 0.8167 (tt) REVERT: E 335 ILE cc_start: 0.8909 (pt) cc_final: 0.8545 (tp) REVERT: E 344 VAL cc_start: 0.7270 (t) cc_final: 0.6920 (t) REVERT: E 347 CYS cc_start: 0.8148 (p) cc_final: 0.7171 (p) REVERT: E 398 MET cc_start: 0.6104 (ptt) cc_final: 0.5604 (ptt) REVERT: F 53 TYR cc_start: 0.3898 (m-80) cc_final: 0.3460 (m-80) REVERT: F 66 ILE cc_start: 0.9351 (mm) cc_final: 0.9099 (mm) REVERT: F 116 ASP cc_start: 0.7391 (m-30) cc_final: 0.7131 (m-30) REVERT: F 139 HIS cc_start: 0.7880 (p90) cc_final: 0.7441 (p90) REVERT: F 163 ASP cc_start: 0.7561 (p0) cc_final: 0.7258 (p0) REVERT: F 166 MET cc_start: 0.7503 (mmp) cc_final: 0.7218 (mmm) REVERT: F 209 LEU cc_start: 0.9093 (mt) cc_final: 0.8875 (mt) REVERT: F 217 LEU cc_start: 0.8162 (mm) cc_final: 0.7698 (mm) REVERT: F 356 CYS cc_start: 0.5211 (t) cc_final: 0.4951 (t) REVERT: F 398 MET cc_start: 0.7529 (mtp) cc_final: 0.6591 (ptp) REVERT: F 432 TYR cc_start: 0.5826 (m-80) cc_final: 0.5065 (m-10) REVERT: G 209 ILE cc_start: 0.9201 (mt) cc_final: 0.8983 (mt) REVERT: G 271 THR cc_start: 0.6326 (m) cc_final: 0.3676 (m) REVERT: H 20 PHE cc_start: 0.8286 (t80) cc_final: 0.8054 (t80) REVERT: H 21 TRP cc_start: 0.7679 (m100) cc_final: 0.6327 (m100) REVERT: H 132 LEU cc_start: 0.8910 (tp) cc_final: 0.8001 (tp) REVERT: H 153 LEU cc_start: 0.9191 (mt) cc_final: 0.8864 (mt) REVERT: H 240 THR cc_start: 0.8027 (m) cc_final: 0.7553 (m) REVERT: H 259 MET cc_start: 0.7334 (mmp) cc_final: 0.7129 (mmm) REVERT: H 269 MET cc_start: 0.4816 (ptt) cc_final: 0.4415 (ptt) REVERT: H 372 LYS cc_start: 0.7951 (mmpt) cc_final: 0.7617 (mmmt) REVERT: H 388 PHE cc_start: 0.6186 (m-80) cc_final: 0.5668 (m-10) REVERT: I 20 CYS cc_start: 0.9078 (p) cc_final: 0.8453 (p) REVERT: I 53 PHE cc_start: 0.7581 (m-80) cc_final: 0.6803 (m-80) REVERT: I 75 ILE cc_start: 0.8309 (mm) cc_final: 0.7182 (tt) REVERT: I 83 TYR cc_start: 0.6177 (m-10) cc_final: 0.5788 (m-10) REVERT: I 92 LEU cc_start: 0.9221 (mt) cc_final: 0.8832 (tt) REVERT: I 269 LEU cc_start: 0.5666 (mt) cc_final: 0.5147 (mt) REVERT: I 286 LEU cc_start: 0.8039 (tp) cc_final: 0.7775 (tp) REVERT: I 352 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7731 (mppt) REVERT: I 376 CYS cc_start: 0.7568 (t) cc_final: 0.7202 (t) REVERT: I 377 MET cc_start: 0.7703 (tmm) cc_final: 0.7437 (tmm) REVERT: I 386 GLU cc_start: 0.7795 (mp0) cc_final: 0.7382 (mp0) REVERT: J 21 TRP cc_start: 0.7648 (m100) cc_final: 0.6631 (m100) REVERT: J 66 ILE cc_start: 0.8768 (mm) cc_final: 0.8563 (mm) REVERT: J 75 MET cc_start: 0.7281 (tpt) cc_final: 0.6946 (tpp) REVERT: J 120 ASP cc_start: 0.8170 (t70) cc_final: 0.7830 (t70) REVERT: J 165 ILE cc_start: 0.8494 (pt) cc_final: 0.8141 (pt) REVERT: J 205 ASP cc_start: 0.8205 (t0) cc_final: 0.7876 (t0) REVERT: J 239 THR cc_start: 0.8290 (t) cc_final: 0.7915 (t) REVERT: J 248 LEU cc_start: 0.7118 (mm) cc_final: 0.6805 (mt) REVERT: J 252 LEU cc_start: 0.8611 (mt) cc_final: 0.8341 (mt) REVERT: J 257 VAL cc_start: 0.9157 (t) cc_final: 0.8794 (p) REVERT: J 266 HIS cc_start: 0.8380 (p90) cc_final: 0.7925 (p-80) REVERT: J 291 LEU cc_start: 0.8576 (mt) cc_final: 0.7896 (mm) REVERT: J 327 GLU cc_start: 0.7329 (pt0) cc_final: 0.7033 (pt0) REVERT: J 349 ASN cc_start: 0.9120 (m-40) cc_final: 0.8879 (t0) REVERT: K 16 ILE cc_start: 0.7854 (pt) cc_final: 0.7383 (pt) REVERT: K 78 VAL cc_start: 0.8791 (t) cc_final: 0.8244 (t) REVERT: K 118 VAL cc_start: 0.8844 (t) cc_final: 0.8628 (t) REVERT: K 121 ARG cc_start: 0.7434 (mmp80) cc_final: 0.6342 (mmp80) REVERT: K 122 ILE cc_start: 0.7677 (mt) cc_final: 0.7434 (mt) REVERT: K 149 PHE cc_start: 0.6952 (t80) cc_final: 0.6101 (t80) REVERT: K 166 LYS cc_start: 0.6912 (mppt) cc_final: 0.6472 (mptt) REVERT: K 292 THR cc_start: 0.8970 (p) cc_final: 0.8518 (p) REVERT: K 335 ILE cc_start: 0.8735 (pt) cc_final: 0.7809 (tp) REVERT: K 352 LYS cc_start: 0.7955 (tptt) cc_final: 0.7182 (tptm) REVERT: L 21 TRP cc_start: 0.7962 (m100) cc_final: 0.7054 (m100) REVERT: L 53 TYR cc_start: 0.5154 (m-10) cc_final: 0.4892 (m-80) REVERT: L 92 PHE cc_start: 0.6931 (m-80) cc_final: 0.6658 (m-80) REVERT: L 163 ASP cc_start: 0.6638 (p0) cc_final: 0.6339 (m-30) REVERT: L 355 VAL cc_start: 0.7433 (t) cc_final: 0.7080 (t) REVERT: L 356 CYS cc_start: 0.6096 (t) cc_final: 0.4919 (t) REVERT: M 21 TRP cc_start: 0.8142 (m100) cc_final: 0.7724 (m100) REVERT: M 123 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7419 (mmm-85) REVERT: M 291 ILE cc_start: 0.8290 (mt) cc_final: 0.7742 (mt) REVERT: M 316 CYS cc_start: 0.5265 (p) cc_final: 0.4279 (p) REVERT: N 14 ASN cc_start: 0.8486 (m-40) cc_final: 0.8219 (m110) REVERT: N 21 TRP cc_start: 0.8616 (m100) cc_final: 0.8110 (m100) REVERT: N 119 LEU cc_start: 0.8302 (pp) cc_final: 0.8039 (pp) REVERT: N 166 MET cc_start: 0.3941 (ptt) cc_final: 0.3594 (ptt) REVERT: N 213 CYS cc_start: 0.6730 (p) cc_final: 0.6402 (p) REVERT: N 292 THR cc_start: 0.7410 (p) cc_final: 0.6841 (t) REVERT: N 333 LEU cc_start: 0.7228 (tp) cc_final: 0.6959 (tp) REVERT: N 384 ILE cc_start: 0.7596 (mp) cc_final: 0.6779 (mp) REVERT: O 21 TRP cc_start: 0.8470 (m100) cc_final: 0.7983 (m100) REVERT: O 33 ASP cc_start: 0.8171 (p0) cc_final: 0.7910 (p0) REVERT: O 36 MET cc_start: 0.3166 (ttp) cc_final: 0.2414 (ttp) REVERT: O 53 PHE cc_start: 0.6756 (m-80) cc_final: 0.6376 (m-80) REVERT: O 62 VAL cc_start: 0.7081 (p) cc_final: 0.6836 (p) REVERT: O 68 VAL cc_start: 0.8767 (t) cc_final: 0.8507 (t) REVERT: O 76 ASP cc_start: 0.7761 (m-30) cc_final: 0.7410 (t70) REVERT: O 86 LEU cc_start: 0.8622 (tp) cc_final: 0.8389 (tp) REVERT: O 239 THR cc_start: 0.6843 (p) cc_final: 0.6475 (p) REVERT: O 398 MET cc_start: 0.7627 (mtp) cc_final: 0.6638 (mmt) REVERT: O 429 GLU cc_start: 0.7758 (tt0) cc_final: 0.7422 (tt0) REVERT: P 14 ASN cc_start: 0.7929 (m-40) cc_final: 0.7479 (m110) REVERT: P 115 VAL cc_start: 0.9283 (t) cc_final: 0.8993 (t) REVERT: P 154 ILE cc_start: 0.8739 (mt) cc_final: 0.8499 (mt) REVERT: P 259 MET cc_start: 0.7374 (mmm) cc_final: 0.6548 (mmp) REVERT: P 268 PHE cc_start: 0.6943 (m-80) cc_final: 0.5352 (m-80) REVERT: P 292 THR cc_start: 0.7444 (p) cc_final: 0.6992 (p) REVERT: P 384 ILE cc_start: 0.8019 (mt) cc_final: 0.7729 (mt) REVERT: P 398 MET cc_start: 0.7751 (ptm) cc_final: 0.7423 (ptm) REVERT: P 425 MET cc_start: 0.8319 (tpp) cc_final: 0.7631 (tpp) REVERT: Q 76 ASP cc_start: 0.7805 (m-30) cc_final: 0.7073 (t0) REVERT: Q 86 LEU cc_start: 0.8675 (tp) cc_final: 0.8294 (tp) REVERT: Q 154 MET cc_start: 0.7352 (tmm) cc_final: 0.6975 (tmm) REVERT: Q 378 LEU cc_start: 0.7565 (mm) cc_final: 0.6636 (mm) REVERT: Q 391 LEU cc_start: 0.9036 (mm) cc_final: 0.8651 (tp) REVERT: Q 398 MET cc_start: 0.7274 (ptm) cc_final: 0.6947 (ttp) REVERT: Q 429 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7088 (mm-30) REVERT: Q 431 ASP cc_start: 0.5518 (m-30) cc_final: 0.5280 (m-30) REVERT: R 60 LYS cc_start: 0.7157 (pttt) cc_final: 0.6493 (pttt) REVERT: R 115 VAL cc_start: 0.9052 (p) cc_final: 0.8620 (p) REVERT: R 120 ASP cc_start: 0.7957 (m-30) cc_final: 0.7524 (m-30) REVERT: R 139 HIS cc_start: 0.7093 (p90) cc_final: 0.6667 (p-80) REVERT: R 154 ILE cc_start: 0.8913 (mt) cc_final: 0.8672 (mt) REVERT: R 259 MET cc_start: 0.7698 (mmm) cc_final: 0.6132 (mmt) REVERT: R 268 PHE cc_start: 0.7030 (m-80) cc_final: 0.4495 (m-80) REVERT: R 269 MET cc_start: 0.5050 (tpt) cc_final: 0.4544 (tpt) REVERT: R 314 THR cc_start: 0.7824 (p) cc_final: 0.7100 (p) REVERT: R 315 VAL cc_start: 0.7769 (t) cc_final: 0.7452 (t) REVERT: R 332 MET cc_start: 0.5917 (tmm) cc_final: 0.5595 (tmm) REVERT: R 398 MET cc_start: 0.7969 (ptm) cc_final: 0.7235 (ttp) outliers start: 6 outliers final: 2 residues processed: 1565 average time/residue: 0.5774 time to fit residues: 1526.1780 Evaluate side-chains 1194 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1192 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 10.0000 chunk 698 optimal weight: 20.0000 chunk 636 optimal weight: 8.9990 chunk 679 optimal weight: 30.0000 chunk 697 optimal weight: 20.0000 chunk 408 optimal weight: 30.0000 chunk 295 optimal weight: 50.0000 chunk 533 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 613 optimal weight: 7.9990 chunk 642 optimal weight: 20.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN C 356 ASN C 380 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 249 ASN D 334 ASN ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 GLN F 249 ASN F 309 HIS ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 HIS N 334 ASN ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 HIS O 85 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 249 ASN R 394 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.8662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 62262 Z= 0.216 Angle : 0.672 10.205 84582 Z= 0.352 Chirality : 0.047 0.372 9216 Planarity : 0.005 0.071 11043 Dihedral : 11.061 179.779 8595 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.09 % Allowed : 0.53 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 7632 helix: 0.71 (0.09), residues: 3564 sheet: 0.66 (0.14), residues: 1296 loop : 0.17 (0.13), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP R 21 HIS 0.013 0.001 HIS O 8 PHE 0.030 0.002 PHE F 395 TYR 0.033 0.002 TYR K 24 ARG 0.010 0.001 ARG L 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1521 time to evaluate : 5.