Starting phenix.real_space_refine on Thu Sep 26 04:30:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/09_2024/3j6e_5895.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/09_2024/3j6e_5895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/09_2024/3j6e_5895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/09_2024/3j6e_5895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/09_2024/3j6e_5895.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6e_5895/09_2024/3j6e_5895.cif" } resolution = 4.7 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= 0.468 sd= 1.871 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 54 5.49 5 Mg 18 5.21 5 S 414 5.16 5 C 38223 2.51 5 N 10395 2.21 5 O 11880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 315 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 60984 Number of models: 1 Model: "" Number of chains: 22 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "B" 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: "D" 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: "F" 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: "H" 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: "J" 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: "L" 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: "N" 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: "P" 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} Chain: "R" 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: 13.76, per 1000 atoms: 0.23 Number of scatterers: 60984 At special positions: 0 Unit cell: (168.78, 88.74, 295.8, 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 54 15.00 Mg 18 11.99 O 11880 8.00 N 10395 7.00 C 38223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.25 Conformation dependent library (CDL) restraints added in 5.9 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: 369 helices and 45 sheets defined 55.5% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.617A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.645A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 147 through 161 removed outlier: 3.856A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.544A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (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 339 Processing helix chain 'A' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.649A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.590A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (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: 3.730A pdb=" N GLU B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 161 removed outlier: 4.067A pdb=" N GLY B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN B 282 " --> pdb=" O ARG B 278 " (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 306 through 310 Processing helix chain 'B' and resid 324 through 339 Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 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: 4.617A pdb=" N ILE C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 removed outlier: 3.646A pdb=" N GLN C 85 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 147 through 161 removed outlier: 3.856A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.601A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 4.544A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (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 339 Processing helix chain 'C' and resid 383 through 402 removed outlier: 4.157A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 401 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.650A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.589A pdb=" N MET D 75 " --> pdb=" O GLU D 71 " (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: 3.730A pdb=" N GLU D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 removed outlier: 4.066A pdb=" N GLY D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS D 229 " --> pdb=" O GLY D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 244 Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN D 282 " --> pdb=" O ARG D 278 " (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 306 through 310 Processing helix chain 'D' and resid 324 through 339 Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 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: 4.616A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 86 removed outlier: 3.645A pdb=" N GLN E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 147 through 161 removed outlier: 3.855A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 244 removed outlier: 4.545A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (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 339 Processing helix chain 'E' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 437 removed outlier: 3.650A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 Processing helix chain 'F' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.590A pdb=" N MET F 75 " --> pdb=" O GLU F 71 " (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: 3.730A pdb=" N GLU F 113 " --> pdb=" O THR F 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 161 removed outlier: 4.068A pdb=" N GLY F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 216 Processing helix chain 'F' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS F 229 " --> pdb=" O GLY F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 244 Processing helix chain 'F' and resid 251 through 260 Processing helix chain 'F' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN F 282 " --> pdb=" O ARG F 278 " (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 306 through 310 Processing helix chain 'F' and resid 324 through 339 Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 384 through 402 removed outlier: 3.630A pdb=" N PHE F 388 " --> pdb=" O ILE F 384 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG F 401 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 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: 4.616A pdb=" N ILE G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 86 removed outlier: 3.645A pdb=" N GLN G 85 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 110 through 113 Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 147 through 161 removed outlier: 3.856A pdb=" N VAL G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Processing helix chain 'G' and resid 223 through 244 removed outlier: 4.544A pdb=" N SER G 241 " --> pdb=" O SER G 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 242 " --> pdb=" O ILE G 238 " (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 339 Processing helix chain 'G' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA G 387 " --> pdb=" O ALA G 383 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS G 401 " --> pdb=" O LEU G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 Processing helix chain 'G' and resid 414 through 437 removed outlier: 3.650A pdb=" N PHE G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 40 through 48 removed outlier: 3.837A pdb=" N LEU H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.590A pdb=" N MET H 75 " --> pdb=" O GLU H 71 " (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: 3.730A pdb=" N GLU H 113 " --> pdb=" O THR H 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 161 removed outlier: 4.067A pdb=" N GLY H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 198 removed outlier: 4.126A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 216 Processing helix chain 'H' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS H 229 " --> pdb=" O GLY H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 244 Processing helix chain 'H' and resid 251 through 260 Processing helix chain 'H' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN H 282 " --> pdb=" O ARG H 278 " (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 306 through 310 Processing helix chain 'H' and resid 324 through 339 Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE H 388 " --> pdb=" O ILE H 384 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG H 401 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 410 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: 4.617A pdb=" N ILE I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 86 removed outlier: 3.645A pdb=" N GLN I 85 " --> pdb=" O THR I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'I' and resid 102 through 108 Processing helix chain 'I' and resid 110 through 113 Processing helix chain 'I' and resid 114 through 129 Processing helix chain 'I' and resid 147 through 161 removed outlier: 3.856A pdb=" N VAL I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 216 Processing helix chain 'I' and resid 223 through 244 removed outlier: 4.544A pdb=" N SER I 241 " --> pdb=" O SER I 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU I 242 " --> pdb=" O ILE I 238 " (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 339 Processing helix chain 'I' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA I 387 " --> pdb=" O ALA I 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS I 401 " --> pdb=" O LEU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 410 Processing helix chain 'I' and resid 414 through 437 removed outlier: 3.649A pdb=" N PHE I 418 " --> pdb=" O GLU I 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 29 Processing helix chain 'J' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU J 44 " --> pdb=" O SER J 40 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.590A pdb=" N MET J 75 " --> pdb=" O GLU J 71 " (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: 3.730A pdb=" N GLU J 113 " --> pdb=" O THR J 109 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 143 through 161 removed outlier: 4.066A pdb=" N GLY J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 216 Processing helix chain 'J' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS J 229 " --> pdb=" O GLY J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 Processing helix chain 'J' and resid 251 through 260 Processing helix chain 'J' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN J 282 " --> pdb=" O ARG J 278 " (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 306 through 310 Processing helix chain 'J' and resid 324 through 339 Processing helix chain 'J' and resid 340 through 343 Processing helix chain 'J' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE J 388 " --> pdb=" O ILE J 384 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG J 401 " --> pdb=" O ALA J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 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: 4.617A pdb=" N ILE K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 86 removed outlier: 3.646A pdb=" N GLN K 85 " --> pdb=" O THR K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 110 through 113 Processing helix chain 'K' and resid 114 through 129 Processing helix chain 'K' and resid 147 through 161 removed outlier: 3.855A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 198 removed outlier: 3.601A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 Processing helix chain 'K' and resid 223 through 244 removed outlier: 4.545A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (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 339 Processing helix chain 'K' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS K 401 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 414 through 437 removed outlier: 3.649A pdb=" N PHE K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 29 Processing helix chain 'L' and resid 40 through 48 removed outlier: 3.837A pdb=" N LEU L 44 " --> pdb=" O SER L 40 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.589A pdb=" N MET L 75 " --> pdb=" O GLU L 71 " (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: 3.730A pdb=" N GLU L 113 " --> pdb=" O THR L 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 143 through 161 removed outlier: 4.067A pdb=" N GLY L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 216 Processing helix chain 'L' and resid 223 through 238 removed outlier: 3.716A pdb=" N HIS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 Processing helix chain 'L' and resid 251 through 260 Processing helix chain 'L' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN L 282 " --> pdb=" O ARG L 278 " (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 306 through 310 Processing helix chain 'L' and resid 324 through 339 Processing helix chain 'L' and resid 340 through 343 Processing helix chain 'L' and resid 384 through 402 removed outlier: 3.632A pdb=" N PHE L 388 " --> pdb=" O ILE L 384 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG L 401 " --> pdb=" O ALA L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 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: 4.617A pdb=" N ILE M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 86 removed outlier: 3.646A pdb=" N GLN M 85 " --> pdb=" O THR M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'M' and resid 102 through 108 Processing helix chain 'M' and resid 110 through 113 Processing helix chain 'M' and resid 114 through 129 Processing helix chain 'M' and resid 147 through 161 removed outlier: 3.855A pdb=" N VAL M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR M 193 " --> pdb=" O LEU M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 216 Processing helix chain 'M' and resid 223 through 244 removed outlier: 4.544A pdb=" N SER M 241 " --> pdb=" O SER M 237 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU M 242 " --> pdb=" O ILE M 238 " (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 339 Processing helix chain 'M' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS M 401 " --> pdb=" O LEU M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 410 Processing helix chain 'M' and resid 414 through 437 removed outlier: 3.650A pdb=" N PHE M 418 " --> pdb=" O GLU M 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 29 Processing helix chain 'N' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU N 44 " --> pdb=" O SER N 40 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.590A pdb=" N MET N 75 " --> pdb=" O GLU N 71 " (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: 3.730A pdb=" N GLU N 113 " --> pdb=" O THR N 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU N 114 " --> pdb=" O GLU N 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER N 117 " --> pdb=" O GLU N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 161 removed outlier: 4.067A pdb=" N GLY N 150 " --> pdb=" O GLY N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU N 196 " --> pdb=" O HIS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 216 Processing helix chain 'N' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 244 Processing helix chain 'N' and resid 251 through 260 Processing helix chain 'N' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN N 282 " --> pdb=" O ARG N 278 " (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 306 through 310 Processing helix chain 'N' and resid 324 through 339 Processing helix chain 'N' and resid 340 through 343 Processing helix chain 'N' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE N 388 " --> pdb=" O ILE N 384 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG N 401 " --> pdb=" O ALA N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 410 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: 4.616A pdb=" N ILE O 75 " --> pdb=" O GLU O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 86 removed outlier: 3.645A pdb=" N GLN O 85 " --> pdb=" O THR O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'O' and resid 102 through 108 Processing helix chain 'O' and resid 110 through 113 Processing helix chain 'O' and resid 114 through 129 Processing helix chain 'O' and resid 147 through 161 removed outlier: 3.856A pdb=" N VAL O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR O 193 " --> pdb=" O LEU O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 216 Processing helix chain 'O' and resid 223 through 244 removed outlier: 4.544A pdb=" N SER O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU O 242 " --> pdb=" O ILE O 238 " (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 339 Processing helix chain 'O' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA O 387 " --> pdb=" O ALA O 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS O 401 " --> pdb=" O LEU O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 410 Processing helix chain 'O' and resid 414 through 437 removed outlier: 3.650A pdb=" N PHE O 418 " --> pdb=" O GLU O 414 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 29 Processing helix chain 'P' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU P 44 " --> pdb=" O SER P 40 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.590A pdb=" N MET P 75 " --> pdb=" O GLU P 71 " (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: 3.730A pdb=" N GLU P 113 " --> pdb=" O THR P 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU P 114 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 143 through 161 removed outlier: 4.066A pdb=" N GLY P 150 " --> pdb=" O GLY P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 198 removed outlier: 4.127A pdb=" N GLU P 196 " --> pdb=" O HIS P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 216 Processing helix chain 'P' and resid 223 through 238 removed outlier: 3.717A pdb=" N HIS P 229 " --> pdb=" O GLY P 225 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 244 Processing helix chain 'P' and resid 251 through 260 Processing helix chain 'P' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN P 282 " --> pdb=" O ARG P 278 " (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 306 through 310 Processing helix chain 'P' and resid 324 through 339 Processing helix chain 'P' and resid 340 through 343 Processing helix chain 'P' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE P 388 " --> pdb=" O ILE P 384 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG P 401 " --> pdb=" O ALA P 397 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 410 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: 4.616A pdb=" N ILE Q 75 " --> pdb=" O GLU Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 86 removed outlier: 3.646A pdb=" N GLN Q 85 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 90 No H-bonds generated for 'chain 'Q' and resid 88 through 90' Processing helix chain 'Q' and resid 102 through 108 Processing helix chain 'Q' and resid 110 through 113 Processing helix chain 'Q' and resid 114 through 129 Processing helix chain 'Q' and resid 147 through 161 removed outlier: 3.856A pdb=" N VAL Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 182 through 198 removed outlier: 3.602A