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7904 (m-80) cc_final: 0.7516 (m-80) REVERT: A 66 VAL cc_start: 0.8545 (t) cc_final: 0.8275 (t) REVERT: A 75 ILE cc_start: 0.9089 (mm) cc_final: 0.8467 (tt) REVERT: A 152 LEU cc_start: 0.8385 (tp) cc_final: 0.8029 (tp) REVERT: A 193 THR cc_start: 0.8970 (p) cc_final: 0.7472 (t) REVERT: A 291 ILE cc_start: 0.9313 (mt) cc_final: 0.8135 (tp) REVERT: A 317 LEU cc_start: 0.7611 (mt) cc_final: 0.7394 (mt) REVERT: A 347 CYS cc_start: 0.8326 (p) cc_final: 0.8094 (p) REVERT: A 352 LYS cc_start: 0.8126 (tptt) cc_final: 0.7620 (tptp) REVERT: A 353 VAL cc_start: 0.9277 (t) cc_final: 0.9070 (m) REVERT: A 355 ILE cc_start: 0.9476 (mp) cc_final: 0.9252 (mp) REVERT: A 408 TYR cc_start: 0.5849 (m-80) cc_final: 0.5474 (m-80) REVERT: A 415 GLU cc_start: 0.8281 (mp0) cc_final: 0.8059 (pm20) REVERT: B 14 ASN cc_start: 0.7874 (m110) cc_final: 0.7632 (m110) REVERT: B 21 TRP cc_start: 0.7884 (m100) cc_final: 0.7601 (m100) REVERT: B 22 GLU cc_start: 0.6564 (tp30) cc_final: 0.6316 (tp30) REVERT: B 119 LEU cc_start: 0.8309 (mt) cc_final: 0.7899 (mt) REVERT: B 139 HIS cc_start: 0.8049 (p90) cc_final: 0.7500 (p90) REVERT: B 185 TYR cc_start: 0.5588 (m-10) cc_final: 0.4567 (m-80) REVERT: B 215 ARG cc_start: 0.7634 (tmm160) cc_final: 0.6777 (ttp80) REVERT: B 217 LEU cc_start: 0.8841 (mm) cc_final: 0.8375 (mm) REVERT: B 389 LYS cc_start: 0.8907 (ptpp) cc_final: 0.8523 (ptpp) REVERT: B 398 MET cc_start: 0.7334 (ptm) cc_final: 0.5640 (ptm) REVERT: B 405 LEU cc_start: 0.8797 (mm) cc_final: 0.8436 (tt) REVERT: B 422 GLU cc_start: 0.8608 (pt0) cc_final: 0.8046 (pp20) REVERT: C 75 ILE cc_start: 0.8444 (mm) cc_final: 0.6996 (tt) REVERT: C 217 LEU cc_start: 0.8330 (mm) cc_final: 0.7982 (mm) REVERT: C 257 THR cc_start: 0.7230 (t) cc_final: 0.7003 (t) REVERT: C 295 CYS cc_start: 0.9308 (t) cc_final: 0.9083 (t) REVERT: C 316 CYS cc_start: 0.6700 (t) cc_final: 0.6196 (t) REVERT: C 435 VAL cc_start: 0.8949 (t) cc_final: 0.8590 (t) REVERT: D 21 TRP cc_start: 0.7986 (m100) cc_final: 0.7770 (m100) REVERT: D 86 ILE cc_start: 0.9175 (pt) cc_final: 0.8547 (tt) REVERT: D 119 LEU cc_start: 0.8672 (mt) cc_final: 0.8119 (mt) REVERT: D 120 ASP cc_start: 0.7188 (m-30) cc_final: 0.6960 (m-30) REVERT: D 139 HIS cc_start: 0.7781 (p90) cc_final: 0.7154 (p90) REVERT: D 165 ILE cc_start: 0.8637 (mt) cc_final: 0.8204 (mt) REVERT: D 207 GLU cc_start: 0.8389 (mp0) cc_final: 0.8057 (mp0) REVERT: D 259 MET cc_start: 0.8451 (mmm) cc_final: 0.8148 (mmm) REVERT: D 260 VAL cc_start: 0.9103 (t) cc_final: 0.8894 (t) REVERT: D 264 ARG cc_start: 0.6560 (mtt180) cc_final: 0.5834 (mtt180) REVERT: E 14 VAL cc_start: 0.8971 (m) cc_final: 0.8595 (p) REVERT: E 21 TRP cc_start: 0.8339 (m100) cc_final: 0.7801 (m100) REVERT: E 33 ASP cc_start: 0.7500 (p0) cc_final: 0.6660 (p0) REVERT: E 75 ILE cc_start: 0.8969 (mm) cc_final: 0.8620 (mm) REVERT: E 193 THR cc_start: 0.8651 (p) cc_final: 0.8355 (p) REVERT: E 291 ILE cc_start: 0.9222 (mt) cc_final: 0.8258 (tt) REVERT: E 335 ILE cc_start: 0.8956 (pt) cc_final: 0.8587 (tp) REVERT: E 343 PHE cc_start: 0.6297 (p90) cc_final: 0.6005 (p90) REVERT: E 347 CYS cc_start: 0.8435 (p) cc_final: 0.7601 (p) REVERT: E 352 LYS cc_start: 0.8689 (tptp) cc_final: 0.8268 (tptp) REVERT: E 398 MET cc_start: 0.6021 (ptt) cc_final: 0.5641 (ptt) REVERT: F 66 ILE cc_start: 0.9142 (mm) cc_final: 0.8933 (mm) REVERT: F 116 ASP cc_start: 0.7245 (m-30) cc_final: 0.7006 (m-30) REVERT: F 129 CYS cc_start: 0.7672 (m) cc_final: 0.7159 (m) REVERT: F 139 HIS cc_start: 0.7820 (p90) cc_final: 0.7313 (p90) REVERT: F 163 ASP cc_start: 0.7672 (p0) cc_final: 0.6808 (p0) REVERT: F 217 LEU cc_start: 0.8225 (mm) cc_final: 0.7657 (mm) REVERT: F 425 MET cc_start: 0.7847 (tpp) cc_final: 0.7452 (tpp) REVERT: F 432 TYR cc_start: 0.5992 (m-80) cc_final: 0.5321 (m-10) REVERT: G 212 ILE cc_start: 0.8884 (pt) cc_final: 0.8674 (pt) REVERT: G 217 LEU cc_start: 0.7576 (mt) cc_final: 0.7288 (mt) REVERT: G 230 LEU cc_start: 0.9372 (pp) cc_final: 0.9152 (pp) REVERT: G 271 THR cc_start: 0.7298 (m) cc_final: 0.6828 (t) REVERT: G 291 ILE cc_start: 0.8256 (mt) cc_final: 0.7644 (mt) REVERT: G 322 ASP cc_start: 0.7519 (p0) cc_final: 0.7064 (p0) REVERT: G 431 ASP cc_start: 0.7662 (m-30) cc_final: 0.7412 (m-30) REVERT: G 435 VAL cc_start: 0.8905 (t) cc_final: 0.8428 (t) REVERT: H 20 PHE cc_start: 0.8361 (t80) cc_final: 0.8067 (t80) REVERT: H 21 TRP cc_start: 0.7671 (m100) cc_final: 0.6529 (m100) REVERT: H 132 LEU cc_start: 0.8944 (tp) cc_final: 0.8622 (tp) REVERT: H 153 LEU cc_start: 0.9235 (mt) cc_final: 0.8854 (mt) REVERT: H 240 THR cc_start: 0.7909 (m) cc_final: 0.7467 (m) REVERT: H 259 MET cc_start: 0.7517 (mmp) cc_final: 0.7266 (mmm) REVERT: H 264 ARG cc_start: 0.3988 (mtt180) cc_final: 0.3766 (mtt180) REVERT: H 269 MET cc_start: 0.4995 (ptt) cc_final: 0.4618 (ptt) REVERT: H 288 VAL cc_start: 0.8983 (t) cc_final: 0.8130 (t) REVERT: H 325 MET cc_start: 0.7479 (pmm) cc_final: 0.7240 (pmm) REVERT: H 388 PHE cc_start: 0.6282 (m-80) cc_final: 0.5588 (m-10) REVERT: I 20 CYS cc_start: 0.9074 (p) cc_final: 0.8470 (p) REVERT: I 53 PHE cc_start: 0.7736 (m-80) cc_final: 0.7112 (m-80) REVERT: I 75 ILE cc_start: 0.8388 (mm) cc_final: 0.7905 (mm) REVERT: I 83 TYR cc_start: 0.6068 (m-10) cc_final: 0.5806 (m-10) REVERT: I 92 LEU cc_start: 0.9331 (mt) cc_final: 0.9018 (tp) REVERT: I 286 LEU cc_start: 0.8076 (tp) cc_final: 0.7783 (tp) REVERT: I 291 ILE cc_start: 0.8312 (mt) cc_final: 0.8029 (mt) REVERT: I 296 PHE cc_start: 0.8669 (m-10) cc_final: 0.8275 (m-10) REVERT: I 386 GLU cc_start: 0.7732 (mp0) cc_final: 0.7363 (mp0) REVERT: J 21 TRP cc_start: 0.7818 (m100) cc_final: 0.7214 (m100) REVERT: J 66 ILE cc_start: 0.8748 (mm) cc_final: 0.8510 (mm) REVERT: J 132 LEU cc_start: 0.8604 (mm) cc_final: 0.8339 (mm) REVERT: J 165 ILE cc_start: 0.8605 (pt) cc_final: 0.8210 (pt) REVERT: J 205 ASP cc_start: 0.8834 (t0) cc_final: 0.8545 (t0) REVERT: J 239 THR cc_start: 0.8232 (t) cc_final: 0.7872 (t) REVERT: J 248 LEU cc_start: 0.7452 (mm) cc_final: 0.6986 (mt) REVERT: J 257 VAL cc_start: 0.9190 (t) cc_final: 0.8885 (p) REVERT: J 266 HIS cc_start: 0.8503 (p90) cc_final: 0.7962 (p-80) REVERT: J 291 LEU cc_start: 0.8428 (mt) cc_final: 0.7679 (mm) REVERT: J 327 GLU cc_start: 0.7156 (pt0) cc_final: 0.6618 (pt0) REVERT: J 349 ASN cc_start: 0.9170 (m-40) cc_final: 0.8846 (t0) REVERT: K 120 ASP cc_start: 0.8056 (m-30) cc_final: 0.6887 (t70) REVERT: K 121 ARG cc_start: 0.6454 (mmp80) cc_final: 0.6224 (mmp80) REVERT: K 149 PHE cc_start: 0.7056 (t80) cc_final: 0.6134 (t80) REVERT: K 166 LYS cc_start: 0.6665 (mppt) cc_final: 0.6234 (mptt) REVERT: K 335 ILE cc_start: 0.8620 (pt) cc_final: 0.7981 (tp) REVERT: K 352 LYS cc_start: 0.8146 (tptt) cc_final: 0.7461 (tptm) REVERT: K 377 MET cc_start: 0.7352 (ttp) cc_final: 0.7109 (tpt) REVERT: L 21 TRP cc_start: 0.7925 (m100) cc_final: 0.6620 (m100) REVERT: L 22 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7876 (mt-10) REVERT: L 53 TYR cc_start: 0.5540 (m-10) cc_final: 0.5257 (m-80) REVERT: L 120 ASP cc_start: 0.7729 (t70) cc_final: 0.7266 (t70) REVERT: L 138 THR cc_start: 0.5104 (p) cc_final: 0.4767 (p) REVERT: L 163 ASP cc_start: 0.6812 (p0) cc_final: 0.6390 (m-30) REVERT: L 356 CYS cc_start: 0.6170 (t) cc_final: 0.4984 (t) REVERT: M 21 TRP cc_start: 0.8213 (m100) cc_final: 0.7737 (m100) REVERT: M 123 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.7559 (mmm-85) REVERT: M 291 ILE cc_start: 0.8739 (mt) cc_final: 0.8435 (mt) REVERT: M 316 CYS cc_start: 0.5105 (p) cc_final: 0.4209 (p) REVERT: N 21 TRP cc_start: 0.8782 (m100) cc_final: 0.8143 (m100) REVERT: N 119 LEU cc_start: 0.8522 (pp) cc_final: 0.8258 (pp) REVERT: N 166 MET cc_start: 0.3838 (ptt) cc_final: 0.3350 (ptt) REVERT: N 213 CYS cc_start: 0.6766 (p) cc_final: 0.6560 (p) REVERT: N 227 LEU cc_start: 0.8343 (mt) cc_final: 0.7872 (mt) REVERT: N 292 THR cc_start: 0.7487 (p) cc_final: 0.6816 (t) REVERT: N 355 VAL cc_start: 0.6452 (t) cc_final: 0.5856 (t) REVERT: N 384 ILE cc_start: 0.8204 (mp) cc_final: 0.7741 (mp) REVERT: O 21 TRP cc_start: 0.8544 (m100) cc_final: 0.7852 (m100) REVERT: O 33 ASP cc_start: 0.8300 (p0) cc_final: 0.7780 (p0) REVERT: O 36 MET cc_start: 