pdb=" N THR Q 193 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 216 Processing helix chain 'Q' and resid 223 through 244 removed outlier: 4.543A pdb=" N SER Q 241 " --> pdb=" O SER Q 237 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU Q 242 " --> pdb=" O ILE Q 238 " (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 339 Processing helix chain 'Q' and resid 383 through 402 removed outlier: 4.156A pdb=" N ALA Q 387 " --> pdb=" O ALA Q 383 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS Q 401 " --> pdb=" O LEU Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 410 Processing helix chain 'Q' and resid 414 through 437 removed outlier: 3.649A pdb=" N PHE Q 418 " --> pdb=" O GLU Q 414 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 29 Processing helix chain 'R' and resid 40 through 48 removed outlier: 3.836A pdb=" N LEU R 44 " --> pdb=" O SER R 40 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.589A pdb=" N MET R 75 " --> pdb=" O GLU R 71 " (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: 3.730A pdb=" N GLU R 113 " --> pdb=" O THR R 109 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER R 117 " --> pdb=" O GLU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 161 removed outlier: 4.067A pdb=" N GLY R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 198 removed outlier: 4.126A pdb=" N GLU R 196 " --> pdb=" O HIS R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 216 Processing helix chain 'R' and resid 223 through 238 removed outlier: 3.716A pdb=" N HIS R 229 " --> pdb=" O GLY R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 244 Processing helix chain 'R' and resid 251 through 260 Processing helix chain 'R' and resid 277 through 282 removed outlier: 3.830A pdb=" N GLN R 282 " --> pdb=" O ARG R 278 " (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 306 through 310 Processing helix chain 'R' and resid 324 through 339 Processing helix chain 'R' and resid 340 through 343 Processing helix chain 'R' and resid 384 through 402 removed outlier: 3.631A pdb=" N PHE R 388 " --> pdb=" O ILE R 384 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG R 401 " --> pdb=" O ALA R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 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: 7.980A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 137 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 7 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 355 " --> pdb=" O GLN B 247 " (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: 7.980A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU C 3 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE C 135 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE C 5 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N VAL C 137 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE C 7 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS C 139 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL C 9 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN C 133 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU C 167 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.353A pdb=" N ALA C 374 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR C 319 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS C 376 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU C 317 " --> pdb=" O CYS C 376 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 378 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS C 315 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN C 380 " --> pdb=" O MET C 313 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain 'D' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU D 3 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE D 135 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL D 5 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU D 137 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE D 7 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS D 139 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA D 9 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER D 374 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 319 " --> pdb=" O SER D 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR D 376 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 317 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 378 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN D 380 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL D 355 " --> pdb=" O GLN D 247 " (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: 7.980A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA E 374 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR E 319 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS E 376 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU E 317 " --> pdb=" O CYS E 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU E 378 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS E 315 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN E 380 " --> pdb=" O MET E 313 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'F' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU F 3 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE F 135 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 5 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU F 137 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE F 7 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS F 139 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA F 9 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER F 374 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE F 319 " --> pdb=" O SER F 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR F 376 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA F 317 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE F 378 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL F 315 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN F 380 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL F 355 " --> pdb=" O GLN F 247 " (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: 7.980A pdb=" N ILE G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE G 67 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU G 3 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE G 135 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE G 5 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL G 137 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE G 7 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS G 139 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL G 9 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN G 133 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N LEU G 167 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE G 135 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE G 169 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL G 137 " --> pdb=" O PHE G 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE G 171 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA G 374 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR G 319 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS G 376 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU G 317 " --> pdb=" O CYS G 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU G 378 " --> pdb=" O CYS G 315 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS G 315 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN G 380 " --> pdb=" O MET G 313 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain 'H' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU H 3 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE H 135 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL H 5 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU H 137 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE H 7 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS H 139 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA H 9 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER H 374 " --> pdb=" O PHE H 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE H 319 " --> pdb=" O SER H 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR H 376 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA H 317 " --> pdb=" O THR H 376 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE H 378 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL H 315 " --> pdb=" O ILE H 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN H 380 " --> pdb=" O LEU H 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL H 355 " --> pdb=" O GLN H 247 " (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: 7.980A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU I 3 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE I 135 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE I 5 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL I 137 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE I 7 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS I 139 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL I 9 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN I 133 " --> pdb=" O SER I 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU I 167 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE I 135 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE I 169 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL I 137 " --> pdb=" O PHE I 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE I 171 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.351A pdb=" N ALA I 374 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR I 319 " --> pdb=" O ALA I 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS I 376 " --> pdb=" O LEU I 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU I 317 " --> pdb=" O CYS I 376 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU I 378 " --> pdb=" O CYS I 315 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS I 315 " --> pdb=" O LEU I 378 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN I 380 " --> pdb=" O MET I 313 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 67 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE J 66 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS J 6 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL J 68 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU J 3 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE J 135 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL J 5 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU J 137 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE J 7 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS J 139 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA J 9 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE J 267 " --> pdb=" O SER J 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER J 381 " --> pdb=" O PHE J 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER J 374 " --> pdb=" O PHE J 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE J 319 " --> pdb=" O SER J 374 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR J 376 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA J 317 " --> pdb=" O THR J 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE J 378 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL J 315 " --> pdb=" O ILE J 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN J 380 " --> pdb=" O LEU J 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL J 355 " --> pdb=" O GLN J 247 " (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: 7.980A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU K 3 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE K 135 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE K 5 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL K 137 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE K 7 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS K 139 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL K 9 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N GLN K 133 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU K 167 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE K 135 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE K 169 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL K 137 " --> pdb=" O PHE K 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE K 171 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA K 374 " --> pdb=" O TYR K 319 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TYR K 319 " --> pdb=" O ALA K 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS K 376 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU K 317 " --> pdb=" O CYS K 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU K 378 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS K 315 " --> pdb=" O LEU K 378 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN K 380 " --> pdb=" O MET K 313 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU L 67 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE L 66 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS L 6 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL L 68 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU L 3 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N PHE L 135 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL L 5 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU L 137 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE L 7 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS L 139 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA L 9 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE L 267 " --> pdb=" O SER L 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER L 381 " --> pdb=" O PHE L 267 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER L 374 " --> pdb=" O PHE L 319 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE L 319 " --> pdb=" O SER L 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR L 376 " --> pdb=" O ALA L 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA L 317 " --> pdb=" O THR L 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE L 378 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL L 315 " --> pdb=" O ILE L 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN L 380 " --> pdb=" O LEU L 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL L 355 " --> pdb=" O GLN L 247 " (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: 7.980A pdb=" N ILE M 93 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N PHE M 67 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU M 3 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N PHE M 135 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE M 5 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL M 137 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE M 7 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS M 139 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL M 9 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN M 133 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU M 167 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE M 135 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE M 169 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL M 137 " --> pdb=" O PHE M 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE M 171 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 7.708A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA M 374 " --> pdb=" O TYR M 319 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR M 319 " --> pdb=" O ALA M 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS M 376 " --> pdb=" O LEU M 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU M 317 " --> pdb=" O CYS M 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU M 378 " --> pdb=" O CYS M 315 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS M 315 " --> pdb=" O LEU M 378 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN M 380 " --> pdb=" O MET M 313 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'N' and resid 92 through 94 removed outlier: 8.160A pdb=" N VAL N 93 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU N 67 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE N 66 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS N 6 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL N 68 " --> pdb=" O HIS N 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN N 8 " --> pdb=" O VAL N 68 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU N 3 " --> pdb=" O GLN N 133 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE N 135 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL N 5 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU N 137 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE N 7 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS N 139 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ALA N 9 " --> pdb=" O HIS N 139 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE N 267 " --> pdb=" O SER N 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER N 381 " --> pdb=" O PHE N 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER N 374 " --> pdb=" O PHE N 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE N 319 " --> pdb=" O SER N 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR N 376 " --> pdb=" O ALA N 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA N 317 " --> pdb=" O THR N 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE N 378 " --> pdb=" O VAL N 315 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL N 315 " --> pdb=" O ILE N 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN N 380 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL N 355 " --> pdb=" O GLN N 247 " (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: 7.981A pdb=" N ILE O 93 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE O 67 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU O 3 " --> pdb=" O GLN O 133 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE O 135 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE O 5 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL O 137 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE O 7 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS O 139 " --> pdb=" O ILE O 7 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL O 9 " --> pdb=" O HIS O 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN O 133 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU O 167 " --> pdb=" O GLN O 133 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE O 135 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE O 169 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL O 137 " --> pdb=" O PHE O 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE O 171 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 