0.3358 (ttp) cc_final: 0.2743 (ttp) REVERT: O 53 PHE cc_start: 0.6842 (m-80) cc_final: 0.6578 (m-80) REVERT: O 62 VAL cc_start: 0.7217 (p) cc_final: 0.6872 (p) REVERT: O 76 ASP cc_start: 0.7972 (m-30) cc_final: 0.7183 (t70) REVERT: O 120 ASP cc_start: 0.8602 (m-30) cc_final: 0.8338 (m-30) REVERT: O 122 ILE cc_start: 0.7261 (mt) cc_final: 0.6936 (mt) REVERT: O 154 MET cc_start: 0.8016 (tmm) cc_final: 0.7684 (tmm) REVERT: O 214 ARG cc_start: 0.5007 (ptp-110) cc_final: 0.4228 (ptp-110) REVERT: O 317 LEU cc_start: 0.6938 (mt) cc_final: 0.6719 (mt) REVERT: O 398 MET cc_start: 0.7665 (mtp) cc_final: 0.6780 (mmp) REVERT: O 429 GLU cc_start: 0.7719 (tt0) cc_final: 0.7424 (tt0) REVERT: O 431 ASP cc_start: 0.7238 (m-30) cc_final: 0.6926 (m-30) REVERT: P 14 ASN cc_start: 0.8052 (m-40) cc_final: 0.7551 (m110) REVERT: P 115 VAL cc_start: 0.9313 (t) cc_final: 0.9066 (t) REVERT: P 259 MET cc_start: 0.7616 (mmm) cc_final: 0.6697 (mmp) REVERT: P 268 PHE cc_start: 0.7007 (m-80) cc_final: 0.5521 (m-80) REVERT: P 269 MET cc_start: 0.6314 (tpt) cc_final: 0.5882 (tpt) REVERT: P 292 THR cc_start: 0.7595 (p) cc_final: 0.7082 (p) REVERT: P 414 ASP cc_start: 0.8091 (t0) cc_final: 0.7479 (m-30) REVERT: P 425 MET cc_start: 0.8380 (tpp) cc_final: 0.7656 (tpp) REVERT: Q 76 ASP cc_start: 0.7793 (m-30) cc_final: 0.7216 (t0) REVERT: Q 86 LEU cc_start: 0.8830 (tp) cc_final: 0.8184 (tp) REVERT: Q 122 ILE cc_start: 0.8545 (pt) cc_final: 0.8287 (pt) REVERT: Q 154 MET cc_start: 0.7396 (tmm) cc_final: 0.7095 (tmm) REVERT: Q 391 LEU cc_start: 0.8987 (mm) cc_final: 0.8597 (tp) REVERT: Q 429 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7133 (mm-30) REVERT: Q 431 ASP cc_start: 0.6102 (m-30) cc_final: 0.5826 (m-30) REVERT: R 60 LYS cc_start: 0.7372 (pttt) cc_final: 0.6700 (pttt) REVERT: R 75 MET cc_start: 0.6832 (mmp) cc_final: 0.6608 (mmm) REVERT: R 115 VAL cc_start: 0.9081 (p) cc_final: 0.8624 (p) REVERT: R 120 ASP cc_start: 0.8134 (m-30) cc_final: 0.7676 (m-30) REVERT: R 135 PHE cc_start: 0.7561 (m-80) cc_final: 0.6262 (m-80) REVERT: R 139 HIS cc_start: 0.7258 (p90) cc_final: 0.6643 (p90) REVERT: R 154 ILE cc_start: 0.8993 (mt) cc_final: 0.8770 (mt) REVERT: R 179 ASP cc_start: 0.7561 (m-30) cc_final: 0.6233 (p0) REVERT: R 259 MET cc_start: 0.7755 (mmm) cc_final: 0.5871 (tpp) REVERT: R 268 PHE cc_start: 0.6811 (m-80) cc_final: 0.3667 (m-80) REVERT: R 269 MET cc_start: 0.4762 (tpt) cc_final: 0.4406 (tpt) REVERT: R 278 ARG cc_start: 0.6857 (tpm170) cc_final: 0.6464 (tpp80) REVERT: R 332 MET cc_start: 0.5155 (tmm) cc_final: 0.4742 (tmm) REVERT: R 398 MET cc_start: 0.7921 (ptm) cc_final: 0.7165 (ttp) outliers start: 6 outliers final: 1 residues processed: 1521 average time/residue: 0.5843 time to fit residues: 1505.6878 Evaluate side-chains 1147 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1146 time to evaluate : 5.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 40.0000 chunk 445 optimal weight: 4.9990 chunk 718 optimal weight: 7.9990 chunk 438 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 499 optimal weight: 0.7980 chunk 753 optimal weight: 7.9990 chunk 693 optimal weight: 10.0000 chunk 599 optimal weight: 6.9990 chunk 62 optimal weight: 50.0000 chunk 463 optimal weight: 40.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN C 380 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 249 ASN D 309 HIS ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN F 309 HIS ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 380 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 ASN ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 197 HIS ** O 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN Q 61 HIS ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 249 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.8897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62262 Z= 0.198 Angle : 0.675 12.646 84582 Z= 0.351 Chirality : 0.047 0.340 9216 Planarity : 0.005 0.076 11043 Dihedral : 10.936 179.318 8595 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.11 % Allowed : 0.24 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 7632 helix: 0.69 (0.09), residues: 3591 sheet: 0.54 (0.14), residues: 1323 loop : 0.11 (0.13), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 21 HIS 0.012 0.001 HIS E 283 PHE 0.031 0.001 PHE F 395 TYR 0.042 0.002 TYR D 161 ARG 0.024 0.001 ARG F 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1520 time to evaluate : 5.