7.709A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA O 374 " --> pdb=" O TYR O 319 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N TYR O 319 " --> pdb=" O ALA O 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS O 376 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU O 317 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU O 378 " --> pdb=" O CYS O 315 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N CYS O 315 " --> pdb=" O LEU O 378 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASN O 380 " --> pdb=" O MET O 313 " (cutoff:3.500A) Processing sheet with id=AM, first strand: chain 'P' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL P 93 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU P 67 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE P 66 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS P 6 " --> pdb=" O ILE P 66 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL P 68 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN P 8 " --> pdb=" O VAL P 68 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU P 3 " --> pdb=" O GLN P 133 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE P 135 " --> pdb=" O GLU P 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL P 5 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU P 137 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE P 7 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS P 139 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA P 9 " --> pdb=" O HIS P 139 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N PHE P 267 " --> pdb=" O SER P 381 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER P 381 " --> pdb=" O PHE P 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER P 374 " --> pdb=" O PHE P 319 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE P 319 " --> pdb=" O SER P 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR P 376 " --> pdb=" O ALA P 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA P 317 " --> pdb=" O THR P 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE P 378 " --> pdb=" O VAL P 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL P 315 " --> pdb=" O ILE P 378 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN P 380 " --> pdb=" O LEU P 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL P 355 " --> pdb=" O GLN P 247 " (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: 7.980A pdb=" N ILE Q 93 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N PHE Q 67 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU Q 3 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N PHE Q 135 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE Q 5 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL Q 137 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE Q 7 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N HIS Q 139 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL Q 9 " --> pdb=" O HIS Q 139 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N GLN Q 133 " --> pdb=" O SER Q 165 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LEU Q 167 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N PHE Q 135 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE Q 169 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL Q 137 " --> pdb=" O PHE Q 169 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE Q 171 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 7.709A 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 269 through 273 removed outlier: 6.352A pdb=" N ALA Q 374 " --> pdb=" O TYR Q 319 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N TYR Q 319 " --> pdb=" O ALA Q 374 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS Q 376 " --> pdb=" O LEU Q 317 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU Q 317 " --> pdb=" O CYS Q 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU Q 378 " --> pdb=" O CYS Q 315 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS Q 315 " --> pdb=" O LEU Q 378 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN Q 380 " --> pdb=" O MET Q 313 " (cutoff:3.500A) Processing sheet with id=AR, first strand: chain 'R' and resid 92 through 94 removed outlier: 8.161A pdb=" N VAL R 93 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU R 67 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ILE R 66 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N HIS R 6 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL R 68 " --> pdb=" O HIS R 6 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN R 8 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU R 3 " --> pdb=" O GLN R 133 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N PHE R 135 " --> pdb=" O GLU R 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL R 5 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU R 137 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE R 7 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS R 139 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA R 9 " --> pdb=" O HIS R 139 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE R 267 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER R 381 " --> pdb=" O PHE R 267 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER R 374 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE R 319 " --> pdb=" O SER R 374 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR R 376 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA R 317 " --> pdb=" O THR R 376 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE R 378 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL R 315 " --> pdb=" O ILE R 378 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN R 380 " --> pdb=" O LEU R 313 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL R 355 " --> pdb=" O GLN R 247 " (cutoff:3.500A) Processing sheet with id=AS, first strand: chain 'R' and resid 53 through 56 3159 hydrogen bonds defined for protein. 9099 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: 25.44 Time building geometry restraints manager: 14.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 10970 1.30 - 1.43: 17265 1.43 - 1.56: 33235 1.56 - 1.68: 171 1.68 - 1.81: 657 Bond restraints: 62298 Sorted by residual: bond pdb=" CA THR K 349 " pdb=" C THR K 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.10e+02 bond pdb=" CA THR C 349 " pdb=" C THR C 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.10e+02 bond pdb=" CA THR E 349 " pdb=" C THR E 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.09e+02 bond pdb=" CA THR I 349 " pdb=" C THR I 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.09e+02 bond pdb=" CA THR O 349 " pdb=" C THR O 349 " ideal model delta sigma weight residual 1.520 1.316 0.204 1.16e-02 7.43e+03 3.08e+02 ... (remaining 62293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.41: 80612 5.41 - 10.82: 3755 10.82 - 16.23: 215 16.23 - 21.64: 54 21.64 - 27.05: 9 Bond angle restraints: 84645 Sorted by residual: angle pdb=" CA ARG M 339 " pdb=" C ARG M 339 " pdb=" N THR M 340 " ideal model delta sigma weight residual 115.21 93.87 21.34 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG I 339 " pdb=" C ARG I 339 " pdb=" N THR I 340 " ideal model delta sigma weight residual 115.21 93.87 21.34 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG O 339 " pdb=" C ARG O 339 " pdb=" N THR O 340 " ideal model delta sigma weight residual 115.21 93.87 21.34 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG G 339 " pdb=" C ARG G 339 " pdb=" N THR G 340 " ideal model delta sigma weight residual 115.21 93.88 21.33 1.33e+00 5.65e-01 2.57e+02 angle pdb=" CA ARG C 339 " pdb=" C ARG C 339 " pdb=" N THR C 340 " ideal model delta sigma weight residual 115.21 93.88 21.33 1.33e+00 5.65e-01 2.57e+02 ... (remaining 84640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.15: 36475 33.15 - 66.30: 533 66.30 - 99.45: 135 99.45 - 132.60: 18 132.60 - 165.75: 18 Dihedral angle restraints: 37179 sinusoidal: 15012 harmonic: 22167 Sorted by residual: dihedral pdb=" C PHE N 83 " pdb=" N PHE N 83 " pdb=" CA PHE N 83 " pdb=" CB PHE N 83 " ideal model delta harmonic sigma weight residual -122.60 -143.51 20.91 0 2.50e+00 1.60e-01 7.00e+01 dihedral pdb=" C PHE R 83 " pdb=" N PHE R 83 " pdb=" CA PHE R 83 " pdb=" CB PHE R 83 " ideal model delta harmonic sigma weight residual -122.60 -143.49 20.89 0 2.50e+00 1.60e-01 6.98e+01 dihedral pdb=" C PHE F 83 " pdb=" N PHE F 83 " pdb=" CA PHE F 83 " pdb=" CB PHE F 83 " ideal model delta harmonic sigma weight residual -122.60 -143.48 20.88 0 2.50e+00 1.60e-01 6.98e+01 ... (remaining 37176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 8210 0.193 - 0.386: 853 0.386 - 0.579: 108 0.579 - 0.772: 36 0.772 - 0.965: 9 Chirality restraints: 9216 Sorted by residual: chirality pdb=" CA PHE N 83 " pdb=" N PHE N 83 " pdb=" C PHE N 83 " pdb=" CB PHE N 83 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA PHE F 83 " pdb=" N PHE F 83 " pdb=" C PHE F 83 " pdb=" CB PHE F 83 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA PHE H 83 " pdb=" N PHE H 83 " pdb=" C PHE H 83 " pdb=" CB PHE H 83 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.97 2.00e-01 2.50e+01 2.33e+01 ... (remaining 9213 not shown) Planarity restraints: 11043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP R 437 " 0.040 2.00e-02 2.50e+03 8.19e-02 6.70e+01 pdb=" C ASP R 437 " -0.142 2.00e-02 2.50e+03 pdb=" O ASP R 437 " 0.052 2.00e-02 2.50e+03 pdb=" OXT ASP R 437 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 437 " 0.040 2.00e-02 2.50e+03 8.18e-02 6.69e+01 pdb=" C ASP F 437 " -0.141 2.00e-02 2.50e+03 pdb=" O ASP F 437 " 0.052 2.00e-02 2.50e+03 pdb=" OXT ASP F 437 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP J 437 " 0.040 2.00e-02 2.50e+03 8.18e-02 6.69e+01 pdb=" C ASP J 437 " -0.141 2.00e-02 2.50e+03 pdb=" O ASP J 437 " 0.052 2.00e-02 2.50e+03 pdb=" OXT ASP J 437 " 0.049 2.00e-02 2.50e+03 ... (remaining 11040 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.21: 45 2.21 - 2.88: 27412 2.88 - 3.56: 93622 3.56 - 4.23: 161517 4.23 - 4.90: 266185 Nonbonded interactions: 548781 Sorted by model distance: nonbonded pdb="MG MG E 502 " pdb=" O HOH E 604 " model vdw 1.539 2.170 nonbonded pdb="MG MG Q 502 " pdb=" O HOH Q 604 " model vdw 1.539 2.170 nonbonded pdb="MG MG C 502 " pdb=" O HOH C 604 " model vdw 1.540 2.170 nonbonded pdb="MG MG M 502 " pdb=" O HOH M 604 " model vdw 1.540 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH A 604 " model vdw 1.540 2.170 ... (remaining 548776 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: 0.050 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: 0.070 Extract box with map and model: 1.680 Check model and map are aligned: 0.360 Set scattering table: 0.440 Process input model: 96.420 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.260 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 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 0.253 62298 Z= 1.354 Angle : 2.598 27.047 84645 Z= 1.704 Chirality : 0.134 0.965 9216 Planarity : 0.008 0.082 11043 Dihedral : 13.517 165.753 22977 Min Nonbonded Distance : 1.539 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.42 % Favored : 96.23 % Rotamer: Outliers : 0.28 % Allowed : 0.41 % Favored : 99.31 % Cbeta Deviations : 0.25 % 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: -0.68 (0.09), residues: 7632 helix: -0.52 (0.07), residues: 3510 sheet: 1.04 (0.13), residues: 1197 loop : -0.83 (0.11), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.007 TRP R 103 HIS 0.012 0.002 HIS Q 139 PHE 0.019 0.004 PHE N 267 TYR 0.053 0.007 TYR N 61 ARG 0.008 0.001 ARG P 64 *********************** 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 2736 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 2718 time to evaluate : 5.137 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 14 VAL cc_start: 0.9005 (t) cc_final: 0.8744 (p) REVERT: A 24 TYR cc_start: 0.8333 (m-80) cc_final: 0.8093 (m-80) REVERT: A 74 VAL cc_start: 0.8038 (t) cc_final: 0.7748 (t) REVERT: A 75 ILE cc_start: 0.9048 (mm) cc_final: 0.8684 (mm) REVERT: A 118 VAL cc_start: 0.9402 (t) cc_final: 0.9072 (t) REVERT: A 167 LEU cc_start: 0.8545 (mt) cc_final: 0.8199 (mt) REVERT: A 188 ILE cc_start: 0.8618 (mt) cc_final: 0.8191 (mm) REVERT: A 207 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.4331 (mp0) REVERT: A 217 LEU cc_start: 0.8701 (mt) cc_final: 0.8473 (tp) REVERT: A 224 TYR cc_start: 0.6543 (m-80) cc_final: 0.5789 (m-10) REVERT: A 302 MET cc_start: 0.8237 (mmt) cc_final: 0.7438 (mpp) REVERT: A 315 CYS cc_start: 0.8097 (t) cc_final: 0.7861 (m) REVERT: A 344 VAL cc_start: 0.8043 (t) cc_final: 0.7499 (t) REVERT: A 378 LEU cc_start: 0.8334 (mt) cc_final: 0.7956 (mp) REVERT: A 384 ILE cc_start: 0.7868 (tt) cc_final: 0.6936 (tp) REVERT: A 391 LEU cc_start: 0.8639 (mt) cc_final: 0.8338 (mt) REVERT: A 413 MET cc_start: 0.7468 (mmm) cc_final: 0.6950 (mmp) REVERT: B 5 VAL cc_start: 0.9244 (t) cc_final: 0.8703 (t) REVERT: B 14 ASN cc_start: 0.8673 (m-40) cc_final: 0.8165 (m-40) REVERT: B 44 LEU cc_start: 0.8278 (mt) cc_final: 0.7911 (mt) REVERT: B 122 VAL cc_start: 0.9484 (t) cc_final: 0.9079 (t) REVERT: B 153 LEU cc_start: 0.8290 (tp) cc_final: 0.7716 (tp) REVERT: B 213 CYS cc_start: 0.8380 (m) cc_final: 0.8097 (m) REVERT: B 222 PRO cc_start: 0.8067 (Cg_exo) cc_final: 0.7751 (Cg_endo) REVERT: B 230 LEU cc_start: 0.9268 (mt) cc_final: 0.8684 (tt) REVERT: B 326 LYS cc_start: 0.7146 (tptp) cc_final: 0.6178 (ttpp) REVERT: B 378 ILE cc_start: 0.8391 (mt) cc_final: 0.8065 (mt) REVERT: B 391 ILE cc_start: 0.8744 (mt) cc_final: 0.8523 (mt) REVERT: B 413 MET cc_start: 0.7482 (mmm) cc_final: 0.7226 (mmt) REVERT: B 417 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7307 (tt0) REVERT: C 24 TYR cc_start: 0.8288 (m-80) cc_final: 0.7905 (m-80) REVERT: C 137 VAL cc_start: 0.7615 (t) cc_final: 0.7129 (t) REVERT: C 155 GLU cc_start: 0.6963 (tp30) cc_final: 0.6675 (tp30) REVERT: C 167 LEU cc_start: 0.7349 (mt) cc_final: 0.5806 (mt) REVERT: C 171 ILE cc_start: 0.9288 (mm) cc_final: 0.9043 (mm) REVERT: C 217 LEU cc_start: 0.8418 (mt) cc_final: 0.7929 (tt) REVERT: C 318 LEU cc_start: 0.8017 (mt) cc_final: 0.7692 (mm) REVERT: C 391 LEU cc_start: 0.8264 (mt) cc_final: 0.7942 (mt) REVERT: D 14 ASN cc_start: 0.8684 (m-40) cc_final: 0.8324 (m-40) REVERT: D 24 ILE cc_start: 0.8943 (mm) cc_final: 0.8490 (mm) REVERT: D 44 LEU cc_start: 0.7606 (mt) cc_final: 0.7141 (mp) REVERT: D 53 TYR cc_start: 0.5790 (m-80) cc_final: 0.5588 (m-80) REVERT: D 120 ASP cc_start: 0.5817 (m-30) cc_final: 0.5420 (m-30) REVERT: D 235 MET cc_start: 0.7347 (mtp) cc_final: 0.7138 (ttm) REVERT: D 248 LEU cc_start: 0.7637 (mt) cc_final: 0.7426 (mp) REVERT: D 283 TYR cc_start: 0.6231 (m-80) cc_final: 0.5809 (m-80) REVERT: D 378 ILE cc_start: 0.7902 (mt) cc_final: 0.7424 (mt) REVERT: D 398 MET cc_start: 0.7104 (mtp) cc_final: 0.4353 (mtp) REVERT: E 24 TYR cc_start: 0.7826 (m-80) cc_final: 0.7235 (m-10) REVERT: E 80 THR cc_start: 0.7552 (p) cc_final: 0.7296 (t) REVERT: E 157 LEU cc_start: 0.8540 (mt) cc_final: 0.8200 (mt) REVERT: E 167 LEU cc_start: 0.7529 (mt) cc_final: 0.6707 (mt) REVERT: E 171 ILE cc_start: 0.8528 (mm) cc_final: 0.8140 (mm) REVERT: E 209 ILE cc_start: 0.9499 (mt) cc_final: 0.9261 (mp) REVERT: E 227 LEU cc_start: 0.9380 (mt) cc_final: 0.9134 (mt) REVERT: E 302 MET cc_start: 0.8486 (mmt) cc_final: 0.7629 (mpp) REVERT: E 352 LYS cc_start: 0.8200 (tttp) cc_final: 0.7706 (ttpt) REVERT: E 378 LEU cc_start: 0.8586 (mt) cc_final: 0.7355 (mp) REVERT: E 413 MET cc_start: 0.7920 (mmm) cc_final: 0.7285 (mmp) REVERT: F 14 ASN cc_start: 0.8518 (m-40) cc_final: 0.8218 (m110) REVERT: F 24 ILE cc_start: 0.9209 (mm) cc_final: 0.8550 (mm) REVERT: F 53 TYR cc_start: 0.5198 (m-80) cc_final: 0.4957 (m-80) REVERT: F 72 PRO cc_start: 0.8061 (Cg_exo) cc_final: 0.7547 (Cg_endo) REVERT: F 115 VAL cc_start: 0.9338 (t) cc_final: 0.8981 (p) REVERT: F 119 LEU cc_start: 0.8759 (tp) cc_final: 0.8333 (tp) REVERT: F 122 VAL cc_start: 0.9573 (t) cc_final: 0.9235 (t) REVERT: F 192 HIS cc_start: 0.8292 (t-170) cc_final: 0.8081 (t-90) REVERT: F 209 LEU cc_start: 0.8346 (mt) cc_final: 0.6878 (mt) REVERT: F 230 LEU cc_start: 0.9194 (mt) cc_final: 0.8969 (mt) REVERT: F 305 CYS cc_start: 0.6448 (t) cc_final: 0.5557 (t) REVERT: F 335 VAL cc_start: 0.7401 (t) cc_final: 0.6113 (t) REVERT: F 351 VAL cc_start: 0.8422 (t) cc_final: 0.7267 (t) REVERT: F 413 MET cc_start: 0.7059 (mmm) cc_final: 0.6776 (mmt) REVERT: G 14 VAL cc_start: 0.8430 (t) cc_final: 0.7668 (p) REVERT: G 16 ILE cc_start: 0.9245 (mt) cc_final: 0.8942 (tp) REVERT: G 75 ILE cc_start: 0.7997 (mm) cc_final: 0.6496 (mm) REVERT: G 115 ILE cc_start: 0.8574 (tp) cc_final: 0.8251 (tp) REVERT: G 118 VAL cc_start: 0.9238 (t) cc_final: 0.8898 (t) REVERT: G 129 CYS cc_start: 0.6655 (m) cc_final: 0.6270 (t) REVERT: G 132 LEU cc_start: 0.8207 (tp) cc_final: 0.7951 (tp) REVERT: G 137 VAL cc_start: 0.8091 (t) cc_final: 0.7516 (t) REVERT: G 153 LEU cc_start: 0.8753 (tp) cc_final: 0.8457 (tt) REVERT: G 167 LEU cc_start: 0.7620 (mt) cc_final: 0.6790 (mt) REVERT: G 195 LEU cc_start: 0.7785 (tp) cc_final: 0.7057 (tt) REVERT: G 207 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: G 218 ASP cc_start: 0.6492 (m-30) cc_final: 0.6073 (m-30) REVERT: G 267 PHE cc_start: 0.7518 (m-80) cc_final: 0.6915 (m-80) REVERT: G 295 CYS cc_start: 0.9347 (m) cc_final: 0.8867 (m) REVERT: G 316 CYS cc_start: 0.8497 (t) cc_final: 0.6608 (m) REVERT: G 378 LEU cc_start: 0.7961 (mt) cc_final: 0.7581 (mp) REVERT: G 384 ILE cc_start: 0.6140 (tt) cc_final: 0.5857 (pt) REVERT: H 5 VAL cc_start: 0.8572 (t) cc_final: 0.8367 (t) REVERT: H 14 ASN cc_start: 0.8778 (m-40) cc_final: 0.7906 (t0) REVERT: H 122 VAL cc_start: 0.9377 (t) cc_final: 0.8809 (t) REVERT: H 209 LEU cc_start: 0.8081 (mt) cc_final: 0.6194 (tp) REVERT: H 242 LEU cc_start: 0.7547 (tp) cc_final: 0.7245 (tp) REVERT: H 248 LEU cc_start: 0.6848 (mt) cc_final: 0.6038 (mp) REVERT: H 332 MET cc_start: 0.7472 (mmm) cc_final: 0.6914 (mmm) REVERT: H 391 ILE cc_start: 0.9095 (mt) cc_final: 0.8774 (mm) REVERT: I 22 GLU cc_start: 0.5877 (tt0) cc_final: 0.5637 (tt0) REVERT: I 119 LEU cc_start: 0.7008 (tp) cc_final: 0.6655 (mt) REVERT: I 120 ASP cc_start: 0.5264 (t70) cc_final: 0.4414 (t0) REVERT: I 122 ILE cc_start: 0.9052 (mt) cc_final: 0.8750 (mt) REVERT: I 132 LEU cc_start: 0.7904 (tp) cc_final: 0.7456 (tp) REVERT: I 181 VAL cc_start: 0.7900 (m) cc_final: 0.7605 (p) REVERT: I 186 ASN cc_start: 0.8025 (m-40) cc_final: 0.7684 (t0) REVERT: I 212 ILE cc_start: 0.8375 (mt) cc_final: 0.8160 (mt) REVERT: I 224 TYR cc_start: 0.7424 (m-80) cc_final: 0.7076 (m-80) REVERT: I 286 LEU cc_start: 0.8676 (mt) cc_final: 0.8322 (mt) REVERT: I 378 LEU cc_start: 0.8802 (mt) cc_final: 0.8528 (mp) REVERT: I 395 PHE cc_start: 0.7750 (t80) cc_final: 0.7546 (t80) REVERT: J 14 ASN cc_start: 0.8643 (m-40) cc_final: 0.7925 (t0) REVERT: J 62 VAL cc_start: 0.8153 (t) cc_final: 0.7877 (p) REVERT: J 72 PRO cc_start: 0.8852 (Cg_exo) cc_final: 0.8307 (Cg_endo) REVERT: J 119 LEU cc_start: 0.9030 (tp) cc_final: 0.8662 (tp) REVERT: J 122 VAL cc_start: 0.9090 (t) cc_final: 0.8835 (t) REVERT: J 209 LEU cc_start: 0.8014 (mt) cc_final: 0.7029 (mt) REVERT: J 266 HIS cc_start: 0.7185 (p-80) cc_final: 0.6720 (p-80) REVERT: J 295 MET cc_start: 0.8061 (mtm) cc_final: 0.7706 (ptm) REVERT: J 332 MET cc_start: 0.7396 (mmm) cc_final: 0.7069 (mmt) REVERT: J 376 THR cc_start: 0.8250 (m) cc_final: 0.7739 (p) REVERT: K 56 THR cc_start: 0.3881 (p) cc_final: 0.3277 (p) REVERT: K 75 ILE cc_start: 0.7526 (mm) cc_final: 0.6222 (mm) REVERT: K 207 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6145 (tm-30) REVERT: K 219 ILE cc_start: 0.8555 (mt) cc_final: 0.8300 (mm) REVERT: K 295 CYS cc_start: 0.9092 (m) cc_final: 0.8822 (m) REVERT: K 377 MET cc_start: 0.7921 (ttt) cc_final: 0.7691 (tmm) REVERT: K 378 LEU cc_start: 0.8591 (mt) cc_final: 0.8225 (mt) REVERT: L 14 ASN cc_start: 0.8519 (m-40) cc_final: 0.7581 (t0) REVERT: L 242 LEU cc_start: 0.7534 (tp) cc_final: 0.6840 (tp) REVERT: L 248 LEU cc_start: 0.7271 (mt) cc_final: 0.6933 (mp) REVERT: L 300 ASN cc_start: 0.6582 (m-40) cc_final: 0.6189 (m-40) REVERT: M 66 VAL cc_start: 0.7848 (t) cc_final: 0.7601 (t) REVERT: M 75 ILE cc_start: 0.8601 (mm) cc_final: 0.8297 (mm) REVERT: M 119 LEU cc_start: 0.8671 (tp) cc_final: 0.8399 (tp) REVERT: M 121 ARG cc_start: 0.8141 (mmp-170) cc_final: 0.7921 (mmp80) REVERT: M 132 LEU cc_start: 0.8045 (tp) cc_final: 0.7712 (tp) REVERT: M 167 LEU cc_start: 0.7610 (mt) cc_final: 0.7125 (mp) REVERT: M 212 ILE cc_start: 0.8100 (mt) cc_final: 0.6736 (mt) REVERT: M 316 CYS cc_start: 0.6300 (t) cc_final: 0.5982 (t) REVERT: M 357 TYR cc_start: 0.6117 (m-80) cc_final: 0.5548 (m-80) REVERT: M 384 ILE cc_start: 0.8451 (tt) cc_final: 0.6597 (tp) REVERT: M 391 LEU cc_start: 0.6667 (mt) cc_final: 0.6357 (mm) REVERT: N 4 ILE cc_start: 0.8967 (mt) cc_final: 0.8625 (mm) REVERT: N 14 ASN cc_start: 0.8019 (m-40) cc_final: 0.6916 (m-40) REVERT: N 24 ILE cc_start: 0.9436 (mm) cc_final: 0.9057 (mm) REVERT: N 220 THR cc_start: 0.6854 (p) cc_final: 0.6188 (p) REVERT: N 235 MET cc_start: 0.7425 (mtp) cc_final: 0.6748 (ttt) REVERT: N 244 PHE cc_start: 0.6849 (m-80) cc_final: 0.6648 (m-10) REVERT: N 301 MET cc_start: 0.7149 (mmp) cc_final: 0.6743 (mmm) REVERT: N 398 MET cc_start: 0.5945 (mtp) cc_final: 0.3968 (mtp) REVERT: N 405 LEU cc_start: 0.8138 (tp) cc_final: 0.7853 (tp) REVERT: O 6 SER cc_start: 0.7974 (t) cc_final: 0.7599 (p) REVERT: O 14 VAL cc_start: 0.8997 (t) cc_final: 0.8737 (p) REVERT: O 23 LEU cc_start: 0.9077 (tp) cc_final: 0.8625 (mm) REVERT: O 60 LYS cc_start: 0.8066 (mmtt) cc_final: 0.6424 (mmmt) REVERT: O 75 ILE cc_start: 0.8596 (mm) cc_final: 0.8337 (mm) REVERT: O 138 PHE cc_start: 0.7242 (m-80) cc_final: 0.6941 (m-80) REVERT: O 171 ILE cc_start: 0.7881 (mm) cc_final: 0.7637 (mm) REVERT: O 303 VAL cc_start: 0.8882 (t) cc_final: 0.8672 (p) REVERT: O 343 PHE cc_start: 0.6626 (m-80) cc_final: 0.6199 (m-80) REVERT: O 384 ILE cc_start: 0.8385 (tt) cc_final: 0.7344 (tp) REVERT: O 391 LEU cc_start: 0.7074 (mt) cc_final: 0.6668 (mm) REVERT: P 4 ILE cc_start: 0.8875 (mt) cc_final: 0.8660 (mm) REVERT: P 14 ASN cc_start: 0.8077 (m-40) cc_final: 0.7407 (m-40) REVERT: P 24 ILE cc_start: 0.9604 (mm) cc_final: 0.9076 (mm) REVERT: P 107 HIS cc_start: 0.7083 (t70) cc_final: 0.6769 (t-90) REVERT: P 192 HIS cc_start: 0.7519 (t-170) cc_final: 0.6331 (t-90) REVERT: P 288 VAL cc_start: 0.9004 (t) cc_final: 0.8460 (t) REVERT: P 301 MET cc_start: 0.6161 (mmp) cc_final: 0.5194 (mmp) REVERT: P 306 ASP cc_start: 0.4149 (t0) cc_final: 0.2553 (t70) REVERT: P 377 PHE cc_start: 0.6493 (t80) cc_final: 0.5607 (t80) REVERT: P 384 ILE cc_start: 0.8083 (mt) cc_final: 0.7659 (tp) REVERT: P 391 ILE cc_start: 0.8111 (mt) cc_final: 0.7880 (mt) REVERT: Q 5 ILE cc_start: 0.7809 (mt) cc_final: 0.7375 (mm) REVERT: Q 6 SER cc_start: 0.7647 (t) cc_final: 0.7397 (p) REVERT: Q 23 LEU cc_start: 0.8985 (tp) cc_final: 0.8707 (mm) REVERT: Q 66 VAL cc_start: 0.7655 (t) cc_final: 0.7098 (t) REVERT: Q 132 LEU cc_start: 0.7764 (tp) cc_final: 0.7228 (tt) REVERT: Q 167 LEU cc_start: 0.7531 (mt) cc_final: 0.7192 (mt) REVERT: Q 302 MET cc_start: 0.7850 (mmt) cc_final: 0.6973 (mpp) REVERT: Q 303 VAL cc_start: 0.9070 (t) cc_final: 0.8550 (p) REVERT: Q 355 ILE cc_start: 0.9091 (mt) cc_final: 0.8807 (tp) REVERT: Q 384 ILE cc_start: 0.8724 (tt) cc_final: 0.6861 (tp) REVERT: Q 391 LEU cc_start: 0.6330 (mt) cc_final: 0.5818 (mt) REVERT: R 24 ILE cc_start: 0.9570 (mm) cc_final: 0.8587 (tp) REVERT: R 86 ILE cc_start: 0.7893 (tt) cc_final: 0.7658 (tt) REVERT: R 103 TRP cc_start: 0.5760 (t60) cc_final: 0.4529 (t60) REVERT: R 199 ASP cc_start: 0.7082 (m-30) cc_final: 0.6513 (m-30) REVERT: R 221 THR cc_start: 0.5261 (p) cc_final: 0.4692 (p) REVERT: R 378 ILE cc_start: 0.7390 (mt) cc_final: 0.6857 (mt) REVERT: R 380 ASN cc_start: 0.6343 (t0) cc_final: 0.6136 (t0) outliers start: 18 outliers final: 2 residues processed: 2730 average time/residue: 0.6630 time to fit residues: 2940.6461 Evaluate side-chains 1432 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1427 time to evaluate : 5.234 ------------------------------------------------------------------------------- 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: 7.9990 chunk 573 optimal weight: 5.9990 chunk 317 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 386 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 592 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 441 optimal weight: 7.9990 chunk 686 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN B 102 ASN B 133 GLN B 136 GLN B 192 HIS B 331 GLN C 11 GLN C 28 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 15 GLN D 102 ASN D 133 GLN D 192 HIS D 349 ASN E 11 GLN E 28 HIS E 31 GLN ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN F 101 ASN F 102 ASN F 133 GLN F 206 ASN F 281 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 GLN H 37 HIS H 102 ASN H 133 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 85 GLN I 309 HIS J 6 HIS J 37 HIS J 133 GLN J 192 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 433 GLN K 11 GLN K 31 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS L 15 GLN L 37 HIS L 102 ASN L 133 GLN L 192 HIS L 331 GLN M 15 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN N 229 HIS N 281 GLN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 35 GLN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN P 28 HIS ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN ** P 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 331 GLN Q 15 GLN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 ASN R 15 GLN R 101 ASN R 102 ASN R 192 HIS R 339 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 62298 Z= 0.254 Angle : 0.723 8.706 84645 Z= 0.390 Chirality : 0.048 0.277 9216 Planarity : 0.006 0.115 11043 Dihedral : 12.515 174.406 8784 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.15 % Allowed : 2.67 % Favored : 97.17 % 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: 0.71 (0.09), residues: 7632 helix: 0.66 (0.08), residues: 3600 sheet: 1.69 (0.14), residues: 1134 loop : -0.14 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP M 388 HIS 0.016 0.002 HIS H 28 PHE 0.032 0.002 PHE H 92 TYR 0.025 0.002 TYR Q 224 ARG 0.010 0.001 ARG D 401 *********************** 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 2005 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1995 time to evaluate : 5.178 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: A 16 ILE cc_start: 0.9214 (mt) cc_final: 0.8955 (mt) REVERT: A 66 VAL cc_start: 0.7751 (t) cc_final: 0.7509 (t) REVERT: A 209 ILE cc_start: 0.9098 (mp) cc_final: 0.7208 (mp) REVERT: A 210 TYR cc_start: 0.8634 (m-80) cc_final: 0.7956 (m-80) REVERT: A 221 ARG cc_start: 0.7329 (mmt180) cc_final: 0.6825 (mmt180) REVERT: A 344 VAL cc_start: 0.8324 (t) cc_final: 0.7999 (t) REVERT: A 376 CYS cc_start: 0.8967 (t) cc_final: 0.8624 (p) REVERT: A 377 MET cc_start: 0.8919 (tmm) cc_final: 0.8324 (tmm) REVERT: A 378 LEU cc_start: 0.8207 (mt) cc_final: 0.7592 (mp) REVERT: A 384 ILE cc_start: 0.8289 (tt) cc_final: 0.7979 (tp) REVERT: B 3 GLU cc_start: 0.7182 (mp0) cc_final: 0.6967 (mp0) REVERT: B 5 VAL cc_start: 0.8863 (t) cc_final: 0.8622 (t) REVERT: B 6 HIS cc_start: 0.7845 (t70) cc_final: 0.7485 (t70) REVERT: B 14 ASN cc_start: 0.8941 (m-40) cc_final: 0.8645 (m-40) REVERT: B 75 MET cc_start: 0.8653 (mmp) cc_final: 0.8423 (mmp) REVERT: B 115 VAL cc_start: 0.8722 (t) cc_final: 0.7924 (t) REVERT: B 120 ASP cc_start: 0.6908 (t0) cc_final: 0.6504 (t70) REVERT: B 124 LYS cc_start: 0.6871 (pptt) cc_final: 0.6201 (ttpp) REVERT: B 230 LEU cc_start: 0.9262 (mt) cc_final: 0.9026 (tt) REVERT: B 254 LYS cc_start: 0.7357 (mtpp) cc_final: 0.7050 (mmtm) REVERT: B 268 PHE cc_start: 0.8211 (m-80) cc_final: 0.7938 (m-10) REVERT: B 269 MET cc_start: 0.7817 (tpp) cc_final: 0.7578 (tpp) REVERT: B 291 LEU cc_start: 0.9152 (mm) cc_final: 0.8684 (tp) REVERT: B 356 CYS cc_start: 0.8145 (p) cc_final: 0.7581 (t) REVERT: B 372 LYS cc_start: 0.8867 (mmpt) cc_final: 0.8581 (tttt) REVERT: B 389 LYS cc_start: 0.9156 (mtmt) cc_final: 0.8744 (ttmm) REVERT: B 417 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7148 (tt0) REVERT: C 77 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7845 (mt-10) REVERT: C 118 VAL cc_start: 0.9363 (t) cc_final: 0.9079 (t) REVERT: C 132 LEU cc_start: 0.8177 (tp) cc_final: 0.7441 (mp) REVERT: C 217 LEU cc_start: 0.8339 (mt) cc_final: 0.8113 (mt) REVERT: C 221 ARG cc_start: 0.7752 (mpt90) cc_final: 0.6666 (mmt180) REVERT: C 268 PRO cc_start: 0.7328 (Cg_endo) cc_final: 0.7113 (Cg_exo) REVERT: C 291 ILE cc_start: 0.8829 (mt) cc_final: 0.8584 (tt) REVERT: C 318 LEU cc_start: 0.7885 (mt) cc_final: 0.7662 (mp) REVERT: C 377 MET cc_start: 0.8378 (tmm) cc_final: 0.7854 (tmm) REVERT: D 14 ASN cc_start: 0.8809 (m-40) cc_final: 0.8067 (m-40) REVERT: D 115 VAL cc_start: 0.8850 (t) cc_final: 0.8282 (t) REVERT: D 132 LEU cc_start: 0.8209 (mt) cc_final: 0.7889 (mt) REVERT: D 210 TYR cc_start: 0.6526 (m-80) cc_final: 0.6203 (m-80) REVERT: D 219 LEU cc_start: 0.8588 (tp) cc_final: 0.8062 (tp) REVERT: D 269 MET cc_start: 0.8267 (tpp) cc_final: 0.8032 (tpp) REVERT: D 286 LEU cc_start: 0.7851 (mt) cc_final: 0.7497 (mt) REVERT: D 288 VAL cc_start: 0.8862 (t) cc_final: 0.8634 (t) REVERT: D 291 LEU cc_start: 0.8877 (mm) cc_final: 0.8436 (mm) REVERT: D 301 MET cc_start: 0.6603 (mmm) cc_final: 0.6323 (mmm) REVERT: D 323 MET cc_start: 0.6913 (mtm) cc_final: 0.6692 (mpp) REVERT: D 325 MET cc_start: 0.6398 (mmm) cc_final: 0.5647 (mmt) REVERT: D 335 VAL cc_start: 0.6268 (t) cc_final: 0.5990 (t) REVERT: D 422 GLU cc_start: 0.7737 (tp30) cc_final: 0.7325 (tp30) REVERT: D 432 TYR cc_start: 0.6845 (m-80) cc_final: 0.5976 (m-10) REVERT: E 5 ILE cc_start: 0.7145 (mm) cc_final: 0.6917 (mm) REVERT: E 14 VAL cc_start: 0.8566 (p) cc_final: 0.8090 (p) REVERT: E 80 THR cc_start: 0.7764 (p) cc_final: 0.7558 (t) REVERT: E 116 ASP cc_start: 0.7527 (p0) cc_final: 0.7293 (p0) REVERT: E 199 ASP cc_start: 0.6989 (m-30) cc_final: 0.6719 (m-30) REVERT: E 209 ILE cc_start: 0.9310 (mt) cc_final: 0.8992 (mt) REVERT: E 352 LYS cc_start: 0.8004 (tttp) cc_final: 0.7112 (ttpt) REVERT: E 377 MET cc_start: 0.8219 (tmm) cc_final: 0.7577 (tmm) REVERT: E 378 LEU cc_start: 0.8199 (mt) cc_final: 0.7360 (mp) REVERT: E 380 ASN cc_start: 0.7689 (t0) cc_final: 0.7288 (t0) REVERT: E 384 ILE cc_start: 0.8787 (tp) cc_final: 0.8432 (tp) REVERT: E 422 ARG cc_start: 0.6328 (ttp80) cc_final: 0.5911 (ttp80) REVERT: F 14 ASN cc_start: 0.8177 (m-40) cc_final: 0.7455 (m-40) REVERT: F 24 ILE cc_start: 0.9103 (mm) cc_final: 0.8639 (mm) REVERT: F 115 VAL cc_start: 0.9523 (t) cc_final: 0.8719 (t) REVERT: F 127 GLU cc_start: 0.7684 (pp20) cc_final: 0.6760 (pp20) REVERT: F 235 MET cc_start: 0.7926 (mtt) cc_final: 0.7399 (ttm) REVERT: F 248 LEU cc_start: 0.7450 (mp) cc_final: 0.6873 (mp) REVERT: F 259 MET cc_start: 0.6220 (mmm) cc_final: 0.5946 (mmm) REVERT: F 268 PHE cc_start: 0.7502 (m-80) cc_final: 0.6718 (m-80) REVERT: F 269 MET cc_start: 0.6749 (tpp) cc_final: 0.6460 (tpp) REVERT: F 291 LEU cc_start: 0.8951 (mm) cc_final: 0.8596 (tp) REVERT: F 327 GLU cc_start: 0.6760 (pt0) cc_final: 0.6206 (pt0) REVERT: F 328 VAL cc_start: 0.8928 (t) cc_final: 0.8590 (p) REVERT: F 329 ASP cc_start: 0.7348 (t0) cc_final: 0.6406 (t0) REVERT: F 332 MET cc_start: 0.7718 (ttp) cc_final: 0.7509 (tmm) REVERT: F 351 VAL cc_start: 0.7715 (t) cc_final: 0.7274 (t) REVERT: F 395 PHE cc_start: 0.7582 (t80) cc_final: 0.6310 (t80) REVERT: F 398 MET cc_start: 0.6697 (mtm) cc_final: 0.4850 (mtt) REVERT: F 422 GLU cc_start: 0.7483 (tp30) cc_final: 0.6555 (tp30) REVERT: G 25 CYS cc_start: 0.7126 (m) cc_final: 0.6858 (m) REVERT: G 66 VAL cc_start: 0.6693 (t) cc_final: 0.6288 (t) REVERT: G 113 GLU cc_start: 0.7555 (pp20) cc_final: 0.7082 (pp20) REVERT: G 129 CYS cc_start: 0.7815 (m) cc_final: 0.7547 (t) REVERT: G 169 PHE cc_start: 0.6008 (m-80) cc_final: 0.5475 (m-80) REVERT: G 181 VAL cc_start: 0.7011 (m) cc_final: 0.6580 (m) REVERT: G 191 THR cc_start: 0.6536 (p) cc_final: 0.6016 (p) REVERT: G 252 LEU cc_start: 0.6916 (pp) cc_final: 0.6197 (pp) REVERT: G 291 ILE cc_start: 0.9101 (mt) cc_final: 0.7942 (tt) REVERT: G 315 CYS cc_start: 0.7464 (t) cc_final: 0.6562 (t) REVERT: G 317 LEU cc_start: 0.7477 (mt) cc_final: 0.7133 (mt) REVERT: H 14 ASN cc_start: 0.8513 (m-40) cc_final: 0.7740 (t0) REVERT: H 62 VAL cc_start: 0.8045 (m) cc_final: 0.7551 (m) REVERT: H 124 LYS cc_start: 0.8974 (pptt) cc_final: 0.8714 (tttp) REVERT: H 209 LEU cc_start: 0.8332 (mt) cc_final: 0.7918 (mt) REVERT: H 259 MET cc_start: 0.7231 (mmm) cc_final: 0.6845 (mmm) REVERT: H 267 PHE cc_start: 0.6906 (m-80) cc_final: 0.6555 (m-10) REVERT: H 283 TYR cc_start: 0.7322 (m-80) cc_final: 0.7079 (m-10) REVERT: H 332 MET cc_start: 0.7177 (mmm) cc_final: 0.6536 (mmm) REVERT: H 384 ILE cc_start: 0.8414 (mt) cc_final: 0.8205 (mt) REVERT: I 24 TYR cc_start: 0.8104 (m-80) cc_final: 0.7618 (m-80) REVERT: I 36 MET cc_start: 0.2545 (tmm) cc_final: 0.2027 (tmm) REVERT: I 118 VAL cc_start: 0.8809 (t) cc_final: 0.8472 (t) REVERT: I 122 ILE cc_start: 0.8619 (mt) cc_final: 0.8409 (mt) REVERT: I 181 VAL cc_start: 0.7573 (m) cc_final: 0.7151 (p) REVERT: I 186 ASN cc_start: 0.7685 (m-40) cc_final: 0.7421 (t0) REVERT: I 191 THR cc_start: 0.7014 (p) cc_final: 0.6489 (p) REVERT: I 237 SER cc_start: 0.7614 (p) cc_final: 0.7361 (m) REVERT: I 346 TRP cc_start: 0.5914 (m-10) cc_final: 0.5475 (m-10) REVERT: I 347 CYS cc_start: 0.7656 (t) cc_final: 0.7311 (t) REVERT: I 417 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6090 (tt0) REVERT: J 14 ASN cc_start: 0.8229 (m-40) cc_final: 0.7872 (t0) REVERT: J 69 ASP cc_start: 0.6598 (t0) cc_final: 0.6134 (t70) REVERT: J 120 ASP cc_start: 0.7061 (t0) cc_final: 0.6751 (t70) REVERT: J 227 LEU cc_start: 0.9342 (mt) cc_final: 0.8474 (mp) REVERT: J 267 PHE cc_start: 0.7409 (m-80) cc_final: 0.6836 (m-80) REVERT: J 305 CYS cc_start: 0.5648 (t) cc_final: 0.5303 (t) REVERT: J 315 VAL cc_start: 0.7899 (t) cc_final: 0.7688 (t) REVERT: J 376 THR cc_start: 0.8520 (m) cc_final: 0.8137 (p) REVERT: K 7 ILE cc_start: 0.8714 (mm) cc_final: 0.8325 (mm) REVERT: K 114 ILE cc_start: 0.8336 (mm) cc_final: 0.8011 (mm) REVERT: K 122 ILE cc_start: 0.8652 (mt) cc_final: 0.7980 (mt) REVERT: K 125 LEU cc_start: 0.9329 (mm) cc_final: 0.9019 (mm) REVERT: K 286 LEU cc_start: 0.8218 (mt) cc_final: 0.7886 (mp) REVERT: K 291 ILE cc_start: 0.8896 (mt) cc_final: 0.7921 (tt) REVERT: K 334 THR cc_start: 0.8072 (m) cc_final: 0.7750 (p) REVERT: K 335 ILE cc_start: 0.7256 (mm) cc_final: 0.6837 (mm) REVERT: K 377 MET cc_start: 0.7094 (ttt) cc_final: 0.6683 (tmm) REVERT: K 435 VAL cc_start: 0.8279 (t) cc_final: 0.7741 (t) REVERT: L 14 ASN cc_start: 0.8524 (m-40) cc_final: 0.7527 (t0) REVERT: L 19 LYS cc_start: 0.8911 (mmpt) cc_final: 0.8696 (mmmm) REVERT: L 21 TRP cc_start: 0.7083 (m100) cc_final: 0.6546 (m100) REVERT: L 191 VAL cc_start: 0.8718 (t) cc_final: 0.8112 (p) REVERT: L 267 PHE cc_start: 0.7007 (m-80) cc_final: 0.6208 (m-10) REVERT: L 269 MET cc_start: 0.7084 (mtm) cc_final: 0.6650 (mtt) REVERT: L 275 LEU cc_start: 0.7698 (pt) cc_final: 0.7478 (pt) REVERT: M 21 TRP cc_start: 0.7809 (m100) cc_final: 0.7548 (m100) REVERT: M 25 CYS cc_start: 0.7986 (t) cc_final: 0.7146 (t) REVERT: M 75 ILE cc_start: 0.8449 (mm) cc_final: 0.7920 (tp) REVERT: M 122 ILE cc_start: 0.8894 (mt) cc_final: 0.8575 (mt) REVERT: M 132 LEU cc_start: 0.7004 (tp) cc_final: 0.6729 (tp) REVERT: M 167 LEU cc_start: 0.6914 (mt) cc_final: 0.6175 (mt) REVERT: M 334 THR cc_start: 0.7981 (m) cc_final: 0.7680 (p) REVERT: M 431 ASP cc_start: 0.7557 (m-30) cc_final: 0.7282 (m-30) REVERT: N 24 ILE cc_start: 0.9204 (mm) cc_final: 0.8979 (mm) REVERT: N 49 ILE cc_start: 0.7867 (tp) cc_final: 0.7646 (tp) REVERT: N 53 TYR cc_start: 0.7053 (m-80) cc_final: 0.6772 (m-10) REVERT: N 119 LEU cc_start: 0.8108 (tp) cc_final: 0.5590 (tp) REVERT: N 123 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7544 (mtt-85) REVERT: N 124 LYS cc_start: 0.9034 (pptt) cc_final: 0.8687 (pptt) REVERT: N 156 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7910 (mmtm) REVERT: N 202 TYR cc_start: 0.6688 (m-80) cc_final: 0.6175 (m-80) REVERT: N 227 LEU cc_start: 0.8937 (mt) cc_final: 0.8734 (mt) REVERT: N 244 PHE cc_start: 0.6802 (m-80) cc_final: 0.6428 (m-80) REVERT: N 268 PHE cc_start: 0.5832 (m-80) cc_final: 0.5505 (m-80) REVERT: N 300 ASN cc_start: 0.7960 (m-40) cc_final: 0.7505 (t0) REVERT: N 332 MET cc_start: 0.6283 (mmt) cc_final: 0.6013 (mmt) REVERT: N 398 MET cc_start: 0.6141 (mtp) cc_final: 0.5350 (mtt) REVERT: N 428 LEU cc_start: 0.8472 (mt) cc_final: 0.8219 (mp) REVERT: O 6 SER cc_start: 0.8147 (t) cc_final: 0.7685 (t) REVERT: O 23 LEU cc_start: 0.8654 (tp) cc_final: 0.8045 (tt) REVERT: O 28 HIS cc_start: 0.6332 (m-70) cc_final: 0.5383 (m-70) REVERT: O 138 PHE cc_start: 0.6935 (m-80) cc_final: 0.6715 (m-80) REVERT: O 154 MET cc_start: 0.7277 (ttp) cc_final: 0.7017 (ppp) REVERT: O 172 TYR cc_start: 0.6042 (t80) cc_final: 0.5837 (t80) REVERT: O 318 LEU cc_start: 0.8162 (mt) cc_final: 0.7956 (mt) REVERT: O 384 ILE cc_start: 0.8239 (tt) cc_final: 0.6873 (tp) REVERT: O 398 MET cc_start: 0.6239 (mmm) cc_final: 0.5961 (mmp) REVERT: P 5 VAL cc_start: 0.8919 (t) cc_final: 0.8705 (t) REVERT: P 14 ASN cc_start: 0.8075 (m-40) cc_final: 0.7530 (m-40) REVERT: P 24 ILE cc_start: 0.9292 (mm) cc_final: 0.9055 (mm) REVERT: P 154 ILE cc_start: 0.9146 (tp) cc_final: 0.8741 (tp) REVERT: P 266 HIS cc_start: 0.7981 (p-80) cc_final: 0.7778 (p-80) REVERT: P 268 PHE cc_start: 0.6151 (m-80) cc_final: 0.5861 (m-80) REVERT: P 300 ASN cc_start: 0.8698 (m110) cc_final: 0.8251 (t0) REVERT: P 306 ASP cc_start: 0.5323 (t0) cc_final: 0.4347 (t0) REVERT: P 325 MET cc_start: 0.7568 (mmm) cc_final: 0.6417 (mmm) REVERT: P 332 MET cc_start: 0.6313 (mmt) cc_final: 0.5661 (mmt) REVERT: P 377 PHE cc_start: 0.5491 (t80) cc_final: 0.5194 (t80) REVERT: P 382 THR cc_start: 0.8190 (p) cc_final: 0.7683 (t) REVERT: P 384 ILE cc_start: 0.8724 (mt) cc_final: 0.8320 (tp) REVERT: P 413 MET cc_start: 0.8352 (mmm) cc_final: 0.7719 (mmm) REVERT: P 428 LEU cc_start: 0.8462 (mt) cc_final: 0.8184 (mt) REVERT: Q 6 SER cc_start: 0.8103 (t) cc_final: 0.7884 (p) REVERT: Q 23 LEU cc_start: 0.8883 (tp) cc_final: 0.8012 (mm) REVERT: Q 24 TYR cc_start: 0.8039 (m-10) cc_final: 0.7594 (m-10) REVERT: Q 25 CYS cc_start: 0.7828 (m) cc_final: 0.7397 (m) REVERT: Q 120 ASP cc_start: 0.6445 (t70) cc_final: 0.5661 (t70) REVERT: Q 203 MET cc_start: 0.6512 (mtm) cc_final: 0.6302 (mtt) REVERT: Q 217 LEU cc_start: 0.8427 (mm) cc_final: 0.8108 (mm) REVERT: Q 302 MET cc_start: 0.7613 (mmt) cc_final: 0.7295 (mpp) REVERT: Q 318 LEU cc_start: 0.6232 (mt) cc_final: 0.5510 (mt) REVERT: Q 377 MET cc_start: 0.7407 (tmm) cc_final: 0.6979 (tmm) REVERT: Q 384 ILE cc_start: 0.7940 (tt) cc_final: 0.7358 (tp) REVERT: Q 431 ASP cc_start: 0.6744 (m-30) cc_final: 0.6481 (m-30) REVERT: R 5 VAL cc_start: 0.7984 (t) cc_final: 0.7721 (t) REVERT: R 6 HIS cc_start: 0.8899 (t-90) cc_final: 0.8067 (t-90) REVERT: R 14 ASN cc_start: 0.8399 (m110) cc_final: 0.8083 (m-40) REVERT: R 20 PHE cc_start: 0.8599 (t80) cc_final: 0.8327 (t80) REVERT: R 24 ILE cc_start: 0.9245 (mm) cc_final: 0.8798 (mm) REVERT: R 122 VAL cc_start: 0.9505 (t) cc_final: 0.9231 (t) REVERT: R 130 ASP cc_start: 0.6429 (m-30) cc_final: 0.6215 (m-30) REVERT: R 139 HIS cc_start: 0.7950 (p90) cc_final: 0.6877 (p90) REVERT: R 270 PRO cc_start: 0.8220 (Cg_endo) cc_final: 0.7811 (Cg_exo) REVERT: R 328 VAL cc_start: 0.7749 (m) cc_final: 0.7334 (p) REVERT: R 378 ILE cc_start: 0.7529 (mt) cc_final: 0.7216 (mt) REVERT: R 428 LEU cc_start: 0.8488 (mt) cc_final: 0.8154 (mt) outliers start: 10 outliers final: 3 residues processed: 2002 average time/residue: 0.6026 time to fit residues: 2014.8846 Evaluate side-chains 1332 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1329 time to evaluate : 5.266 ------------------------------------------------------------------------------- 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: 40.0000 chunk 571 optimal weight: 30.0000 chunk 467 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 687 optimal weight: 8.9990 chunk 742 optimal weight: 0.2980 chunk 612 optimal weight: 9.9990 chunk 682 optimal weight: 5.9990 chunk 234 optimal weight: 50.0000 chunk 551 optimal weight: 40.0000 overall best weight: 6.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN C 11 GLN ** C 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN D 193 GLN D 380 ASN E 11 GLN E 256 GLN F 15 GLN F 133 GLN F 136 GLN F 206 ASN F 281 GLN F 380 ASN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 HIS ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS H 337 ASN J 6 HIS J 193 GLN J 331 GLN J 339 ASN J 406 HIS J 424 ASN K 11 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN L 6 HIS M 11 GLN M 15 GLN M 91 GLN ** M 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 102 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 GLN N 300 ASN ** O 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN P 107 HIS P 193 GLN P 337 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 GLN R 133 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 62298 Z= 0.224 Angle : 0.649 11.533 84645 Z= 0.345 Chirality : 0.045 0.252 9216 Planarity : 0.005 0.070 11043 Dihedral : 12.039 179.869 8784 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 2.86 % Favored : 97.00 % 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: 0.73 (0.08), residues: 3627 sheet: 1.08 (0.14), residues: 1314 loop : 0.06 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP K 21 HIS 0.016 0.001 HIS N 6 PHE 0.049 0.002 PHE N 169 TYR 0.029 0.002 TYR A 24 ARG 0.016 0.001 ARG J 215 *********************** 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 1671 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1662 time to evaluate : 5.350 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: A 21 TRP cc_start: 0.8481 (m100) cc_final: 0.7796 (m100) REVERT: A 24 TYR cc_start: 0.7964 (m-80) cc_final: 0.7226 (m-80) REVERT: A 66 VAL cc_start: 0.7759 (t) cc_final: 0.7171 (t) REVERT: A 122 ILE cc_start: 0.8891 (mt) cc_final: 0.8648 (mt) REVERT: A 169 PHE cc_start: 0.6619 (m-80) cc_final: 0.6404 (m-80) REVERT: A 190 THR cc_start: 0.8375 (m) cc_final: 0.8115 (m) REVERT: A 203 MET cc_start: 0.7721 (mpp) cc_final: 0.7334 (tpp) REVERT: A 210 TYR cc_start: 0.8417 (m-80) cc_final: 0.8088 (m-80) REVERT: A 217 LEU cc_start: 0.8733 (tp) cc_final: 0.8291 (tp) REVERT: A 221 ARG cc_start: 0.7277 (mmt180) cc_final: 0.6807 (mmt180) REVERT: A 224 TYR cc_start: 0.7432 (m-10) cc_final: 0.5930 (m-80) REVERT: A 377 MET cc_start: 0.8877 (tmm) cc_final: 0.8423 (tmm) REVERT: A 378 LEU cc_start: 0.7785 (mt) cc_final: 0.7408 (mp) REVERT: A 418 PHE cc_start: 0.7656 (m-80) cc_final: 0.7367 (m-10) REVERT: B 41 ASP cc_start: 0.7404 (p0) cc_final: 0.6877 (m-30) REVERT: B 44 LEU cc_start: 0.8959 (mt) cc_final: 0.8751 (mt) REVERT: B 166 MET cc_start: 0.6093 (mmp) cc_final: 0.5520 (mmm) REVERT: B 177 VAL cc_start: 0.7822 (t) cc_final: 0.6819 (p) REVERT: B 235 MET cc_start: 0.8500 (mtt) cc_final: 0.7989 (ttt) REVERT: B 291 LEU cc_start: 0.9319 (mm) cc_final: 0.8777 (tp) REVERT: B 325 MET cc_start: 0.6908 (mmm) cc_final: 0.6343 (mmt) REVERT: B 326 LYS cc_start: 0.8159 (tptp) cc_final: 0.7388 (ttpt) REVERT: B 327 GLU cc_start: 0.7524 (tt0) cc_final: 0.6976 (tt0) REVERT: B 356 CYS cc_start: 0.8014 (p) cc_final: 0.6382 (t) REVERT: B 372 LYS cc_start: 0.9008 (mmpt) cc_final: 0.8707 (tttt) REVERT: C 118 VAL cc_start: 0.9301 (t) cc_final: 0.8837 (t) REVERT: C 209 ILE cc_start: 0.9611 (mp) cc_final: 0.8960 (tt) REVERT: C 377 MET cc_start: 0.8257 (tmm) cc_final: 0.7910 (tmm) REVERT: D 5 VAL cc_start: 0.8868 (t) cc_final: 0.8651 (t) REVERT: D 14 ASN cc_start: 0.8276 (m-40) cc_final: 0.7852 (m110) REVERT: D 19 LYS cc_start: 0.8134 (mmmt) cc_final: 0.7679 (tppt) REVERT: D 55 GLU cc_start: 0.6133 (tp30) cc_final: 0.5913 (tm-30) REVERT: D 149 MET cc_start: 0.6308 (ptt) cc_final: 0.6001 (ppp) REVERT: D 210 TYR cc_start: 0.6465 (m-80) cc_final: 0.6126 (m-80) REVERT: D 295 MET cc_start: 0.8521 (mmm) cc_final: 0.8233 (mmm) REVERT: D 325 MET cc_start: 0.6776 (mmm) cc_final: 0.6027 (mmt) REVERT: D 395 PHE cc_start: 0.7937 (t80) cc_final: 0.6446 (t80) REVERT: D 422 GLU cc_start: 0.7514 (tp30) cc_final: 0.6698 (tp30) REVERT: E 80 THR cc_start: 0.7919 (p) cc_final: 0.7707 (t) REVERT: E 120 ASP cc_start: 0.5567 (t70) cc_final: 0.5287 (t70) REVERT: E 209 ILE cc_start: 0.9325 (mt) cc_final: 0.9038 (mt) REVERT: E 292 THR cc_start: 0.8524 (p) cc_final: 0.8292 (p) REVERT: E 357 TYR cc_start: 0.7483 (m-80) cc_final: 0.7075 (m-80) REVERT: E 377 MET cc_start: 0.8259 (tmm) cc_final: 0.7826 (tmm) REVERT: E 378 LEU cc_start: 0.8359 (mt) cc_final: 0.7921 (mp) REVERT: E 380 ASN cc_start: 0.7528 (t0) cc_final: 0.7124 (t0) REVERT: E 384 ILE cc_start: 0.8461 (tp) cc_final: 0.7284 (tp) REVERT: E 422 ARG cc_start: 0.6132 (ttp80) cc_final: 0.5588 (ttp80) REVERT: E 425 MET cc_start: 0.8481 (tpt) cc_final: 0.7321 (tpp) REVERT: F 14 ASN cc_start: 0.7886 (m-40) cc_final: 0.7501 (m-40) REVERT: F 24 ILE cc_start: 0.8942 (mm) cc_final: 0.7995 (mm) REVERT: F 53 TYR cc_start: 0.5104 (m-80) cc_final: 0.4875 (m-80) REVERT: F 75 MET cc_start: 0.8452 (mmm) cc_final: 0.8250 (mmp) REVERT: F 115 VAL cc_start: 0.8973 (t) cc_final: 0.8578 (t) REVERT: F 116 ASP cc_start: 0.8317 (p0) cc_final: 0.8030 (p0) REVERT: F 120 ASP cc_start: 0.6635 (t70) cc_final: 0.6320 (t70) REVERT: F 235 MET cc_start: 0.7975 (mtt) cc_final: 0.7518 (ttm) REVERT: F 286 LEU cc_start: 0.7795 (mt) cc_final: 0.7581 (mt) REVERT: F 288 VAL cc_start: 0.9185 (t) cc_final: 0.8793 (t) REVERT: F 299 LYS cc_start: 0.8408 (tmmt) cc_final: 0.8207 (tmmt) REVERT: F 327 GLU cc_start: 0.7188 (pt0) cc_final: 0.5998 (pt0) REVERT: F 328 VAL cc_start: 0.8824 (t) cc_final: 0.8151 (p) REVERT: F 373 MET cc_start: 0.8367 (pmm) cc_final: 0.7865 (pmm) REVERT: F 425 MET cc_start: 0.5908 (tmm) cc_final: 0.5675 (tmm) REVERT: G 113 GLU cc_start: 0.7170 (pp20) cc_final: 0.6929 (pp20) REVERT: G 169 PHE cc_start: 0.5630 (m-80) cc_final: 0.5425 (m-10) REVERT: G 171 ILE cc_start: 0.8188 (mm) cc_final: 0.7960 (mm) REVERT: G 209 ILE cc_start: 0.9413 (mp) cc_final: 0.8793 (tt) REVERT: G 254 GLU cc_start: 0.7048 (mp0) cc_final: 0.6150 (mm-30) REVERT: G 288 VAL cc_start: 0.7433 (t) cc_final: 0.7161 (p) REVERT: G 291 ILE cc_start: 0.8967 (mt) cc_final: 0.8749 (mt) REVERT: G 295 CYS cc_start: 0.8991 (m) cc_final: 0.8752 (m) REVERT: G 305 CYS cc_start: 0.7749 (m) cc_final: 0.7462 (m) REVERT: G 315 CYS cc_start: 0.7877 (t) cc_final: 0.7094 (t) REVERT: G 418 PHE cc_start: 0.7419 (m-10) cc_final: 0.7155 (m-80) REVERT: H 14 ASN cc_start: 0.8477 (m-40) cc_final: 0.7593 (t0) REVERT: H 62 VAL cc_start: 0.6909 (m) cc_final: 0.6649 (m) REVERT: H 124 LYS cc_start: 0.8574 (pptt) cc_final: 0.7634 (tttp) REVERT: H 262 PHE cc_start: 0.6098 (t80) cc_final: 0.5851 (t80) REVERT: H 283 TYR cc_start: 0.7238 (m-80) cc_final: 0.6956 (m-80) REVERT: H 292 THR cc_start: 0.8303 (p) cc_final: 0.7564 (p) REVERT: H 295 MET cc_start: 0.8218 (ppp) cc_final: 0.7986 (ppp) REVERT: H 297 ASP cc_start: 0.7231 (t0) cc_final: 0.6619 (t0) REVERT: H 332 MET cc_start: 0.6684 (mmm) cc_final: 0.6438 (mmm) REVERT: H 425 MET cc_start: 0.7279 (tpt) cc_final: 0.7076 (mmt) REVERT: H 428 LEU cc_start: 0.7880 (mt) cc_final: 0.7255 (mt) REVERT: I 26 LEU cc_start: 0.8820 (mt) cc_final: 0.8552 (mt) REVERT: I 237 SER cc_start: 0.7410 (p) cc_final: 0.6931 (m) REVERT: I 280 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8351 (mmmt) REVERT: I 291 ILE cc_start: 0.8597 (mm) cc_final: 0.7939 (tt) REVERT: I 378 LEU cc_start: 0.8547 (mp) cc_final: 0.8095 (mp) REVERT: J 3 GLU cc_start: 0.6715 (mp0) cc_final: 0.5771 (mp0) REVERT: J 166 MET cc_start: 0.2944 (mtm) cc_final: 0.2276 (mtm) REVERT: J 203 CYS cc_start: 0.7967 (m) cc_final: 0.7504 (m) REVERT: J 227 LEU cc_start: 0.9237 (mt) cc_final: 0.9020 (mp) REVERT: J 230 LEU cc_start: 0.8404 (tp) cc_final: 0.8138 (tp) REVERT: J 235 MET cc_start: 0.8467 (mtp) cc_final: 0.8052 (mtt) REVERT: J 241 CYS cc_start: 0.8275 (t) cc_final: 0.8060 (t) REVERT: J 286 LEU cc_start: 0.7949 (mt) cc_final: 0.7687 (mt) REVERT: J 297 ASP cc_start: 0.7551 (t0) cc_final: 0.7322 (t0) REVERT: J 305 CYS cc_start: 0.6151 (t) cc_final: 0.5929 (t) REVERT: J 376 THR cc_start: 0.8617 (m) cc_final: 0.8239 (p) REVERT: J 395 PHE cc_start: 0.8130 (t80) cc_final: 0.7380 (t80) REVERT: K 113 GLU cc_start: 0.6620 (pp20) cc_final: 0.6387 (pp20) REVERT: K 114 ILE cc_start: 0.8060 (mm) cc_final: 0.7591 (mm) REVERT: K 121 ARG cc_start: 0.8676 (mmp80) cc_final: 0.8459 (mmt-90) REVERT: K 209 ILE cc_start: 0.8875 (mp) cc_final: 0.8351 (mp) REVERT: K 286 LEU cc_start: 0.7915 (mt) cc_final: 0.7391 (mp) REVERT: K 291 ILE cc_start: 0.8997 (mt) cc_final: 0.8318 (tt) REVERT: K 377 MET cc_start: 0.7306 (ttt) cc_final: 0.6857 (tmm) REVERT: L 14 ASN cc_start: 0.8820 (m-40) cc_final: 0.6576 (t0) REVERT: L 21 TRP cc_start: 0.7121 (m100) cc_final: 0.6703 (m100) REVERT: L 267 PHE cc_start: 0.7340 (m-80) cc_final: 0.6551 (m-10) REVERT: L 269 MET cc_start: 0.7567 (mtm) cc_final: 0.6758 (mtm) REVERT: L 291 LEU cc_start: 0.8419 (mt) cc_final: 0.7192 (mp) REVERT: L 332 MET cc_start: 0.7199 (mmm) cc_final: 0.6899 (mmt) REVERT: M 21 TRP cc_start: 0.8014 (m100) cc_final: 0.7735 (m100) REVERT: M 75 ILE cc_start: 0.8362 (mm) cc_final: 0.7944 (tp) REVERT: M 186 ASN cc_start: 0.7220 (m-40) cc_final: 0.6823 (m-40) REVERT: M 334 THR cc_start: 0.7836 (m) cc_final: 0.7362 (p) REVERT: M 378 LEU cc_start: 0.8240 (mp) cc_final: 0.8000 (mp) REVERT: M 384 ILE cc_start: 0.8239 (tp) cc_final: 0.7915 (tp) REVERT: N 50 ASN cc_start: 0.8797 (p0) cc_final: 0.8470 (p0) REVERT: N 119 LEU cc_start: 0.7969 (tp) cc_final: 0.6090 (tp) REVERT: N 231 VAL cc_start: 0.8842 (t) cc_final: 0.8235 (t) REVERT: N 259 MET cc_start: 0.8039 (mmp) cc_final: 0.7681 (mmm) REVERT: N 268 PHE cc_start: 0.7153 (m-80) cc_final: 0.6046 (m-80) REVERT: N 278 ARG cc_start: 0.5398 (pmt-80) cc_final: 0.5153 (pmt-80) REVERT: N 391 ILE cc_start: 0.8345 (mm) cc_final: 0.8132 (mm) REVERT: N 432 TYR cc_start: 0.6282 (m-10) cc_final: 0.5977 (m-80) REVERT: O 6 SER cc_start: 0.8426 (t) cc_final: 0.8173 (t) REVERT: O 154 MET cc_start: 0.7315 (ttp) cc_final: 0.6660 (ppp) REVERT: O 191 THR cc_start: 0.8206 (m) cc_final: 0.7922 (p) REVERT: O 209 ILE cc_start: 0.9159 (mp) cc_final: 0.8893 (mp) REVERT: O 230 LEU cc_start: 0.8749 (tp) cc_final: 0.8368 (mm) REVERT: O 355 ILE cc_start: 0.9379 (mm) cc_final: 0.9178 (mm) REVERT: O 384 ILE cc_start: 0.8354 (tt) cc_final: 0.7668 (tp) REVERT: O 425 MET cc_start: 0.8152 (mmp) cc_final: 0.6625 (mmm) REVERT: P 5 VAL cc_start: 0.8591 (t) cc_final: 0.8335 (t) REVERT: P 6 HIS cc_start: 0.7077 (t-90) cc_final: 0.6807 (t-90) REVERT: P 14 ASN cc_start: 0.7997 (m-40) cc_final: 0.7558 (m-40) REVERT: P 75 MET cc_start: 0.8878 (mmp) cc_final: 0.8303 (mmp) REVERT: P 118 VAL cc_start: 0.7678 (t) cc_final: 0.7350 (t) REVERT: P 202 TYR cc_start: 0.6711 (m-80) cc_final: 0.6161 (m-10) REVERT: P 224 TYR cc_start: 0.7669 (m-10) cc_final: 0.6828 (m-80) REVERT: P 235 MET cc_start: 0.8104 (mtp) cc_final: 0.7780 (mtp) REVERT: P 266 HIS cc_start: 0.8230 (p-80) cc_final: 0.7581 (p-80) REVERT: P 302 MET cc_start: 0.7207 (mtm) cc_final: 0.6651 (mtp) REVERT: P 325 MET cc_start: 0.7422 (mmm) cc_final: 0.6540 (mmm) REVERT: P 377 PHE cc_start: 0.5172 (t80) cc_final: 0.4782 (t80) REVERT: P 413 MET cc_start: 0.7848 (mmm) cc_final: 0.7496 (mmm) REVERT: Q 25 CYS cc_start: 0.8082 (m) cc_final: 0.7309 (m) REVERT: Q 191 THR cc_start: 0.8154 (p) cc_final: 0.7747 (p) REVERT: Q 209 ILE cc_start: 0.9137 (mp) cc_final: 0.8140 (mp) REVERT: Q 217 LEU cc_start: 0.8089 (mm) cc_final: 0.7781 (mm) REVERT: Q 271 THR cc_start: 0.6397 (p) cc_final: 0.5919 (t) REVERT: Q 318 LEU cc_start: 0.5836 (mt) cc_final: 0.5620 (mt) REVERT: Q 360 PRO cc_start: 0.8841 (Cg_exo) cc_final: 0.8488 (Cg_endo) REVERT: R 14 ASN cc_start: 0.7374 (m110) cc_final: 0.6810 (m-40) REVERT: R 20 PHE cc_start: 0.8672 (t80) cc_final: 0.8196 (t80) REVERT: R 24 ILE cc_start: 0.8856 (mm) cc_final: 0.8541 (mm) REVERT: R 231 VAL cc_start: 0.8967 (t) cc_final: 0.8704 (t) REVERT: R 295 MET cc_start: 0.8249 (ttt) cc_final: 0.7445 (tpp) REVERT: R 323 MET cc_start: 0.8743 (mpp) cc_final: 0.8183 (mpp) REVERT: R 425 MET cc_start: 0.8026 (tmm) cc_final: 0.7781 (tmm) outliers start: 9 outliers final: 6 residues processed: 1671 average time/residue: 0.5937 time to fit residues: 1665.5041 Evaluate side-chains 1205 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1199 time to evaluate : 5.204 ------------------------------------------------------------------------------- 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: 40.0000 chunk 517 optimal weight: 50.0000 chunk 356 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 328 optimal weight: 0.0010 chunk 461 optimal weight: 8.9990 chunk 690 optimal weight: 20.0000 chunk 730 optimal weight: 8.9990 chunk 360 optimal weight: 7.9990 chunk 654 optimal weight: 5.9990 chunk 196 optimal weight: 50.0000 overall best weight: 4.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 266 HIS C 128 GLN C 309 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN F 136 GLN F 192 HIS F 193 GLN ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 380 ASN G 301 GLN ** H 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 ASN J 6 HIS J 37 HIS ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 HIS ** L 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 HIS M 380 ASN N 15 GLN ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 GLN P 107 HIS P 294 GLN ** P 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 331 GLN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62298 Z= 0.193 Angle : 0.627 9.936 84645 Z= 0.328 Chirality : 0.045 0.299 9216 Planarity : 0.005 0.065 11043 Dihedral : 11.816 177.596 8784 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.09 % Allowed : 2.57 % Favored : 97.34 % 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: 0.81 (0.10), residues: 7632 helix: 0.77 (0.08), residues: 3582 sheet: 1.05 (0.14), residues: 1314 loop : 0.17 (0.13), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.003 TRP Q 388 HIS 0.013 0.001 HIS N 6 PHE 0.022 0.002 PHE L 169 TYR 0.031 0.002 TYR F 210 ARG 0.012 0.001 ARG F 390 *********************** 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 1580 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1574 time to evaluate : 5.222 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: A 21 TRP cc_start: 0.8497 (m100) cc_final: 0.8150 (m100) REVERT: A 22 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: A 60 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7967 (mmmt) REVERT: A 118 VAL cc_start: 0.9039 (t) cc_final: 0.8769 (p) REVERT: A 155 GLU cc_start: 0.8187 (pp20) cc_final: 0.7961 (pp20) REVERT: A 169 PHE cc_start: 0.6549 (m-80) cc_final: 0.6217 (m-80) REVERT: A 207 GLU cc_start: 0.7527 (mp0) cc_final: 0.6892 (mm-30) REVERT: A 210 TYR cc_start: 0.8648 (m-80) cc_final: 0.8214 (m-80) REVERT: A 217 LEU cc_start: 0.8720 (tp) cc_final: 0.8476 (tp) REVERT: A 224 TYR cc_start: 0.7345 (m-10) cc_final: 0.6410 (m-80) REVERT: A 378 LEU cc_start: 0.7851 (mt) cc_final: 0.7500 (mp) REVERT: A 384 ILE cc_start: 0.8353 (tp) cc_final: 0.7830 (tp) REVERT: A 429 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7078 (mm-30) REVERT: B 14 ASN cc_start: 0.8365 (m-40) cc_final: 0.8144 (m110) REVERT: B 41 ASP cc_start: 0.7217 (p0) cc_final: 0.6770 (m-30) REVERT: B 227 LEU cc_start: 0.9214 (mt) cc_final: 0.8792 (mt) REVERT: B 235 MET cc_start: 0.8669 (mtt) cc_final: 0.7897 (ttt) REVERT: B 259 MET cc_start: 0.7032 (mmm) cc_final: 0.6617 (mmm) REVERT: B 268 PHE cc_start: 0.7911 (m-80) cc_final: 0.7485 (m-80) REVERT: B 276 THR cc_start: 0.6810 (p) cc_final: 0.6538 (p) REVERT: B 291 LEU cc_start: 0.9169 (mm) cc_final: 0.8745 (tp) REVERT: B 325 MET cc_start: 0.6516 (mmm) cc_final: 0.6244 (mmt) REVERT: B 356 CYS cc_start: 0.8103 (p) cc_final: 0.6518 (t) REVERT: B 372 LYS cc_start: 0.9177 (mmpt) cc_final: 0.8768 (tttp) REVERT: C 118 VAL cc_start: 0.9310 (t) cc_final: 0.8843 (t) REVERT: C 132 LEU cc_start: 0.7364 (mp) cc_final: 0.7158 (mp) REVERT: C 213 CYS cc_start: 0.7185 (m) cc_final: 0.6844 (t) REVERT: C 217 LEU cc_start: 0.7893 (tt) cc_final: 0.7094 (tt) REVERT: C 291 ILE cc_start: 0.9088 (mt) cc_final: 0.8526 (tt) REVERT: C 377 MET cc_start: 0.8114 (tmm) cc_final: 