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 PHE cc_start: 0.7748 (m-80) cc_final: 0.7468 (m-80) REVERT: A 75 ILE cc_start: 0.9200 (mm) cc_final: 0.8606 (tt) REVERT: A 125 LEU cc_start: 0.9302 (tp) cc_final: 0.9052 (tt) REVERT: A 152 LEU cc_start: 0.8308 (tp) cc_final: 0.7983 (tp) REVERT: A 193 THR cc_start: 0.8449 (p) cc_final: 0.8119 (t) REVERT: A 196 GLU cc_start: 0.7692 (pm20) cc_final: 0.7190 (pt0) REVERT: A 291 ILE cc_start: 0.9284 (mt) cc_final: 0.8146 (tp) REVERT: A 347 CYS cc_start: 0.8328 (p) cc_final: 0.8083 (p) REVERT: A 352 LYS cc_start: 0.8185 (tptt) cc_final: 0.7811 (tptp) REVERT: A 408 TYR cc_start: 0.5885 (m-80) cc_final: 0.5310 (m-80) REVERT: A 415 GLU cc_start: 0.8413 (mp0) cc_final: 0.7910 (pm20) REVERT: B 14 ASN cc_start: 0.7872 (m110) cc_final: 0.7548 (m110) REVERT: B 21 TRP cc_start: 0.7741 (m100) cc_final: 0.7537 (m100) REVERT: B 22 GLU cc_start: 0.6552 (tp30) cc_final: 0.6307 (tp30) REVERT: B 119 LEU cc_start: 0.8208 (mt) cc_final: 0.7718 (mt) REVERT: B 139 HIS cc_start: 0.8025 (p90) cc_final: 0.7413 (p90) REVERT: B 185 TYR cc_start: 0.5696 (m-10) cc_final: 0.4824 (m-80) REVERT: B 215 ARG cc_start: 0.7578 (tmm160) cc_final: 0.7059 (ttp80) REVERT: B 217 LEU cc_start: 0.8768 (mm) cc_final: 0.8296 (mm) REVERT: B 235 MET cc_start: 0.8335 (mmp) cc_final: 0.7629 (mmt) REVERT: B 398 MET cc_start: 0.7513 (ptm) cc_final: 0.5792 (ptm) REVERT: B 405 LEU cc_start: 0.8702 (mm) cc_final: 0.8281 (tt) REVERT: C 7 ILE cc_start: 0.8797 (mp) cc_final: 0.8567 (mm) REVERT: C 36 MET cc_start: 0.6765 (mmm) cc_final: 0.5987 (mmm) REVERT: C 75 ILE cc_start: 0.8442 (mm) cc_final: 0.7123 (tt) REVERT: C 196 GLU cc_start: 0.7981 (pm20) cc_final: 0.7545 (mp0) REVERT: C 217 LEU cc_start: 0.8264 (mm) cc_final: 0.7969 (mm) REVERT: C 221 ARG cc_start: 0.7880 (mpp-170) cc_final: 0.7272 (mmm-85) REVERT: C 295 CYS cc_start: 0.9271 (t) cc_final: 0.9066 (t) REVERT: C 316 CYS cc_start: 0.6847 (t) cc_final: 0.6290 (t) REVERT: C 327 ASP cc_start: 0.7370 (m-30) cc_final: 0.7108 (m-30) REVERT: C 435 VAL cc_start: 0.8860 (t) cc_final: 0.8474 (t) REVERT: D 21 TRP cc_start: 0.8092 (m100) cc_final: 0.7624 (m100) REVERT: D 75 MET cc_start: 0.6985 (tmm) cc_final: 0.6683 (tpp) REVERT: D 86 ILE cc_start: 0.9063 (pt) cc_final: 0.8726 (mp) REVERT: D 119 LEU cc_start: 0.8502 (mt) cc_final: 0.8120 (mt) REVERT: D 139 HIS cc_start: 0.7634 (p90) cc_final: 0.7036 (p90) REVERT: D 163 ASP cc_start: 0.7323 (p0) cc_final: 0.6933 (p0) REVERT: D 165 ILE cc_start: 0.8687 (mt) cc_final: 0.8282 (mt) REVERT: D 207 GLU cc_start: 0.8381 (mp0) cc_final: 0.8024 (mp0) REVERT: D 259 MET cc_start: 0.8404 (mmm) cc_final: 0.8077 (mmm) REVERT: D 260 VAL cc_start: 0.9068 (t) cc_final: 0.8825 (t) REVERT: D 264 ARG cc_start: 0.6562 (mtt180) cc_final: 0.5738 (mtt180) REVERT: D 269 MET cc_start: 0.6992 (ttm) cc_final: 0.6569 (ttm) REVERT: D 309 HIS cc_start: 0.5446 (OUTLIER) cc_final: 0.4921 (t-90) REVERT: E 21 TRP cc_start: 0.8283 (m100) cc_final: 0.7828 (m100) REVERT: E 33 ASP cc_start: 0.7361 (p0) cc_final: 0.6615 (p0) REVERT: E 62 VAL cc_start: 0.6311 (p) cc_final: 0.5979 (p) REVERT: E 75 ILE cc_start: 0.8960 (mm) cc_final: 0.8611 (mm) REVERT: E 167 LEU cc_start: 0.6854 (mm) cc_final: 0.6561 (mm) REVERT: E 193 THR cc_start: 0.8879 (p) cc_final: 0.8641 (p) REVERT: E 235 VAL cc_start: 0.8525 (t) cc_final: 0.8219 (t) REVERT: E 291 ILE cc_start: 0.9178 (mt) cc_final: 0.8169 (tt) REVERT: E 335 ILE cc_start: 0.8961 (pt) cc_final: 0.8587 (tp) REVERT: E 347 CYS cc_start: 0.9128 (p) cc_final: 0.8827 (p) REVERT: F 7 ILE cc_start: 0.8808 (mm) cc_final: 0.8417 (mt) REVERT: F 66 ILE cc_start: 0.9147 (mm) cc_final: 0.8941 (mm) REVERT: F 116 ASP cc_start: 0.7197 (m-30) cc_final: 0.6782 (m-30) REVERT: F 120 ASP cc_start: 0.7299 (m-30) cc_final: 0.7086 (m-30) REVERT: F 163 ASP cc_start: 0.7516 (p0) cc_final: 0.6815 (p0) REVERT: F 217 LEU cc_start: 0.8280 (mm) cc_final: 0.7752 (mm) REVERT: F 432 TYR cc_start: 0.5995 (m-80) cc_final: 0.5367 (m-10) REVERT: G 5 ILE cc_start: 0.6412 (pt) cc_final: 0.6151 (pt) REVERT: G 271 THR cc_start: 0.7601 (m) cc_final: 0.7223 (t) REVERT: G 322 ASP cc_start: 0.7622 (p0) cc_final: 0.7224 (p0) REVERT: H 20 PHE cc_start: 0.8307 (t80) cc_final: 0.8072 (t80) REVERT: H 21 TRP cc_start: 0.7650 (m100) cc_final: 0.6646 (m100) REVERT: H 55 GLU cc_start: 0.5076 (tp30) cc_final: 0.4866 (tp30) REVERT: H 60 LYS cc_start: 0.1367 (pttt) cc_final: 0.1025 (pttt) REVERT: H 132 LEU cc_start: 0.9086 (tp) cc_final: 0.8244 (tp) REVERT: H 153 LEU cc_start: 0.9178 (mt) cc_final: 0.8856 (mt) REVERT: H 240 THR cc_start: 0.7764 (m) cc_final: 0.7482 (m) REVERT: H 259 MET cc_start: 0.7470 (mmp) cc_final: 0.7116 (mmm) REVERT: H 264 ARG cc_start: 0.4155 (mtt180) cc_final: 0.3684 (mtt180) REVERT: H 275 LEU cc_start: 0.7729 (pt) cc_final: 0.7486 (pt) REVERT: H 288 VAL cc_start: 0.8820 (t) cc_final: 0.8536 (t) REVERT: H 325 MET cc_start: 0.7647 (pmm) cc_final: 0.7238 (pmm) REVERT: H 386 GLU cc_start: 0.8311 (mp0) cc_final: 0.8099 (pt0) REVERT: H 388 PHE cc_start: 0.6105 (m-80) cc_final: 0.5343 (m-10) REVERT: I 20 CYS cc_start: 0.9064 (p) cc_final: 0.8307 (p) REVERT: I 53 PHE cc_start: 0.7595 (m-80) cc_final: 0.7029 (m-80) REVERT: I 75 ILE cc_start: 0.8355 (mm) cc_final: 0.7473 (tt) REVERT: I 83 TYR cc_start: 0.5975 (m-10) cc_final: 0.5662 (m-10) REVERT: I 92 LEU cc_start: 0.9335 (mt) cc_final: 0.8995 (tt) REVERT: I 237 SER cc_start: 0.7441 (p) cc_final: 0.7227 (p) REVERT: J 16 ILE cc_start: 0.9337 (mt) cc_final: 0.8926 (tp) REVERT: J 21 TRP cc_start: 0.7862 (m100) cc_final: 0.7432 (m100) REVERT: J 66 ILE cc_start: 0.8911 (mm) cc_final: 0.8579 (mm) REVERT: J 132 LEU cc_start: 0.8559 (mm) cc_final: 0.8319 (mm) REVERT: J 138 THR cc_start: 0.7280 (p) cc_final: 0.6557 (p) REVERT: J 165 ILE cc_start: 0.8656 (pt) cc_final: 0.8341 (pt) REVERT: J 205 ASP cc_start: 0.8774 (t0) cc_final: 0.8506 (t0) REVERT: J 239 THR cc_start: 0.8160 (t) cc_final: 0.7707 (t) REVERT: J 248 LEU cc_start: 0.7626 (mm) cc_final: 0.7145 (mt) REVERT: J 257 VAL cc_start: 0.9206 (t) cc_final: 0.8901 (p) REVERT: J 266 HIS cc_start: 0.8388 (p90) cc_final: 0.7968 (p-80) REVERT: K 16 ILE cc_start: 0.7401 (pt) cc_final: 0.7184 (pt) REVERT: K 36 MET cc_start: 0.5822 (mmm) cc_final: 0.5609 (mmm) REVERT: K 149 PHE cc_start: 0.7101 (t80) cc_final: 0.6707 (t80) REVERT: K 166 LYS cc_start: 0.6822 (mppt) cc_final: 0.6622 (mptt) REVERT: K 217 LEU cc_start: 0.6963 (mm) cc_final: 0.6549 (mm) REVERT: K 335 ILE cc_start: 0.8488 (pt) cc_final: 0.7847 (tp) REVERT: K 352 LYS cc_start: 0.8571 (tptt) cc_final: 0.7799 (tptp) REVERT: K 377 MET cc_start: 0.7418 (ttp) cc_final: 0.6978 (tpt) REVERT: L 21 TRP cc_start: 0.8112 (m100) cc_final: 0.7029 (m100) REVERT: L 27 GLU cc_start: 0.6767 (pt0) cc_final: 0.6511 (pt0) REVERT: L 53 TYR cc_start: 0.5737 (m-10) cc_final: 0.5296 (m-80) REVERT: L 138 THR cc_start: 0.5737 (p) cc_final: 0.5241 (p) REVERT: L 163 ASP cc_start: 0.6623 (p0) cc_final: 0.6422 (m-30) REVERT: L 209 LEU cc_start: 0.8972 (mt) cc_final: 0.8737 (mt) REVERT: L 356 CYS cc_start: 0.6162 (t) cc_final: 0.5107 (t) REVERT: M 21 TRP cc_start: 0.8226 (m100) cc_final: 0.7634 (m100) REVERT: M 25 CYS cc_start: 0.6897 (m) cc_final: 0.6641 (m) REVERT: M 122 ILE cc_start: 0.8800 (mt) cc_final: 0.8586 (mt) REVERT: M 123 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.7398 (mmm-85) REVERT: M 231 ILE cc_start: 0.8548 (mt) cc_final: 0.8288 (mm) REVERT: M 291 ILE cc_start: 0.8679 (mt) cc_final: 0.8349 (mt) REVERT: M 316 CYS cc_start: 0.5407 (p) cc_final: 0.4629 (p) REVERT: N 21 TRP cc_start: 0.8842 (m100) cc_final: 0.8033 (m100) REVERT: N 115 VAL cc_start: 0.8367 (t) cc_final: 0.8125 (t) REVERT: N 166 MET cc_start: 0.3776 (ptt) cc_final: 0.3339 (ptt) REVERT: N 192 HIS cc_start: 0.8130 (t70) cc_final: 0.7897 (t70) REVERT: N 213 CYS cc_start: 0.6607 (p) cc_final: 0.6366 (p) REVERT: N 227 LEU cc_start: 0.8287 (mt) cc_final: 0.7872 (mt) REVERT: N 292 THR cc_start: 0.7447 (p) cc_final: 0.6786 (t) REVERT: N 355 VAL cc_start: 0.6350 (t) cc_final: 0.5974 (t) REVERT: N 384 ILE cc_start: 0.8093 (mp) cc_final: 0.7776 (mp) REVERT: N 391 ILE cc_start: 0.8900 (tp) cc_final: 0.8547 (mm) REVERT: O 33 ASP cc_start: 0.8242 (p0) cc_final: 0.7542 (p0) REVERT: O 36 MET cc_start: 0.3219 (ttp) cc_final: 0.2540 (ttp) REVERT: O 53 PHE cc_start: 0.6789 (m-80) cc_final: 0.6427 (m-80) REVERT: O 62 VAL cc_start: 0.6810 (p) cc_final: 0.6530 (p) REVERT: O 76 ASP cc_start: 0.7559 (m-30) cc_final: 0.7161 (t70) REVERT: O 86 LEU cc_start: 0.8638 (tp) cc_final: 0.8344 (tp) REVERT: O 154 MET cc_start: 0.8086 (tmm) cc_final: 0.7601 (tmm) REVERT: O 196 GLU cc_start: 0.6767 (pm20) cc_final: 0.6433 (mt-10) REVERT: O 398 MET cc_start: 0.7724 (mtp) cc_final: 0.6684 (mmp) REVERT: O 429 GLU cc_start: 0.7624 (tt0) cc_final: 0.7351 (tt0) REVERT: P 14 ASN cc_start: 0.7961 (m-40) cc_final: 0.7666 (m110) REVERT: P 94 PHE cc_start: 0.8588 (p90) cc_final: 0.8279 (p90) REVERT: P 115 VAL cc_start: 0.9312 (t) cc_final: 0.8993 (t) REVERT: P 154 ILE cc_start: 0.8893 (mt) cc_final: 0.8622 (mt) REVERT: P 259 MET cc_start: 0.7537 (mmm) cc_final: 0.6466 (mmp) REVERT: P 268 PHE cc_start: 0.7187 (m-80) cc_final: 0.5340 (m-80) REVERT: P 292 THR cc_start: 0.7551 (p) cc_final: 0.7109 (p) REVERT: P 314 THR cc_start: 0.8177 (p) cc_final: 0.7940 (p) REVERT: P 384 ILE cc_start: 0.8428 (mt) cc_final: 0.8214 (mt) REVERT: P 389 LYS cc_start: 0.9018 (ptpp) cc_final: 0.8800 (pttp) REVERT: P 414 ASP cc_start: 0.8010 (t0) cc_final: 0.7330 (m-30) REVERT: P 425 MET cc_start: 0.8360 (tpp) cc_final: 0.7640 (tpp) REVERT: Q 76 ASP cc_start: 0.7807 (m-30) cc_final: 0.6902 (t0) REVERT: Q 86 LEU cc_start: 0.8523 (tp) cc_final: 0.8204 (tp) REVERT: Q 154 MET cc_start: 0.7400 (tmm) cc_final: 0.6890 (tmm) REVERT: Q 429 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7133 (mm-30) REVERT: Q 431 ASP cc_start: 0.6081 (m-30) cc_final: 0.5765 (m-30) REVERT: R 115 VAL cc_start: 0.9035 (p) cc_final: 0.8703 (p) REVERT: R 120 ASP cc_start: 0.8001 (m-30) cc_final: 0.7562 (m-30) REVERT: R 135 PHE cc_start: 0.7467 (m-80) cc_final: 0.6904 (m-80) REVERT: R 136 GLN cc_start: 0.6864 (pt0) cc_final: 0.6654 (pt0) REVERT: R 139 HIS cc_start: 0.7119 (p90) cc_final: 0.6517 (p90) REVERT: R 259 MET cc_start: 0.7861 (mmm) cc_final: 0.6197 (mmt) REVERT: R 268 PHE cc_start: 0.6787 (m-80) cc_final: 0.4134 (m-80) REVERT: R 269 MET cc_start: 0.4897 (tpt) cc_final: 0.4629 (tpt) REVERT: R 314 THR cc_start: 0.7122 (p) cc_final: 0.6344 (p) REVERT: R 332 MET cc_start: 0.5631 (tmm) cc_final: 0.5313 (tmm) REVERT: R 398 MET cc_start: 0.7889 (ptm) cc_final: 0.7204 (ttp) outliers start: 7 outliers final: 1 residues processed: 1520 average time/residue: 0.5802 time to fit residues: 1489.1900 Evaluate side-chains 1156 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1154 time to evaluate : 5.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 0.2980 chunk 476 optimal weight: 10.0000 chunk 638 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 553 optimal weight: 0.0470 chunk 88 optimal weight: 40.0000 chunk 166 optimal weight: 30.0000 chunk 600 optimal weight: 50.0000 chunk 251 optimal weight: 20.0000 chunk 616 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 overall best weight: 4.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 249 ASN C 380 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 249 ASN D 309 HIS D 339 ASN ** D 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 136 GLN F 249 ASN F 309 HIS ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 ASN J 249 ASN K 228 ASN ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 GLN ** L 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 334 ASN ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 HIS ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 249 ASN ** Q 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 249 ASN R 309 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.076456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.061868 restraints weight = 208385.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.064827 restraints weight = 124786.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.066988 restraints weight = 81896.953| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.9123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62262 Z= 0.191 Angle : 0.672 12.797 84582 Z= 0.349 Chirality : 0.047 0.315 9216 Planarity : 0.005 0.067 11043 Dihedral : 10.763 179.732 8595 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.12 % Allowed : 0.21 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.10), residues: 7632 helix: 0.69 (0.09), residues: 3591 sheet: 0.54 (0.14), residues: 1323 loop : 0.09 (0.13), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 21 HIS 0.015 0.001 HIS M 8 PHE 0.044 0.002 PHE J 92 TYR 0.037 0.002 TYR D 161 ARG 0.012 0.001 ARG Q 214 =============================================================================== Job complete usr+sys time: 22458.03 seconds wall clock time: 385 minutes 22.77 seconds (23122.77 seconds total)