0.7661 (tmm) REVERT: D 14 ASN cc_start: 0.8020 (m-40) cc_final: 0.7751 (m-40) REVERT: D 55 GLU cc_start: 0.6053 (tp30) cc_final: 0.5799 (tm-30) REVERT: D 62 VAL cc_start: 0.9193 (t) cc_final: 0.8963 (m) REVERT: D 149 MET cc_start: 0.6205 (ptt) cc_final: 0.5953 (ppp) REVERT: D 163 ASP cc_start: 0.6080 (p0) cc_final: 0.5685 (p0) REVERT: D 166 MET cc_start: 0.6305 (mmp) cc_final: 0.5920 (mmp) REVERT: D 236 SER cc_start: 0.7614 (p) cc_final: 0.7294 (p) REVERT: D 323 MET cc_start: 0.6504 (mpp) cc_final: 0.6218 (mpp) REVERT: D 395 PHE cc_start: 0.7703 (t80) cc_final: 0.6309 (t80) REVERT: D 422 GLU cc_start: 0.7530 (tp30) cc_final: 0.6548 (tp30) REVERT: E 209 ILE cc_start: 0.9244 (mt) cc_final: 0.8819 (mt) REVERT: E 347 CYS cc_start: 0.7857 (t) cc_final: 0.7538 (t) REVERT: E 357 TYR cc_start: 0.7881 (m-80) cc_final: 0.7679 (m-80) REVERT: E 377 MET cc_start: 0.8571 (tmm) cc_final: 0.8015 (tmm) REVERT: E 378 LEU cc_start: 0.8381 (mt) cc_final: 0.7776 (mp) REVERT: E 422 ARG cc_start: 0.5997 (ttp80) cc_final: 0.5530 (ttp80) REVERT: E 425 MET cc_start: 0.8669 (tpt) cc_final: 0.8110 (tpp) REVERT: F 14 ASN cc_start: 0.7697 (m-40) cc_final: 0.7386 (m-40) REVERT: F 49 ILE cc_start: 0.7854 (tp) cc_final: 0.7493 (tp) REVERT: F 120 ASP cc_start: 0.6184 (t70) cc_final: 0.5835 (t70) REVERT: F 154 ILE cc_start: 0.8905 (mm) cc_final: 0.8498 (mm) REVERT: F 210 TYR cc_start: 0.7868 (m-80) cc_final: 0.6640 (m-80) REVERT: F 235 MET cc_start: 0.8012 (mtt) cc_final: 0.7738 (ttm) REVERT: F 295 MET cc_start: 0.8692 (mmm) cc_final: 0.8311 (tpt) REVERT: F 299 LYS cc_start: 0.8523 (tmmt) cc_final: 0.7285 (tttm) REVERT: F 327 GLU cc_start: 0.7353 (pt0) cc_final: 0.6469 (pt0) REVERT: F 328 VAL cc_start: 0.8647 (t) cc_final: 0.8154 (p) REVERT: G 113 GLU cc_start: 0.7084 (pp20) cc_final: 0.6563 (pp20) REVERT: G 129 CYS cc_start: 0.8159 (t) cc_final: 0.7839 (t) REVERT: G 171 ILE cc_start: 0.8195 (mm) cc_final: 0.7891 (mm) REVERT: G 209 ILE cc_start: 0.9450 (mp) cc_final: 0.8743 (tt) REVERT: G 291 ILE cc_start: 0.9098 (mt) cc_final: 0.8773 (mt) REVERT: G 292 THR cc_start: 0.8876 (p) cc_final: 0.8651 (p) REVERT: G 295 CYS cc_start: 0.8980 (m) cc_final: 0.8273 (m) REVERT: G 315 CYS cc_start: 0.7843 (t) cc_final: 0.6125 (t) REVERT: G 317 LEU cc_start: 0.7492 (mt) cc_final: 0.7217 (mt) REVERT: G 378 LEU cc_start: 0.7849 (mp) cc_final: 0.7516 (mp) REVERT: H 124 LYS cc_start: 0.8534 (pptt) cc_final: 0.7808 (tttt) REVERT: H 209 LEU cc_start: 0.7875 (mt) cc_final: 0.7602 (mt) REVERT: H 292 THR cc_start: 0.8401 (p) cc_final: 0.7862 (p) REVERT: H 297 ASP cc_start: 0.7400 (t0) cc_final: 0.6657 (t0) REVERT: H 332 MET cc_start: 0.6853 (mmm) cc_final: 0.6186 (mmm) REVERT: I 26 LEU cc_start: 0.8755 (mt) cc_final: 0.8517 (mt) REVERT: I 75 ILE cc_start: 0.6681 (mm) cc_final: 0.6239 (tt) REVERT: I 129 CYS cc_start: 0.8508 (t) cc_final: 0.8282 (t) REVERT: I 203 MET cc_start: 0.5494 (tpp) cc_final: 0.5029 (tpp) REVERT: I 237 SER cc_start: 0.7537 (p) cc_final: 0.7087 (m) REVERT: I 280 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8514 (mmmt) REVERT: I 295 CYS cc_start: 0.9048 (m) cc_final: 0.8599 (m) REVERT: I 313 MET cc_start: 0.6588 (mmm) cc_final: 0.6275 (mmm) REVERT: I 347 CYS cc_start: 0.7827 (t) cc_final: 0.7400 (t) REVERT: I 377 MET cc_start: 0.8016 (tmm) cc_final: 0.7727 (tmm) REVERT: J 203 CYS cc_start: 0.7819 (m) cc_final: 0.7158 (m) REVERT: J 209 LEU cc_start: 0.8002 (mt) cc_final: 0.7694 (mt) REVERT: J 227 LEU cc_start: 0.9397 (mt) cc_final: 0.9071 (mp) REVERT: J 230 LEU cc_start: 0.8639 (tp) cc_final: 0.8370 (tp) REVERT: J 235 MET cc_start: 0.8242 (mtp) cc_final: 0.7729 (mtm) REVERT: J 241 CYS cc_start: 0.8406 (t) cc_final: 0.8039 (t) REVERT: J 259 MET cc_start: 0.7491 (mmm) cc_final: 0.6975 (mmm) REVERT: J 305 CYS cc_start: 0.6206 (t) cc_final: 0.5689 (t) REVERT: J 395 PHE cc_start: 0.8200 (t80) cc_final: 0.7491 (t80) REVERT: J 432 TYR cc_start: 0.5494 (m-80) cc_final: 0.4594 (m-80) REVERT: K 121 ARG cc_start: 0.8606 (mmp80) cc_final: 0.8192 (mmt180) REVERT: K 209 ILE cc_start: 0.9064 (mp) cc_final: 0.8463 (mp) REVERT: K 286 LEU cc_start: 0.8155 (mt) cc_final: 0.7838 (mp) REVERT: K 291 ILE cc_start: 0.9230 (mt) cc_final: 0.8330 (tt) REVERT: K 335 ILE cc_start: 0.7144 (mm) cc_final: 0.6890 (mm) REVERT: K 378 LEU cc_start: 0.8305 (mt) cc_final: 0.8062 (mt) REVERT: K 384 ILE cc_start: 0.7311 (tp) cc_final: 0.6452 (tp) REVERT: K 435 VAL cc_start: 0.7903 (t) cc_final: 0.7478 (t) REVERT: L 14 ASN cc_start: 0.8795 (m-40) cc_final: 0.7665 (t0) REVERT: L 21 TRP cc_start: 0.7123 (m100) cc_final: 0.6829 (m100) REVERT: L 24 ILE cc_start: 0.8849 (mm) cc_final: 0.8616 (mm) REVERT: L 31 ASP cc_start: 0.8278 (p0) cc_final: 0.8064 (p0) REVERT: L 235 MET cc_start: 0.6388 (mtt) cc_final: 0.5997 (mtt) REVERT: L 242 LEU cc_start: 0.7842 (tp) cc_final: 0.7618 (tp) REVERT: L 267 PHE cc_start: 0.7043 (m-80) cc_final: 0.6457 (m-10) REVERT: L 269 MET cc_start: 0.7416 (mtm) cc_final: 0.6750 (mtm) REVERT: L 332 MET cc_start: 0.7028 (mmm) cc_final: 0.6713 (mmt) REVERT: M 75 ILE cc_start: 0.8289 (mm) cc_final: 0.7961 (tp) REVERT: M 132 LEU cc_start: 0.6897 (tp) cc_final: 0.6664 (tp) REVERT: M 191 THR cc_start: 0.8344 (p) cc_final: 0.7748 (p) REVERT: M 313 MET cc_start: 0.4388 (mmm) cc_final: 0.4057 (mmm) REVERT: M 334 THR cc_start: 0.7279 (m) cc_final: 0.5642 (p) REVERT: M 388 TRP cc_start: 0.5629 (m-10) cc_final: 0.5181 (m100) REVERT: N 14 ASN cc_start: 0.8448 (m-40) cc_final: 0.7523 (m110) REVERT: N 21 TRP cc_start: 0.8594 (m100) cc_final: 0.7958 (m100) REVERT: N 50 ASN cc_start: 0.8780 (p0) cc_final: 0.8405 (p0) REVERT: N 53 TYR cc_start: 0.6765 (m-80) cc_final: 0.6005 (m-10) REVERT: N 62 VAL cc_start: 0.9265 (t) cc_final: 0.8920 (p) REVERT: N 124 LYS cc_start: 0.9094 (pptt) cc_final: 0.8275 (pptt) REVERT: N 231 VAL cc_start: 0.8729 (t) cc_final: 0.8132 (t) REVERT: N 259 MET cc_start: 0.8049 (mmp) cc_final: 0.7744 (mmm) REVERT: N 268 PHE cc_start: 0.7075 (m-80) cc_final: 0.5956 (m-80) REVERT: N 416 MET cc_start: 0.4305 (tpt) cc_final: 0.3633 (tpt) REVERT: O 120 ASP cc_start: 0.7148 (m-30) cc_final: 0.6908 (m-30) REVERT: O 335 ILE cc_start: 0.7716 (mm) cc_final: 0.6738 (mm) REVERT: O 355 ILE cc_start: 0.9415 (mm) cc_final: 0.9179 (mm) REVERT: O 384 ILE cc_start: 0.8751 (tt) cc_final: 0.7039 (tt) REVERT: O 407 TRP cc_start: 0.9068 (m100) cc_final: 0.8788 (m100) REVERT: O 425 MET cc_start: 0.7964 (mmp) cc_final: 0.6451 (mmm) REVERT: P 6 HIS cc_start: 0.7777 (t-90) cc_final: 0.7537 (t-90) REVERT: P 14 ASN cc_start: 0.7964 (m-40) cc_final: 0.7686 (m-40) REVERT: P 53 TYR cc_start: 0.6793 (m-80) cc_final: 0.6109 (m-10) REVERT: P 75 MET cc_start: 0.8976 (mmp) cc_final: 0.8654 (mmm) REVERT: P 192 HIS cc_start: 0.7002 (t-90) cc_final: 0.6504 (t-170) REVERT: P 224 TYR cc_start: 0.7999 (m-10) cc_final: 0.7192 (m-80) REVERT: P 257 VAL cc_start: 0.8678 (m) cc_final: 0.8360 (m) REVERT: P 266 HIS cc_start: 0.8146 (p-80) cc_final: 0.7588 (p-80) REVERT: P 268 PHE cc_start: 0.5675 (m-80) cc_final: 0.5402 (m-80) REVERT: P 295 MET cc_start: 0.7645 (ppp) cc_final: 0.7058 (ttp) REVERT: P 302 MET cc_start: 0.6912 (mtm) cc_final: 0.6582 (mtp) REVERT: P 380 ASN cc_start: 0.6485 (m-40) cc_final: 0.5321 (m-40) REVERT: P 411 GLU cc_start: 0.7357 (mm-30) cc_final: 0.5789 (mt-10) REVERT: P 413 MET cc_start: 0.7692 (mmm) cc_final: 0.7474 (mmm) REVERT: P 416 MET cc_start: 0.6976 (mmp) cc_final: 0.6677 (tpt) REVERT: Q 25 CYS cc_start: 0.8059 (m) cc_final: 0.7284 (m) REVERT: Q 120 ASP cc_start: 0.6320 (t70) cc_final: 0.3856 (t70) REVERT: Q 154 MET cc_start: 0.6835 (ppp) cc_final: 0.6526 (ppp) REVERT: Q 271 THR cc_start: 0.6787 (p) cc_final: 0.6275 (t) REVERT: Q 318 LEU cc_start: 0.5811 (mt) cc_final: 0.5478 (mt) REVERT: Q 360 PRO cc_start: 0.8825 (Cg_exo) cc_final: 0.8551 (Cg_endo) REVERT: R 14 ASN cc_start: 0.7436 (m110) cc_final: 0.7013 (m-40) REVERT: R 20 PHE cc_start: 0.8313 (t80) cc_final: 0.8010 (t80) REVERT: R 124 LYS cc_start: 0.8624 (pptt) cc_final: 0.8355 (pptt) REVERT: R 231 VAL cc_start: 0.9011 (t) cc_final: 0.8675 (t) REVERT: R 235 MET cc_start: 0.8852 (mtp) cc_final: 0.8630 (mtp) REVERT: R 295 MET cc_start: 0.8447 (ttt) cc_final: 0.7585 (tpp) REVERT: R 323 MET cc_start: 0.8565 (mpp) cc_final: 0.8214 (mpp) outliers start: 6 outliers final: 2 residues processed: 1580 average time/residue: 0.5876 time to fit residues: 1563.9273 Evaluate side-chains 1173 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1170 time to evaluate : 5.212 ------------------------------------------------------------------------------- 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: 5.9990 chunk 544 optimal weight: 50.0000 chunk 301 optimal weight: 8.9990 chunk 623 optimal weight: 0.7980 chunk 505 optimal weight: 40.0000 chunk 0 optimal weight: 50.0000 chunk 373 optimal weight: 50.0000 chunk 655 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN F 8 GLN F 136 GLN F 192 HIS ** F 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 ASN H 102 ASN ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS J 309 HIS ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 ASN P 107 HIS P 133 GLN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 ASN Q 293 ASN R 309 HIS R 331 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 62298 Z= 0.192 Angle : 0.621 8.151 84645 Z= 0.326 Chirality : 0.045 0.434 9216 Planarity : 0.005 0.078 11043 Dihedral : 11.684 177.083 8784 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % 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: 0.72 (0.10), residues: 7632 helix: 0.75 (0.08), residues: 3636 sheet: 0.76 (0.14), residues: 1341 loop : 0.17 (0.13), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP O 388 HIS 0.013 0.001 HIS P 6 PHE 0.020 0.002 PHE I 351 TYR 0.046 0.002 TYR A 24 ARG 0.010 0.001 ARG F 401 *********************** 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 1494 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1492 time to evaluate : 5.196 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: A 21 TRP cc_start: 0.8589 (m100) cc_final: 0.7815 (m100) REVERT: A 118 VAL cc_start: 0.9096 (t) cc_final: 0.8809 (p) REVERT: A 169 PHE cc_start: 0.6546 (m-80) cc_final: 0.6251 (m-80) REVERT: A 207 GLU cc_start: 0.7277 (mp0) cc_final: 0.5930 (mp0) REVERT: A 210 TYR cc_start: 0.8502 (m-80) cc_final: 0.8144 (m-80) REVERT: A 217 LEU cc_start: 0.8840 (tp) cc_final: 0.8423 (tp) REVERT: A 384 ILE cc_start: 0.8623 (tp) cc_final: 0.7954 (tp) REVERT: A 418 PHE cc_start: 0.7621 (m-10) cc_final: 0.7151 (m-10) REVERT: B 14 ASN cc_start: 0.8259 (m-40) cc_final: 0.8040 (m110) REVERT: B 41 ASP cc_start: 0.7049 (p0) cc_final: 0.6723 (m-30) REVERT: B 210 TYR cc_start: 0.7638 (m-80) cc_final: 0.7278 (m-80) REVERT: B 227 LEU cc_start: 0.9284 (mt) cc_final: 0.8709 (mt) REVERT: B 235 MET cc_start: 0.8612 (mtt) cc_final: 0.7972 (ttm) REVERT: B 259 MET cc_start: 0.6678 (mmm) cc_final: 0.6267 (mmm) REVERT: B 283 TYR cc_start: 0.6583 (m-80) cc_final: 0.5872 (m-80) REVERT: B 291 LEU cc_start: 0.9164 (mm) cc_final: 0.8781 (tp) REVERT: B 301 MET cc_start: 0.8264 (mmp) cc_final: 0.7964 (mmm) REVERT: B 372 LYS cc_start: 0.9122 (mmpt) cc_final: 0.8806 (tttp) REVERT: C 118 VAL cc_start: 0.9292 (t) cc_final: 0.8843 (t) REVERT: C 132 LEU cc_start: 0.7556 (mp) cc_final: 0.7343 (mp) REVERT: C 209 ILE cc_start: 0.9338 (mp) cc_final: 0.9007 (mp) REVERT: C 213 CYS cc_start: 0.7062 (m) cc_final: 0.6860 (t) REVERT: C 217 LEU cc_start: 0.7935 (tt) cc_final: 0.7468 (tt) REVERT: C 378 LEU cc_start: 0.7964 (tp) cc_final: 0.7664 (mp) REVERT: D 14 ASN cc_start: 0.7927 (m-40) cc_final: 0.7157 (m-40) REVERT: D 62 VAL cc_start: 0.9075 (t) cc_final: 0.8873 (m) REVERT: D 149 MET cc_start: 0.6226 (ptt) cc_final: 0.5839 (ppp) REVERT: D 163 ASP cc_start: 0.6044 (p0) cc_final: 0.5600 (p0) REVERT: D 210 TYR cc_start: 0.6695 (m-80) cc_final: 0.6029 (m-80) REVERT: D 235 MET cc_start: 0.6747 (ttt) cc_final: 0.6489 (ttt) REVERT: D 283 TYR cc_start: 0.4594 (m-10) cc_final: 0.4326 (m-10) REVERT: D 328 VAL cc_start: 0.8150 (t) cc_final: 0.7718 (p) REVERT: E 116 ASP cc_start: 0.7743 (p0) cc_final: 0.7473 (p0) REVERT: E 209 ILE cc_start: 0.9278 (mt) cc_final: 0.8854 (mt) REVERT: E 221 ARG cc_start: 0.7170 (mmt180) cc_final: 0.5976 (mmt180) REVERT: E 347 CYS cc_start: 0.7790 (t) cc_final: 0.7582 (t) REVERT: E 377 MET cc_start: 0.8230 (tmm) cc_final: 0.7750 (tmm) REVERT: E 378 LEU cc_start: 0.8177 (mt) cc_final: 0.7584 (mp) REVERT: E 388 TRP cc_start: 0.5507 (m-10) cc_final: 0.5137 (m-10) REVERT: E 425 MET cc_start: 0.8741 (tpt) cc_final: 0.8181 (tpp) REVERT: F 14 ASN cc_start: 0.8327 (m-40) cc_final: 0.8077 (m-40) REVERT: F 53 TYR cc_start: 0.6250 (m-80) cc_final: 0.5733 (m-80) REVERT: F 116 ASP cc_start: 0.8424 (p0) cc_final: 0.8060 (p0) REVERT: F 136 GLN cc_start: 0.7113 (mt0) cc_final: 0.6878 (mt0) REVERT: F 154 ILE cc_start: 0.8960 (mm) cc_final: 0.8563 (mm) REVERT: F 235 MET cc_start: 0.8110 (mtt) cc_final: 0.7869 (ttm) REVERT: F 327 GLU cc_start: 0.7726 (pt0) cc_final: 0.6479 (pt0) REVERT: F 328 VAL cc_start: 0.8665 (t) cc_final: 0.8334 (p) REVERT: F 373 MET cc_start: 0.8464 (pmm) cc_final: 0.7950 (pmm) REVERT: G 66 VAL cc_start: 0.6442 (t) cc_final: 0.6230 (t) REVERT: G 75 ILE cc_start: 0.7857 (mm) cc_final: 0.7019 (tt) REVERT: G 113 GLU cc_start: 0.6889 (pp20) cc_final: 0.6620 (pp20) REVERT: G 129 CYS cc_start: 0.8202 (t) cc_final: 0.7958 (t) REVERT: G 254 GLU cc_start: 0.7075 (mp0) cc_final: 0.6049 (mm-30) REVERT: G 291 ILE cc_start: 0.9080 (mt) cc_final: 0.8306 (tt) REVERT: G 315 CYS cc_start: 0.8102 (t) cc_final: 0.7556 (t) REVERT: G 425 MET cc_start: 0.8174 (mmm) cc_final: 0.7935 (mmm) REVERT: H 19 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8210 (mmmm) REVERT: H 124 LYS cc_start: 0.8718 (pptt) cc_final: 0.7808 (tttp) REVERT: H 292 THR cc_start: 0.8482 (p) cc_final: 0.8024 (p) REVERT: H 297 ASP cc_start: 0.7635 (t0) cc_final: 0.7230 (t0) REVERT: H 332 MET cc_start: 0.6726 (mmm) cc_final: 0.6284 (mmm) REVERT: I 26 LEU cc_start: 0.8794 (mt) cc_final: 0.8491 (mt) REVERT: I 75 ILE cc_start: 0.6492 (mm) cc_final: 0.6275 (tt) REVERT: I 237 SER cc_start: 0.7847 (p) cc_final: 0.7159 (m) REVERT: I 335 ILE cc_start: 0.7326 (mm) cc_final: 0.7122 (mm) REVERT: I 347 CYS cc_start: 0.7686 (t) cc_final: 0.7267 (t) REVERT: J 203 CYS cc_start: 0.7856 (m) cc_final: 0.7258 (m) REVERT: J 209 LEU cc_start: 0.8080 (mt) cc_final: 0.7681 (mt) REVERT: J 227 LEU cc_start: 0.9267 (mt) cc_final: 0.8625 (mp) REVERT: J 230 LEU cc_start: 0.8557 (tp) cc_final: 0.8331 (tp) REVERT: J 235 MET cc_start: 0.8018 (mtp) cc_final: 0.7423 (mtm) REVERT: J 241 CYS cc_start: 0.8360 (t) cc_final: 0.8070 (t) REVERT: J 259 MET cc_start: 0.7518 (mmm) cc_final: 0.6725 (mmm) REVERT: J 305 CYS cc_start: 0.6243 (t) cc_final: 0.5715 (t) REVERT: J 328 VAL cc_start: 0.8440 (m) cc_final: 0.8125 (m) REVERT: J 395 PHE cc_start: 0.8032 (t80) cc_final: 0.7250 (t80) REVERT: K 116 ASP cc_start: 0.7238 (p0) cc_final: 0.6859 (p0) REVERT: K 121 ARG cc_start: 0.8061 (mmp80) cc_final: 0.7813 (mmp80) REVERT: K 122 ILE cc_start: 0.8234 (pt) cc_final: 0.7355 (pt) REVERT: K 209 ILE cc_start: 0.8985 (mp) cc_final: 0.8457 (mp) REVERT: K 286 LEU cc_start: 0.8293 (mt) cc_final: 0.8020 (mp) REVERT: K 291 ILE cc_start: 0.9202 (mt) cc_final: 0.8405 (tt) REVERT: K 377 MET cc_start: 0.7444 (tmm) cc_final: 0.7196 (ttt) REVERT: K 386 GLU cc_start: 0.7512 (mp0) cc_final: 0.7214 (mp0) REVERT: L 24 ILE cc_start: 0.8814 (mm) cc_final: 0.8405 (tp) REVERT: L 31 ASP cc_start: 0.8300 (p0) cc_final: 0.8022 (p0) REVERT: L 116 ASP cc_start: 0.7662 (m-30) cc_final: 0.7203 (m-30) REVERT: L 207 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6541 (mm-30) REVERT: L 235 MET cc_start: 0.6612 (mtt) cc_final: 0.6366 (mtt) REVERT: L 267 PHE cc_start: 0.6838 (m-80) cc_final: 0.6262 (m-10) REVERT: L 269 MET cc_start: 0.7312 (mtm) cc_final: 0.6767 (mtm) REVERT: L 301 MET cc_start: 0.6075 (tpp) cc_final: 0.5819 (tpp) REVERT: M 75 ILE cc_start: 0.8271 (mm) cc_final: 0.8015 (tp) REVERT: M 186 ASN cc_start: 0.7270 (m-40) cc_final: 0.6964 (m-40) REVERT: M 313 MET cc_start: 0.4716 (mmm) cc_final: 0.4222 (mmm) REVERT: N 14 ASN cc_start: 0.8322 (m-40) cc_final: 0.7370 (m110) REVERT: N 50 ASN cc_start: 0.8766 (p0) cc_final: 0.8381 (p0) REVERT: N 53 TYR cc_start: 0.6892 (m-80) cc_final: 0.6556 (m-10) REVERT: N 124 LYS cc_start: 0.9035 (pptt) cc_final: 0.8791 (ptmm) REVERT: N 259 MET cc_start: 0.7925 (mmp) cc_final: 0.7689 (mmm) REVERT: N 268 PHE cc_start: 0.7274 (m-80) cc_final: 0.5960 (m-80) REVERT: N 398 MET cc_start: 0.5043 (mtm) cc_final: 0.4377 (mtm) REVERT: N 405 LEU cc_start: 0.8234 (tp) cc_final: 0.7922 (tp) REVERT: N 416 MET cc_start: 0.4316 (tpt) cc_final: 0.3691 (tpt) REVERT: O 75 ILE cc_start: 0.8177 (mm) cc_final: 0.7391 (mm) REVERT: O 120 ASP cc_start: 0.7076 (m-30) cc_final: 0.6827 (m-30) REVERT: O 154 MET cc_start: 0.7636 (ttp) cc_final: 0.7174 (tmm) REVERT: O 295 CYS cc_start: 0.9163 (m) cc_final: 0.8691 (m) REVERT: O 384 ILE cc_start: 0.8618 (tt) cc_final: 0.8250 (tt) REVERT: P 14 ASN cc_start: 0.8039 (m-40) cc_final: 0.7689 (m-40) REVERT: P 53 TYR cc_start: 0.6945 (m-80) cc_final: 0.6469 (m-10) REVERT: P 75 MET cc_start: 0.8816 (mmp) cc_final: 0.8343 (mmm) REVERT: P 119 LEU cc_start: 0.7609 (tt) cc_final: 0.7398 (tt) REVERT: P 251 ASP cc_start: 0.5461 (t0) cc_final: 0.5208 (t70) REVERT: P 266 HIS cc_start: 0.8135 (p-80) cc_final: 0.7531 (p90) REVERT: P 295 MET cc_start: 0.7765 (ppp) cc_final: 0.7311 (ttp) REVERT: P 411 GLU cc_start: 0.7580 (mm-30) cc_final: 0.5987 (mt-10) REVERT: Q 25 CYS cc_start: 0.8091 (m) cc_final: 0.7609 (m) REVERT: Q 60 LYS cc_start: 0.7030 (mmtt) cc_final: 0.6660 (mmpt) REVERT: Q 120 ASP cc_start: 0.5828 (t70) cc_final: 0.3908 (t70) REVERT: Q 130 THR cc_start: 0.8108 (p) cc_final: 0.7792 (t) REVERT: Q 154 MET cc_start: 0.6911 (ppp) cc_final: 0.6484 (ppp) REVERT: Q 191 THR cc_start: 0.8371 (p) cc_final: 0.7872 (p) REVERT: Q 271 THR cc_start: 0.6892 (p) cc_final: 0.6598 (t) REVERT: Q 391 LEU cc_start: 0.6191 (mt) cc_final: 0.5954 (mt) REVERT: R 14 ASN cc_start: 0.8003 (m110) cc_final: 0.7271 (m-40) REVERT: R 20 PHE cc_start: 0.8203 (t80) cc_final: 0.7982 (t80) REVERT: R 115 VAL cc_start: 0.8810 (t) cc_final: 0.8605 (t) REVERT: R 231 VAL cc_start: 0.8858 (t) cc_final: 0.8371 (t) REVERT: R 235 MET cc_start: 0.8646 (mtp) cc_final: 0.8294 (mtt) outliers start: 2 outliers final: 0 residues processed: 1494 average time/residue: 0.5773 time to fit residues: 1457.5112 Evaluate side-chains 1115 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1115 time to evaluate : 5.207 ------------------------------------------------------------------------------- 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: 6.9990 chunk 658 optimal weight: 30.0000 chunk 144 optimal weight: 7.9990 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 9.9990 chunk 731 optimal weight: 2.9990 chunk 607 optimal weight: 9.9990 chunk 338 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 384 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS C 309 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN F 192 HIS F 380 ASN G 88 HIS ** G 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 349 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 ASN M 293 ASN ** N 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 HIS ** P 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 133 GLN ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 281 GLN R 309 HIS R 331 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.7361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62298 Z= 0.202 Angle : 0.623 9.564 84645 Z= 0.325 Chirality : 0.045 0.321 9216 Planarity : 0.005 0.069 11043 Dihedral : 11.633 177.856 8784 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.12 % Allowed : 1.50 % Favored : 98.38 % 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: 0.70 (0.10), residues: 7632 helix: 0.78 (0.08), residues: 3663 sheet: 0.88 (0.15), residues: 1224 loop : 0.03 (0.13), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP G 388 HIS 0.025 0.001 HIS P 6 PHE 0.030 0.002 PHE P 169 TYR 0.036 0.002 TYR A 24 ARG 0.006 0.001 ARG A 422 *********************** 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 1487 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1479 time to evaluate : 5.299 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: A 21 TRP cc_start: 0.8456 (m100) cc_final: 0.7869 (m100) REVERT: A 66 VAL cc_start: 0.7654 (t) cc_final: 0.7367 (t) REVERT: A 74 VAL cc_start: 0.8636 (t) cc_final: 0.8425 (t) REVERT: A 75 ILE cc_start: 0.8703 (mt) cc_final: 0.7695 (tt) REVERT: A 122 ILE cc_start: 0.8642 (mt) cc_final: 0.8323 (tp) REVERT: A 132 LEU cc_start: 0.7528 (tp) cc_final: 0.6484 (mp) REVERT: A 169 PHE cc_start: 0.6731 (m-80) cc_final: 0.6279 (m-80) REVERT: A 217 LEU cc_start: 0.8298 (tp) cc_final: 0.8039 (tp) REVERT: A 378 LEU cc_start: 0.7841 (mp) cc_final: 0.7522 (mp) REVERT: A 413 MET cc_start: 0.3134 (mmt) cc_final: 0.2915 (mmt) REVERT: B 14 ASN cc_start: 0.8370 (m-40) cc_final: 0.8153 (m110) REVERT: B 41 ASP cc_start: 0.7057 (p0) cc_final: 0.6766 (m-30) REVERT: B 210 TYR cc_start: 0.7373 (m-80) cc_final: 0.6887 (m-80) REVERT: B 227 LEU cc_start: 0.9273 (mt) cc_final: 0.8694 (mt) REVERT: B 235 MET cc_start: 0.8565 (mtt) cc_final: 0.7730 (ttm) REVERT: B 283 TYR cc_start: 0.6752 (m-80) cc_final: 0.6190 (m-80) REVERT: B 291 LEU cc_start: 0.9114 (mm) cc_final: 0.8792 (tp) REVERT: B 297 ASP cc_start: 0.7559 (t0) cc_final: 0.7195 (t0) REVERT: B 301 MET cc_start: 0.8308 (mmp) cc_final: 0.8085 (mmm) REVERT: B 302 MET cc_start: 0.7077 (mtm) cc_final: 0.6765 (mtm) REVERT: B 326 LYS cc_start: 0.8822 (tppt) cc_final: 0.7734 (ttpt) REVERT: B 372 LYS cc_start: 0.9133 (mmpt) cc_final: 0.8919 (tttp) REVERT: B 399 PHE cc_start: 0.7406 (t80) cc_final: 0.7157 (t80) REVERT: C 213 CYS cc_start: 0.7296 (m) cc_final: 0.7021 (t) REVERT: C 217 LEU cc_start: 0.8053 (tt) cc_final: 0.7404 (tt) REVERT: C 224 TYR cc_start: 0.7282 (m-80) cc_final: 0.6828 (m-80) REVERT: C 291 ILE cc_start: 0.9161 (mt) cc_final: 0.8662 (tt) REVERT: D 14 ASN cc_start: 0.7978 (m-40) cc_final: 0.7217 (m-40) REVERT: D 53 TYR cc_start: 0.6024 (m-80) cc_final: 0.5787 (m-10) REVERT: D 149 MET cc_start: 0.6440 (ptt) cc_final: 0.5839 (ppp) REVERT: D 163 ASP cc_start: 0.6372 (p0) cc_final: 0.5849 (p0) REVERT: D 235 MET cc_start: 0.6397 (ttt) cc_final: 0.5975 (ttt) REVERT: D 262 PHE cc_start: 0.7822 (t80) cc_final: 0.7592 (t80) REVERT: D 328 VAL cc_start: 0.8119 (t) cc_final: 0.7876 (p) REVERT: E 116 ASP cc_start: 0.7523 (p0) cc_final: 0.7145 (p0) REVERT: E 221 ARG cc_start: 0.6981 (mmt180) cc_final: 0.5782 (mmt180) REVERT: E 352 LYS cc_start: 0.7850 (tttp) cc_final: 0.7476 (ttpt) REVERT: E 377 MET cc_start: 0.8277 (tmm) cc_final: 0.7702 (tmm) REVERT: E 378 LEU cc_start: 0.8257 (mt) cc_final: 0.7874 (mp) REVERT: E 388 TRP cc_start: 0.5576 (m-10) cc_final: 0.5363 (m-10) REVERT: E 425 MET cc_start: 0.8759 (tpt) cc_final: 0.8217 (tpp) REVERT: F 14 ASN cc_start: 0.8434 (m-40) cc_final: 0.8138 (m-40) REVERT: F 26 ASP cc_start: 0.6776 (t0) cc_final: 0.6487 (t0) REVERT: F 53 TYR cc_start: 0.6164 (m-80) cc_final: 0.5620 (m-80) REVERT: F 62 VAL cc_start: 0.9116 (t) cc_final: 0.8902 (p) REVERT: F 116 ASP cc_start: 0.8396 (p0) cc_final: 0.8047 (p0) REVERT: F 120 ASP cc_start: 0.5589 (t70) cc_final: 0.5377 (t70) REVERT: F 154 ILE cc_start: 0.8863 (mm) cc_final: 0.8477 (mm) REVERT: F 204 ILE cc_start: 0.8742 (mt) cc_final: 0.8514 (mt) REVERT: F 235 MET cc_start: 0.8158 (mtt) cc_final: 0.7557 (ttm) REVERT: F 302 MET cc_start: 0.6637 (mtp) cc_final: 0.5937 (mtp) REVERT: F 327 GLU cc_start: 0.7969 (pt0) cc_final: 0.6710 (pt0) REVERT: F 328 VAL cc_start: 0.8705 (t) cc_final: 0.8259 (p) REVERT: F 373 MET cc_start: 0.8531 (pmm) cc_final: 0.8228 (pmm) REVERT: G 113 GLU cc_start: 0.6577 (pp20) cc_final: 0.6350 (pp20) REVERT: G 129 CYS cc_start: 0.8314 (t) cc_final: 0.8049 (t) REVERT: G 132 LEU cc_start: 0.8546 (tp) cc_final: 0.8211 (tp) REVERT: G 252 LEU cc_start: 0.7026 (pp) cc_final: 0.6767 (pp) REVERT: G 286 LEU cc_start: 0.8194 (tp) cc_final: 0.7944 (tp) REVERT: G 295 CYS cc_start: 0.8981 (m) cc_final: 0.8449 (m) REVERT: G 315 CYS cc_start: 0.7888 (t) cc_final: 0.6645 (t) REVERT: G 378 LEU cc_start: 0.7442 (mp) cc_final: 0.6776 (mp) REVERT: H 19 LYS cc_start: 0.8203 (mmmm) cc_final: 0.7976 (mmmm) REVERT: H 124 LYS cc_start: 0.8850 (pptt) cc_final: 0.7421 (tttp) REVERT: H 209 LEU cc_start: 0.8028 (mt) cc_final: 0.7797 (mt) REVERT: H 286 LEU cc_start: 0.8507 (pt) cc_final: 0.8283 (pt) REVERT: H 292 THR cc_start: 0.8461 (p) cc_final: 0.8044 (p) REVERT: H 295 MET cc_start: 0.8035 (ppp) cc_final: 0.7705 (ppp) REVERT: H 297 ASP cc_start: 0.7180 (t0) cc_final: 0.6832 (t0) REVERT: H 323 MET cc_start: 0.6498 (mpp) cc_final: 0.5765 (mpp) REVERT: H 332 MET cc_start: 0.6882 (mmm) cc_final: 0.6287 (mmm) REVERT: I 26 LEU cc_start: 0.8817 (mt) cc_final: 0.8588 (mt) REVERT: I 75 ILE cc_start: 0.6530 (mm) cc_final: 0.6235 (tt) REVERT: I 211 ASP cc_start: 0.6544 (t70) cc_final: 0.6215 (t0) REVERT: I 237 SER cc_start: 0.7795 (p) cc_final: 0.7237 (m) REVERT: I 286 LEU cc_start: 0.8466 (mt) cc_final: 0.8108 (mt) REVERT: I 295 CYS cc_start: 0.9242 (p) cc_final: 0.9012 (p) REVERT: I 347 CYS cc_start: 0.7498 (t) cc_final: 0.7195 (t) REVERT: I 377 MET cc_start: 0.8237 (tmm) cc_final: 0.7627 (tmm) REVERT: J 230 LEU cc_start: 0.8535 (tp) cc_final: 0.8272 (tp) REVERT: J 235 MET cc_start: 0.8183 (mtp) cc_final: 0.7409 (mtm) REVERT: J 241 CYS cc_start: 0.8316 (t) cc_final: 0.8056 (t) REVERT: J 259 MET cc_start: 0.7477 (mmm) cc_final: 0.6632 (mmm) REVERT: J 305 CYS cc_start: 0.6318 (t) cc_final: 0.5740 (t) REVERT: J 384 ILE cc_start: 0.7880 (mt) cc_final: 0.7608 (mm) REVERT: J 395 PHE cc_start: 0.7893 (t80) cc_final: 0.7310 (t80) REVERT: J 432 TYR cc_start: 0.4392 (m-10) cc_final: 0.4182 (m-80) REVERT: K 75 ILE cc_start: 0.6731 (mm) cc_final: 0.6372 (tt) REVERT: K 116 ASP cc_start: 0.7747 (p0) cc_final: 0.7393 (p0) REVERT: K 122 ILE cc_start: 0.8032 (pt) cc_final: 0.7722 (pt) REVERT: K 209 ILE cc_start: 0.9019 (mp) cc_final: 0.8352 (mp) REVERT: K 291 ILE cc_start: 0.9234 (mt) cc_final: 0.8653 (tt) REVERT: K 335 ILE cc_start: 0.6812 (mm) cc_final: 0.6601 (mm) REVERT: K 377 MET cc_start: 0.7878 (tmm) cc_final: 0.7395 (tmm) REVERT: L 116 ASP cc_start: 0.7602 (m-30) cc_final: 0.7183 (m-30) REVERT: L 242 LEU cc_start: 0.8001 (tp) cc_final: 0.7785 (tp) REVERT: L 269 MET cc_start: 0.7144 (mtm) cc_final: 0.6747 (mtm) REVERT: L 275 LEU cc_start: 0.7292 (pt) cc_final: 0.7082 (pt) REVERT: L 301 MET cc_start: 0.5938 (tpp) cc_final: 0.5691 (tpp) REVERT: M 75 ILE cc_start: 0.8421 (mm) cc_final: 0.7903 (tt) REVERT: M 186 ASN cc_start: 0.7282 (m-40) cc_final: 0.7072 (m-40) REVERT: M 197 HIS cc_start: 0.6159 (m90) cc_final: 0.5715 (m-70) REVERT: M 216 ASN cc_start: 0.7279 (m110) cc_final: 0.6422 (m110) REVERT: M 271 THR cc_start: 0.7597 (p) cc_final: 0.7096 (t) REVERT: M 282 TYR cc_start: 0.5490 (t80) cc_final: 0.5202 (t80) REVERT: M 305 CYS cc_start: 0.7107 (m) cc_final: 0.6792 (m) REVERT: M 313 MET cc_start: 0.5028 (mmm) cc_final: 0.4486 (mmm) REVERT: M 334 THR cc_start: 0.7558 (m) cc_final: 0.7108 (p) REVERT: M 335 ILE cc_start: 0.7900 (mm) cc_final: 0.7545 (mm) REVERT: M 391 LEU cc_start: 0.6944 (mt) cc_final: 0.6716 (mt) REVERT: M 434 GLU cc_start: 0.6663 (pp20) cc_final: 0.6120 (tm-30) REVERT: N 14 ASN cc_start: 0.8435 (m-40) cc_final: 0.7426 (m110) REVERT: N 50 ASN cc_start: 0.8844 (p0) cc_final: 0.8483 (p0) REVERT: N 217 LEU cc_start: 0.6520 (tp) cc_final: 0.6005 (tt) REVERT: N 231 VAL cc_start: 0.9116 (t) cc_final: 0.8791 (t) REVERT: N 259 MET cc_start: 0.8032 (mmp) cc_final: 0.7514 (mmm) REVERT: N 265 LEU cc_start: 0.7446 (mp) cc_final: 0.6926 (tt) REVERT: N 268 PHE cc_start: 0.7026 (m-80) cc_final: 0.5646 (m-80) REVERT: N 295 MET cc_start: 0.7136 (tpp) cc_final: 0.6172 (tmm) REVERT: N 405 LEU cc_start: 0.8082 (tp) cc_final: 0.7786 (tp) REVERT: N 416 MET cc_start: 0.4559 (tpt) cc_final: 0.4156 (tpt) REVERT: O 22 GLU cc_start: 0.7861 (pt0) cc_final: 0.7645 (pt0) REVERT: O 113 GLU cc_start: 0.7663 (mp0) cc_final: 0.6064 (tp30) REVERT: O 120 ASP cc_start: 0.7091 (m-30) cc_final: 0.6728 (m-30) REVERT: O 154 MET cc_start: 0.7600 (ttp) cc_final: 0.6787 (tmm) REVERT: O 295 CYS cc_start: 0.9234 (m) cc_final: 0.8640 (m) REVERT: P 8 GLN cc_start: 0.6715 (mp10) cc_final: 0.6506 (mp10) REVERT: P 53 TYR cc_start: 0.7330 (m-80) cc_final: 0.6975 (m-10) REVERT: P 75 MET cc_start: 0.8839 (mmp) cc_final: 0.8403 (mmm) REVERT: P 252 LEU cc_start: 0.8133 (mt) cc_final: 0.7526 (pt) REVERT: P 266 HIS cc_start: 0.7658 (p-80) cc_final: 0.7439 (p-80) REVERT: P 288 VAL cc_start: 0.8227 (t) cc_final: 0.7927 (t) REVERT: P 295 MET cc_start: 0.7753 (ppp) cc_final: 0.7254 (ttp) REVERT: P 411 GLU cc_start: 0.7904 (mm-30) cc_final: 0.6358 (mt-10) REVERT: P 416 MET cc_start: 0.3325 (tpt) cc_final: 0.2799 (tpt) REVERT: Q 113 GLU cc_start: 0.8930 (mp0) cc_final: 0.6750 (tm-30) REVERT: Q 120 ASP cc_start: 0.6216 (t70) cc_final: 0.3553 (t70) REVERT: Q 130 THR cc_start: 0.8212 (p) cc_final: 0.7836 (t) REVERT: Q 154 MET cc_start: 0.6850 (ppp) cc_final: 0.6530 (ppp) REVERT: Q 191 THR cc_start: 0.8365 (p) cc_final: 0.7989 (p) REVERT: Q 209 ILE cc_start: 0.9436 (mp) cc_final: 0.9214 (mp) REVERT: Q 271 THR cc_start: 0.6709 (p) cc_final: 0.5772 (t) REVERT: Q 318 LEU cc_start: 0.6197 (mt) cc_final: 0.5667 (mt) REVERT: R 14 ASN cc_start: 0.8116 (m110) cc_final: 0.7592 (m-40) REVERT: R 24 ILE cc_start: 0.8758 (mm) cc_final: 0.8434 (mm) REVERT: R 53 TYR cc_start: 0.5991 (m-80) cc_final: 0.5667 (m-10) REVERT: R 231 VAL cc_start: 0.8917 (t) cc_final: 0.8698 (t) REVERT: R 295 MET cc_start: 0.7975 (ttt) cc_final: 0.7611 (tpp) REVERT: R 300 ASN cc_start: 0.8074 (m-40) cc_final: 0.7102 (t0) outliers start: 8 outliers final: 1 residues processed: 1486 average time/residue: 0.5715 time to fit residues: 1440.8764 Evaluate side-chains 1075 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1074 time to evaluate : 5.163 ------------------------------------------------------------------------------- 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: 20.0000 chunk 82 optimal weight: 3.9990 chunk 416 optimal weight: 8.9990 chunk 534 optimal weight: 40.0000 chunk 413 optimal weight: 40.0000 chunk 615 optimal weight: 40.0000 chunk 408 optimal weight: 0.4980 chunk 728 optimal weight: 50.0000 chunk 456 optimal weight: 50.0000 chunk 444 optimal weight: 0.9990 chunk 336 optimal weight: 8.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN E 107 HIS E 266 HIS E 309 HIS G 293 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS I 85 GLN ** I 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 HIS O 226 ASN P 107 HIS P 133 GLN ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 192 HIS P 380 ASN ** Q 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 136 GLN ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.7686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 62298 Z= 0.186 Angle : 0.630 12.080 84645 Z= 0.325 Chirality : 0.045 0.424 9216 Planarity : 0.005 0.074 11043 Dihedral : 11.504 179.742 8784 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.08 % Allowed : 1.19 % Favored : 98.73 % 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: 0.61 (0.10), residues: 7632 helix: 0.80 (0.08), residues: 3672 sheet: 0.56 (0.14), residues: 1287 loop : -0.04 (0.13), residues: 2673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP O 388 HIS 0.016 0.001 HIS P 6 PHE 0.020 0.001 PHE A 395 TYR 0.038 0.002 TYR A 24 ARG 0.018 0.001 ARG I 339 *********************** 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 1459 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1454 time to evaluate : 5.199 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: A 75 ILE cc_start: 0.8708 (mt) cc_final: 0.7822 (tt) REVERT: A 118 VAL cc_start: 0.9218 (t) cc_final: 0.8701 (p) REVERT: A 122 ILE cc_start: 0.8651 (mt) cc_final: 0.8303 (tp) REVERT: A 132 LEU cc_start: 0.7510 (tp) cc_final: 0.6477 (mp) REVERT: A 169 PHE cc_start: 0.6516 (m-80) cc_final: 0.6282 (m-80) REVERT: A 224 TYR cc_start: 0.5597 (m-10) cc_final: 0.5387 (m-80) REVERT: A 302 MET cc_start: 0.8570 (tpp) cc_final: 0.8098 (mmm) REVERT: A 433 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7006 (tm-30) REVERT: B 5 VAL cc_start: 0.8622 (t) cc_final: 0.8409 (t) REVERT: B 235 MET cc_start: 0.8679 (mtt) cc_final: 0.7627 (ttm) REVERT: B 259 MET cc_start: 0.7724 (mmp) cc_final: 0.6826 (mmm) REVERT: B 291 LEU cc_start: 0.9065 (mm) cc_final: 0.8690 (tp) REVERT: B 302 MET cc_start: 0.7322 (mtm) cc_final: 0.6839 (mtm) REVERT: B 372 LYS cc_start: 0.9046 (mmpt) cc_final: 0.8766 (tttp) REVERT: B 399 PHE cc_start: 0.7548 (t80) cc_final: 0.7150 (t80) REVERT: C 118 VAL cc_start: 0.9308 (t) cc_final: 0.8952 (t) REVERT: C 150 THR cc_start: 0.8965 (p) cc_final: 0.8564 (p) REVERT: C 291 ILE cc_start: 0.9131 (mt) cc_final: 0.8674 (tt) REVERT: D 14 ASN cc_start: 0.7967 (m-40) cc_final: 0.7368 (m-40) REVERT: D 53 TYR cc_start: 0.5986 (m-80) cc_final: 0.5767 (m-10) REVERT: D 149 MET cc_start: 0.5562 (ptt) cc_final: 0.5301 (ppp) REVERT: D 163 ASP cc_start: 0.6331 (p0) cc_final: 0.5818 (p0) REVERT: D 235 MET cc_start: 0.7081 (ttt) cc_final: 0.6721 (ttt) REVERT: D 262 PHE cc_start: 0.7631 (t80) cc_final: 0.7408 (t80) REVERT: E 116 ASP cc_start: 0.7231 (p0) cc_final: 0.7015 (p0) REVERT: E 209 ILE cc_start: 0.9104 (mt) cc_final: 0.8510 (tt) REVERT: E 280 LYS cc_start: 0.1503 (mmtt) cc_final: 0.0582 (tptt) REVERT: E 347 CYS cc_start: 0.8052 (t) cc_final: 0.7803 (t) REVERT: E 352 LYS cc_start: 0.7898 (tttp) cc_final: 0.7579 (ttpt) REVERT: E 377 MET cc_start: 0.8116 (tmm) cc_final: 0.7645 (tmm) REVERT: E 378 LEU cc_start: 0.8263 (mt) cc_final: 0.7794 (mp) REVERT: E 388 TRP cc_start: 0.5276 (m-10) cc_final: 0.4445 (m-90) REVERT: E 398 MET cc_start: 0.5327 (mmt) cc_final: 0.5010 (mmp) REVERT: E 425 MET cc_start: 0.8584 (tpt) cc_final: 0.8301 (tpp) REVERT: F 14 ASN cc_start: 0.8494 (m-40) cc_final: 0.8077 (m-40) REVERT: F 62 VAL cc_start: 0.9022 (t) cc_final: 0.8792 (p) REVERT: F 116 ASP cc_start: 0.8349 (p0) cc_final: 0.8123 (p0) REVERT: F 154 ILE cc_start: 0.8794 (mm) cc_final: 0.8520 (mm) REVERT: F 210 TYR cc_start: 0.7873 (m-80) cc_final: 0.7068 (m-80) REVERT: F 235 MET cc_start: 0.8178 (mtt) cc_final: 0.7628 (ttm) REVERT: F 268 PHE cc_start: 0.7485 (m-80) cc_final: 0.7071 (m-10) REVERT: F 302 MET cc_start: 0.5867 (mtp) cc_final: 0.5597 (mtp) REVERT: F 327 GLU cc_start: 0.7969 (pt0) cc_final: 0.6501 (pt0) REVERT: F 328 VAL cc_start: 0.8794 (t) cc_final: 0.8469 (p) REVERT: F 373 MET cc_start: 0.8493 (pmm) cc_final: 0.8163 (pmm) REVERT: G 113 GLU cc_start: 0.6740 (pp20) cc_final: 0.6086 (pp20) REVERT: G 129 CYS cc_start: 0.8284 (t) cc_final: 0.8030 (t) REVERT: G 169 PHE cc_start: 0.4614 (m-80) cc_final: 0.4250 (m-10) REVERT: G 252 LEU cc_start: 0.7519 (pp) cc_final: 0.7219 (pp) REVERT: G 286 LEU cc_start: 0.8357 (tp) cc_final: 0.8112 (tp) REVERT: G 292 THR cc_start: 0.8970 (p) cc_final: 0.8714 (p) REVERT: G 295 CYS cc_start: 0.8771 (m) cc_final: 0.8556 (m) REVERT: G 315 CYS cc_start: 0.7924 (t) cc_final: 0.6860 (t) REVERT: G 317 LEU cc_start: 0.7497 (mt) cc_final: 0.7258 (mt) REVERT: G 327 ASP cc_start: 0.6600 (p0) cc_final: 0.6020 (p0) REVERT: G 378 LEU cc_start: 0.7147 (mp) cc_final: 0.6488 (mp) REVERT: H 19 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8330 (mmmm) REVERT: H 124 LYS cc_start: 0.8823 (pptt) cc_final: 0.7780 (tttp) REVERT: H 149 MET cc_start: 0.5250 (ppp) cc_final: 0.4608 (ppp) REVERT: H 209 LEU cc_start: 0.7896 (mt) cc_final: 0.7198 (mt) REVERT: H 234 THR cc_start: 0.8746 (p) cc_final: 0.8422 (p) REVERT: H 235 MET cc_start: 0.8075 (mmm) cc_final: 0.7580 (mmt) REVERT: H 301 MET cc_start: 0.6425 (mmm) cc_final: 0.6057 (mmt) REVERT: H 332 MET cc_start: 0.6762 (mmm) cc_final: 0.6376 (mmm) REVERT: I 26 LEU cc_start: 0.8805 (mt) cc_final: 0.8556 (mt) REVERT: I 75 ILE cc_start: 0.6293 (mm) cc_final: 0.5985 (tt) REVERT: I 186 ASN cc_start: 0.7856 (m-40) cc_final: 0.7315 (m-40) REVERT: I 211 ASP cc_start: 0.6513 (t70) cc_final: 0.6248 (t0) REVERT: I 237 SER cc_start: 0.7649 (p) cc_final: 0.7110 (m) REVERT: I 282 TYR cc_start: 0.7844 (m-80) cc_final: 0.7397 (m-80) REVERT: I 335 ILE cc_start: 0.7747 (mm) cc_final: 0.7230 (mm) REVERT: I 347 CYS cc_start: 0.7744 (t) cc_final: 0.7219 (t) REVERT: I 377 MET cc_start: 0.8016 (tmm) cc_final: 0.7460 (tmm) REVERT: J 209 LEU cc_start: 0.8114 (mt) cc_final: 0.7834 (mt) REVERT: J 230 LEU cc_start: 0.8440 (tp) cc_final: 0.8081 (tp) REVERT: J 235 MET cc_start: 0.8343 (mtp) cc_final: 0.7662 (mtm) REVERT: J 241 CYS cc_start: 0.8333 (t) cc_final: 0.7933 (t) REVERT: J 259 MET cc_start: 0.7557 (mmm) cc_final: 0.6531 (mmm) REVERT: J 267 PHE cc_start: 0.7090 (m-10) cc_final: 0.6325 (m-10) REVERT: J 305 CYS cc_start: 0.6088 (t) cc_final: 0.5382 (t) REVERT: J 342 TYR cc_start: 0.6510 (m-80) cc_final: 0.6299 (m-80) REVERT: J 384 ILE cc_start: 0.7792 (mt) cc_final: 0.7476 (mm) REVERT: J 395 PHE cc_start: 0.7862 (t80) cc_final: 0.7271 (t80) REVERT: K 14 VAL cc_start: 0.8872 (m) cc_final: 0.8661 (p) REVERT: K 75 ILE cc_start: 0.6480 (mm) cc_final: 0.6107 (tt) REVERT: K 77 GLU cc_start: 0.8429 (pt0) cc_final: 0.8192 (pt0) REVERT: K 116 ASP cc_start: 0.7844 (p0) cc_final: 0.7151 (p0) REVERT: K 122 ILE cc_start: 0.8246 (pt) cc_final: 0.7625 (pt) REVERT: K 209 ILE cc_start: 0.8853 (mp) cc_final: 0.8197 (mp) REVERT: K 377 MET cc_start: 0.7824 (tmm) cc_final: 0.7214 (tmm) REVERT: L 59 ASN cc_start: 0.3862 (p0) cc_final: 0.3530 (p0) REVERT: L 235 MET cc_start: 0.6328 (mtt) cc_final: 0.6028 (mtt) REVERT: L 267 PHE cc_start: 0.6734 (m-10) cc_final: 0.6382 (m-10) REVERT: L 302 MET cc_start: 0.8292 (mmm) cc_final: 0.7865 (mmt) REVERT: M 74 VAL cc_start: 0.8078 (t) cc_final: 0.7852 (t) REVERT: M 75 ILE cc_start: 0.8390 (mm) cc_final: 0.8016 (tt) REVERT: M 154 MET cc_start: 0.7845 (ttp) cc_final: 0.7371 (tmm) REVERT: M 186 ASN cc_start: 0.7235 (m-40) cc_final: 0.6971 (t0) REVERT: M 191 THR cc_start: 0.8242 (p) cc_final: 0.7824 (p) REVERT: M 209 ILE cc_start: 0.8837 (mp) cc_final: 0.8456 (tt) REVERT: M 231 ILE cc_start: 0.8588 (mm) cc_final: 0.8007 (mm) REVERT: M 313 MET cc_start: 0.5067 (mmm) cc_final: 0.4531 (mmm) REVERT: M 334 THR cc_start: 0.7181 (m) cc_final: 0.5874 (p) REVERT: M 335 ILE cc_start: 0.7817 (mm) cc_final: 0.7207 (mm) REVERT: N 14 ASN cc_start: 0.8397 (m-40) cc_final: 0.7622 (m-40) REVERT: N 50 ASN cc_start: 0.8909 (p0) cc_final: 0.8470 (p0) REVERT: N 107 HIS cc_start: 0.6890 (t70) cc_final: 0.6618 (t70) REVERT: N 262 PHE cc_start: 0.7568 (t80) cc_final: 0.7352 (t80) REVERT: N 265 LEU cc_start: 0.7407 (mp) cc_final: 0.6908 (tt) REVERT: N 268 PHE cc_start: 0.7015 (m-80) cc_final: 0.6115 (m-80) REVERT: N 295 MET cc_start: 0.7055 (tpp) cc_final: 0.6614 (tmm) REVERT: N 299 LYS cc_start: 0.7409 (tmtt) cc_final: 0.7150 (tptp) REVERT: N 405 LEU cc_start: 0.8030 (tp) cc_final: 0.7660 (tp) REVERT: N 416 MET cc_start: 0.4518 (tpt) cc_final: 0.4112 (tpt) REVERT: O 22 GLU cc_start: 0.7896 (pt0) cc_final: 0.7661 (pt0) REVERT: O 295 CYS cc_start: 0.9050 (m) cc_final: 0.8706 (m) REVERT: O 407 TRP cc_start: 0.8681 (m100) cc_final: 0.8388 (m-10) REVERT: P 53 TYR cc_start: 0.7244 (m-80) cc_final: 0.6774 (m-10) REVERT: P 252 LEU cc_start: 0.7626 (mt) cc_final: 0.7137 (pt) REVERT: P 259 MET cc_start: 0.7134 (mmm) cc_final: 0.6638 (mmm) REVERT: Q 113 GLU cc_start: 0.8882 (mp0) cc_final: 0.6803 (tm-30) REVERT: Q 130 THR cc_start: 0.8136 (p) cc_final: 0.7869 (t) REVERT: Q 154 MET cc_start: 0.6811 (ppp) cc_final: 0.6532 (ppp) REVERT: Q 191 THR cc_start: 0.8429 (p) cc_final: 0.7924 (p) REVERT: Q 217 LEU cc_start: 0.7606 (mm) cc_final: 0.7403 (mm) REVERT: Q 313 MET cc_start: 0.3472 (mmm) cc_final: 0.2590 (tpt) REVERT: Q 318 LEU cc_start: 0.6358 (mt) cc_final: 0.5835 (mt) REVERT: R 5 VAL cc_start: 0.7365 (t) cc_final: 0.7138 (t) REVERT: R 6 HIS cc_start: 0.8157 (t-90) cc_final: 0.7766 (t-90) REVERT: R 14 ASN cc_start: 0.8099 (m110) cc_final: 0.7436 (m110) REVERT: R 53 TYR cc_start: 0.5780 (m-80) cc_final: 0.5324 (m-10) REVERT: R 119 LEU cc_start: 0.7531 (mp) cc_final: 0.7015 (mt) REVERT: R 295 MET cc_start: 0.8117 (ttt) cc_final: 0.7548 (tpp) REVERT: R 300 ASN cc_start: 0.7945 (m-40) cc_final: 0.7207 (t0) REVERT: R 377 PHE cc_start: 0.5999 (t80) cc_final: 0.5494 (t80) REVERT: R 413 MET cc_start: 0.6833 (mmm) cc_final: 0.6062 (mmp) outliers start: 5 outliers final: 3 residues processed: 1457 average time/residue: 0.5698 time to fit residues: 1410.0495 Evaluate side-chains 1096 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1093 time to evaluate : 5.165 ------------------------------------------------------------------------------- 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: 50.0000 chunk 290 optimal weight: 30.0000 chunk 435 optimal weight: 40.0000 chunk 219 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 30.0000 chunk 463 optimal weight: 40.0000 chunk 496 optimal weight: 5.9990 chunk 360 optimal weight: 40.0000 chunk 67 optimal weight: 7.9990 chunk 572 optimal weight: 50.0000 overall best weight: 11.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 342 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN B 339 ASN B 380 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS C 342 GLN D 101 ASN D 380 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN F 380 ASN G 61 HIS G 266 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 GLN K 301 GLN K 342 GLN L 14 ASN L 229 HIS M 128 GLN ** N 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 ASN O 8 HIS O 35 GLN O 197 HIS ** P 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 133 GLN ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 139 HIS Q 226 ASN R 14 ASN ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 107 HIS ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 HIS ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.8024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 62298 Z= 0.264 Angle : 0.688 14.571 84645 Z= 0.361 Chirality : 0.047 0.385 9216 Planarity : 0.005 0.130 11043 Dihedral : 11.672 179.690 8784 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.06 % Allowed : 1.05 % Favored : 98.88 % 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: 0.75 (0.08), residues: 3582 sheet: 0.44 (0.14), residues: 1350 loop : 0.08 (0.13), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP G 346 HIS 0.011 0.002 HIS R 192 PHE 0.029 0.002 PHE D 268 TYR 0.041 0.002 TYR G 224 ARG 0.017 0.001 ARG N 401 *********************** 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 1371 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1367 time to evaluate : 5.311 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: A 21 TRP cc_start: 0.8526 (m100) cc_final: 0.7550 (m100) REVERT: A 75 ILE cc_start: 0.8500 (mt) cc_final: 0.7611 (tt) REVERT: A 120 ASP cc_start: 0.6749 (t0) cc_final: 0.6523 (t70) REVERT: A 291 ILE cc_start: 0.9262 (mt) cc_final: 0.9050 (mt) REVERT: A 295 CYS cc_start: 0.9111 (m) cc_final: 0.8868 (m) REVERT: A 302 MET cc_start: 0.8719 (tpp) cc_final: 0.8314 (mmm) REVERT: A 433 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7131 (tm-30) REVERT: B 75 MET cc_start: 0.8855 (mmp) cc_final: 0.8569 (mmp) REVERT: B 210 TYR cc_start: 0.7175 (m-80) cc_final: 0.6934 (m-80) REVERT: B 234 THR cc_start: 0.9241 (p) cc_final: 0.8473 (t) REVERT: B 259 MET cc_start: 0.8059 (mmp) cc_final: 0.7249 (mmm) REVERT: B 268 PHE cc_start: 0.8589 (m-80) cc_final: 0.8120 (m-10) REVERT: B 276 THR cc_start: 0.7421 (p) cc_final: 0.7086 (p) REVERT: B 288 VAL cc_start: 0.9131 (t) cc_final: 0.8819 (t) REVERT: B 351 VAL cc_start: 0.7669 (t) cc_final: 0.7279 (t) REVERT: B 399 PHE cc_start: 0.7772 (t80) cc_final: 0.7341 (t80) REVERT: C 36 MET cc_start: 0.6472 (mpp) cc_final: 0.6134 (mpp) REVERT: C 66 VAL cc_start: 0.7890 (t) cc_final: 0.7686 (t) REVERT: C 217 LEU cc_start: 0.8380 (tp) cc_final: 0.8027 (tp) REVERT: C 291 ILE cc_start: 0.9185 (mt) cc_final: 0.8737 (tt) REVERT: D 14 ASN cc_start: 0.8149 (m-40) cc_final: 0.7450 (m-40) REVERT: D 149 MET cc_start: 0.6034 (ptt) cc_final: 0.5723 (ppp) REVERT: D 163 ASP cc_start: 0.6624 (p0) cc_final: 0.6036 (p0) REVERT: D 204 ILE cc_start: 0.9307 (mp) cc_final: 0.9080 (mt) REVERT: D 235 MET cc_start: 0.6491 (ttt) cc_final: 0.5998 (ttt) REVERT: D 259 MET cc_start: 0.7131 (mmm) cc_final: 0.6888 (mmm) REVERT: E 116 ASP cc_start: 0.7696 (p0) cc_final: 0.7312 (p0) REVERT: E 280 LYS cc_start: 0.2277 (mmtt) cc_final: 0.1140 (mmtt) REVERT: E 352 LYS cc_start: 0.7939 (tttp) cc_final: 0.7266 (ttpt) REVERT: E 377 MET cc_start: 0.7824 (tmm) cc_final: 0.7412 (tmm) REVERT: E 378 LEU cc_start: 0.8187 (mt) cc_final: 0.7925 (mp) REVERT: E 388 TRP cc_start: 0.5685 (m-10) cc_final: 0.4934 (m-90) REVERT: E 425 MET cc_start: 0.8597 (tpt) cc_final: 0.8339 (tpp) REVERT: F 14 ASN cc_start: 0.8831 (m-40) cc_final: 0.8195 (m-40) REVERT: F 116 ASP cc_start: 0.8535 (p0) cc_final: 0.8280 (p0) REVERT: F 154 ILE cc_start: 0.8844 (mm) cc_final: 0.8612 (mm) REVERT: F 235 MET cc_start: 0.8375 (mtt) cc_final: 0.8031 (ttm) REVERT: F 295 MET cc_start: 0.8230 (tpp) cc_final: 0.7803 (tpp) REVERT: F 302 MET cc_start: 0.5998 (mtp) cc_final: 0.5624 (mtp) REVERT: F 327 GLU cc_start: 0.8143 (pt0) cc_final: 0.6435 (pt0) REVERT: F 328 VAL cc_start: 0.8823 (t) cc_final: 0.8491 (p) REVERT: G 16 ILE cc_start: 0.9360 (mt) cc_final: 0.9100 (pt) REVERT: G 113 GLU cc_start: 0.6773 (pp20) cc_final: 0.6118 (pp20) REVERT: G 129 CYS cc_start: 0.8006 (t) cc_final: 0.7708 (t) REVERT: G 132 LEU cc_start: 0.8413 (tp) cc_final: 0.8095 (tp) REVERT: G 169 PHE cc_start: 0.4985 (m-80) cc_final: 0.4768 (m-10) REVERT: G 252 LEU cc_start: 0.7572 (pp) cc_final: 0.7207 (pp) REVERT: G 254 GLU cc_start: 0.7634 (mp0) cc_final: 0.7323 (mp0) REVERT: G 315 CYS cc_start: 0.7990 (t) cc_final: 0.7144 (t) REVERT: G 378 LEU cc_start: 0.7373 (mp) cc_final: 0.6469 (mp) REVERT: H 39 ASP cc_start: 0.6885 (p0) cc_final: 0.6670 (p0) REVERT: H 124 LYS cc_start: 0.9014 (pptt) cc_final: 0.7885 (tttp) REVERT: H 149 MET cc_start: 0.5358 (ppp) cc_final: 0.4838 (ppp) REVERT: H 234 THR cc_start: 0.8734 (p) cc_final: 0.8453 (p) REVERT: H 235 MET cc_start: 0.8007 (mmm) cc_final: 0.7298 (mmt) REVERT: H 295 MET cc_start: 0.8152 (ppp) cc_final: 0.7931 (ppp) REVERT: H 332 MET cc_start: 0.7004 (mmm) cc_final: 0.6569 (mmm) REVERT: I 4 CYS cc_start: 0.4571 (t) cc_final: 0.3985 (t) REVERT: I 116 ASP cc_start: 0.8211 (p0) cc_final: 0.7864 (p0) REVERT: I 160 ASP cc_start: 0.8057 (t0) cc_final: 0.7762 (t0) REVERT: I 186 ASN cc_start: 0.8030 (m-40) cc_final: 0.7505 (m-40) REVERT: I 237 SER cc_start: 0.7658 (p) cc_final: 0.7216 (m) REVERT: I 347 CYS cc_start: 0.8002 (t) cc_final: 0.7602 (t) REVERT: I 378 LEU cc_start: 0.8087 (mp) cc_final: 0.7825 (mp) REVERT: J 85 GLN cc_start: 0.8301 (mp10) cc_final: 0.7958 (mm-40) REVERT: J 203 CYS cc_start: 0.7267 (m) cc_final: 0.6613 (m) REVERT: J 230 LEU cc_start: 0.8501 (tp) cc_final: 0.8266 (tp) REVERT: J 235 MET cc_start: 0.7870 (mtp) cc_final: 0.7490 (mtm) REVERT: J 259 MET cc_start: 0.7593 (mmm) cc_final: 0.6272 (mmm) REVERT: J 432 TYR cc_start: 0.3800 (m-10) cc_final: 0.3343 (m-10) REVERT: K 14 VAL cc_start: 0.8879 (m) cc_final: 0.8672 (p) REVERT: K 75 ILE cc_start: 0.6544 (mm) cc_final: 0.6101 (tt) REVERT: K 116 ASP cc_start: 0.7996 (p0) cc_final: 0.7344 (p0) REVERT: K 122 ILE cc_start: 0.8232 (pt) cc_final: 0.7711 (pt) REVERT: K 209 ILE cc_start: 0.9114 (mp) cc_final: 0.8278 (mp) REVERT: K 335 ILE cc_start: 0.7441 (mm) cc_final: 0.7147 (mm) REVERT: K 377 MET cc_start: 0.8088 (tmm) cc_final: 0.7543 (tmm) REVERT: K 435 VAL cc_start: 0.8379 (t) cc_final: 0.7926 (t) REVERT: L 14 ASN cc_start: 0.8271 (m110) cc_final: 0.7488 (t0) REVERT: L 21 TRP cc_start: 0.7522 (m100) cc_final: 0.7191 (m100) REVERT: L 209 LEU cc_start: 0.8766 (mt) cc_final: 0.8519 (mt) REVERT: L 269 MET cc_start: 0.6233 (mtm) cc_final: 0.5932 (mtm) REVERT: L 301 MET cc_start: 0.6786 (tpt) cc_final: 0.6520 (tpt) REVERT: L 353 THR cc_start: 0.5819 (p) cc_final: 0.5579 (m) REVERT: M 75 ILE cc_start: 0.8430 (mm) cc_final: 0.8018 (tt) REVERT: M 154 MET cc_start: 0.7855 (ttp) cc_final: 0.7472 (tmm) REVERT: M 209 ILE cc_start: 0.8981 (mp) cc_final: 0.8620 (tt) REVERT: M 213 CYS cc_start: 0.5891 (t) cc_final: 0.5580 (t) REVERT: N 14 ASN cc_start: 0.8464 (m-40) cc_final: 0.7674 (m-40) REVERT: N 115 VAL cc_start: 0.8787 (t) cc_final: 0.8545 (t) REVERT: N 217 LEU cc_start: 0.6759 (tp) cc_final: 0.6354 (tt) REVERT: N 268 PHE cc_start: 0.7033 (m-80) cc_final: 0.6227 (m-80) REVERT: N 295 MET cc_start: 0.7248 (tpp) cc_final: 0.6627 (tmm) REVERT: N 299 LYS cc_start: 0.7522 (tmtt) cc_final: 0.7053 (tptm) REVERT: N 413 MET cc_start: 0.5726 (mmp) cc_final: 0.4965 (mmp) REVERT: N 416 MET cc_start: 0.4238 (tpt) cc_final: 0.3701 (tpt) REVERT: O 22 GLU cc_start: 0.8071 (pt0) cc_final: 0.7785 (pt0) REVERT: O 75 ILE cc_start: 0.8462 (mm) cc_final: 0.8245 (mm) REVERT: O 221 ARG cc_start: 0.8239 (mpp80) cc_final: 0.7857 (mtm-85) REVERT: O 295 CYS cc_start: 0.8688 (m) cc_final: 0.8470 (m) REVERT: P 53 TYR cc_start: 0.7635 (m-80) cc_final: 0.7116 (m-10) REVERT: P 296 PHE cc_start: 0.6858 (m-10) cc_final: 0.6460 (m-80) REVERT: Q 130 THR cc_start: 0.8364 (p) cc_final: 0.8068 (t) REVERT: Q 191 THR cc_start: 0.8546 (p) cc_final: 0.7798 (p) REVERT: Q 217 LEU cc_start: 0.7962 (mm) cc_final: 0.7688 (mm) REVERT: Q 248 LEU cc_start: 0.6967 (mt) cc_final: 0.6753 (mm) REVERT: Q 313 MET cc_start: 0.3815 (mmm) cc_final: 0.2847 (tpt) REVERT: Q 318 LEU cc_start: 0.6463 (mt) cc_final: 0.6055 (mt) REVERT: Q 430 LYS cc_start: 0.7510 (mmtm) cc_final: 0.7269 (tmmt) REVERT: R 5 VAL cc_start: 0.7517 (t) cc_final: 0.7135 (t) REVERT: R 6 HIS cc_start: 0.8205 (t-90) cc_final: 0.7851 (t-90) REVERT: R 14 ASN cc_start: 0.7983 (m-40) cc_final: 0.7122 (m110) REVERT: R 166 MET cc_start: 0.5893 (tpp) cc_final: 0.5664 (tpt) REVERT: R 235 MET cc_start: 0.7777 (mtp) cc_final: 0.7559 (mtt) REVERT: R 295 MET cc_start: 0.8501 (ttt) cc_final: 0.7740 (tpp) REVERT: R 300 ASN cc_start: 0.8144 (m-40) cc_final: 0.7447 (t0) REVERT: R 301 MET cc_start: 0.7859 (mtt) cc_final: 0.7450 (mtt) REVERT: R 302 MET cc_start: 0.7385 (mmt) cc_final: 0.6939 (mmm) REVERT: R 413 MET cc_start: 0.6493 (mmm) cc_final: 0.5761 (mmp) outliers start: 4 outliers final: 0 residues processed: 1370 average time/residue: 0.5708 time to fit residues: 1330.4190 Evaluate side-chains 1012 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1012 time to evaluate : 5.212 ------------------------------------------------------------------------------- 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: 6.9990 chunk 698 optimal weight: 9.9990 chunk 636 optimal weight: 9.9990 chunk 679 optimal weight: 8.9990 chunk 697 optimal weight: 10.0000 chunk 408 optimal weight: 8.9990 chunk 295 optimal weight: 40.0000 chunk 533 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 613 optimal weight: 10.0000 chunk 642 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 380 ASN G 139 HIS ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 GLN ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN O 266 HIS ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS P 133 GLN ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 136 GLN R 139 HIS ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 331 GLN ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.8288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62298 Z= 0.197 Angle : 0.665 13.154 84645 Z= 0.344 Chirality : 0.046 0.270 9216 Planarity : 0.005 0.080 11043 Dihedral : 11.493 178.373 8784 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.02 % Allowed : 0.47 % Favored : 99.51 % 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: 0.85 (0.09), residues: 3564 sheet: 0.45 (0.14), residues: 1341 loop : -0.08 (0.13), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP E 346 HIS 0.012 0.001 HIS P 28 PHE 0.041 0.002 PHE M 49 TYR 0.033 0.002 TYR A 24 ARG 0.013 0.001 ARG B 158 *********************** 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 1410 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1409 time to evaluate : 5.245 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: A 36 MET cc_start: 0.6745 (ppp) cc_final: 0.6504 (ptm) REVERT: A 66 VAL cc_start: 0.7695 (t) cc_final: 0.7460 (t) REVERT: A 75 ILE cc_start: 0.8626 (mt) cc_final: 0.7920 (tt) REVERT: A 77 GLU cc_start: 0.7538 (pt0) cc_final: 0.7253 (pt0) REVERT: A 116 ASP cc_start: 0.7601 (p0) cc_final: 0.7274 (p0) REVERT: A 118 VAL cc_start: 0.9173 (t) cc_final: 0.8825 (p) REVERT: A 120 ASP cc_start: 0.6645 (t0) cc_final: 0.6206 (t70) REVERT: A 132 LEU cc_start: 0.7517 (tp) cc_final: 0.6237 (mp) REVERT: A 153 LEU cc_start: 0.8030 (tt) cc_final: 0.7807 (tt) REVERT: A 221 ARG cc_start: 0.6757 (mmt180) cc_final: 0.6435 (mmt180) REVERT: A 291 ILE cc_start: 0.9279 (mt) cc_final: 0.9050 (mt) REVERT: A 302 MET cc_start: 0.8866 (tpp) cc_final: 0.8483 (mmm) REVERT: A 413 MET cc_start: 0.5991 (mmm) cc_final: 0.4538 (mmt) REVERT: A 433 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6832 (tm-30) REVERT: B 119 LEU cc_start: 0.7592 (tp) cc_final: 0.7307 (tp) REVERT: B 123 ARG cc_start: 0.7803 (mtt180) cc_final: 0.7597 (mtt-85) REVERT: B 234 THR cc_start: 0.9101 (p) cc_final: 0.8333 (t) REVERT: B 235 MET cc_start: 0.8405 (mtt) cc_final: 0.7425 (ttm) REVERT: B 259 MET cc_start: 0.7770 (mmp) cc_final: 0.7035 (mmm) REVERT: B 283 TYR cc_start: 0.6265 (m-10) cc_final: 0.6020 (m-10) REVERT: B 288 VAL cc_start: 0.9144 (t) cc_final: 0.8925 (t) REVERT: B 291 LEU cc_start: 0.8956 (mm) cc_final: 0.8573 (tp) REVERT: B 328 VAL cc_start: 0.8364 (t) cc_final: 0.8126 (p) REVERT: B 372 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8699 (tttt) REVERT: B 399 PHE cc_start: 0.7640 (t80) cc_final: 0.7170 (t80) REVERT: C 36 MET cc_start: 0.6304 (mpp) cc_final: 0.5936 (mpp) REVERT: C 217 LEU cc_start: 0.8367 (tp) cc_final: 0.7853 (tp) REVERT: C 224 TYR cc_start: 0.7712 (m-80) cc_final: 0.6559 (m-80) REVERT: C 295 CYS cc_start: 0.8729 (m) cc_final: 0.8435 (m) REVERT: C 315 CYS cc_start: 0.7265 (m) cc_final: 0.6956 (m) REVERT: C 347 CYS cc_start: 0.7109 (t) cc_final: 0.6319 (t) REVERT: D 14 ASN cc_start: 0.8097 (m-40) cc_final: 0.7507 (m-40) REVERT: D 259 MET cc_start: 0.7209 (mmm) cc_final: 0.6710 (mmm) REVERT: D 293 GLN cc_start: 0.8252 (mm110) cc_final: 0.7877 (mm-40) REVERT: D 335 VAL cc_start: 0.7565 (p) cc_final: 0.7310 (m) REVERT: D 398 MET cc_start: 0.6569 (mmm) cc_final: 0.5929 (mmm) REVERT: E 116 ASP cc_start: 0.7484 (p0) cc_final: 0.7200 (p0) REVERT: E 122 ILE cc_start: 0.8788 (pt) cc_final: 0.8551 (pt) REVERT: E 154 MET cc_start: 0.6812 (ppp) cc_final: 0.6487 (tmm) REVERT: E 209 ILE cc_start: 0.9228 (mt) cc_final: 0.8876 (tt) REVERT: E 280 LYS cc_start: 0.2127 (mmtt) cc_final: 0.1043 (mmtt) REVERT: E 352 LYS cc_start: 0.7832 (tttp) cc_final: 0.7089 (ttpt) REVERT: E 377 MET cc_start: 0.7985 (tmm) cc_final: 0.7599 (tmm) REVERT: E 378 LEU cc_start: 0.8325 (mt) cc_final: 0.7972 (mp) REVERT: E 388 TRP cc_start: 0.5860 (m-10) cc_final: 0.5510 (m-90) REVERT: E 425 MET cc_start: 0.8570 (tpt) cc_final: 0.8322 (tpp) REVERT: E 433 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6551 (tm-30) REVERT: F 14 ASN cc_start: 0.8734 (m-40) cc_final: 0.8257 (m-40) REVERT: F 116 ASP cc_start: 0.8574 (p0) cc_final: 0.8359 (p0) REVERT: F 120 ASP cc_start: 0.5667 (t70) cc_final: 0.5393 (t70) REVERT: F 136 GLN cc_start: 0.7141 (mt0) cc_final: 0.6935 (mt0) REVERT: F 154 ILE cc_start: 0.8760 (mm) cc_final: 0.8532 (mm) REVERT: F 204 ILE cc_start: 0.8821 (mt) cc_final: 0.8515 (mt) REVERT: F 235 MET cc_start: 0.8280 (mtt) cc_final: 0.7520 (ttm) REVERT: F 295 MET cc_start: 0.8186 (tpp) cc_final: 0.7899 (tpp) REVERT: F 302 MET cc_start: 0.5914 (mtp) cc_final: 0.5678 (mtp) REVERT: F 327 GLU cc_start: 0.7912 (pt0) cc_final: 0.6869 (pt0) REVERT: F 328 VAL cc_start: 0.8796 (t) cc_final: 0.8315 (p) REVERT: F 351 VAL cc_start: 0.7493 (t) cc_final: 0.6755 (t) REVERT: F 373 MET cc_start: 0.8553 (pmm) cc_final: 0.8336 (pmm) REVERT: G 113 GLU cc_start: 0.6741 (pp20) cc_final: 0.6065 (pp20) REVERT: G 129 CYS cc_start: 0.7953 (t) cc_final: 0.7646 (t) REVERT: G 132 LEU cc_start: 0.8292 (tp) cc_final: 0.8080 (tp) REVERT: G 169 PHE cc_start: 0.4804 (m-80) cc_final: 0.4531 (m-10) REVERT: G 252 LEU cc_start: 0.7735 (pp) cc_final: 0.7393 (pp) REVERT: G 254 GLU cc_start: 0.8041 (mp0) cc_final: 0.7249 (mm-30) REVERT: G 315 CYS cc_start: 0.8021 (t) cc_final: 0.7042 (t) REVERT: G 327 ASP cc_start: 0.6463 (p0) cc_final: 0.5888 (p0) REVERT: G 378 LEU cc_start: 0.7179 (mp) cc_final: 0.6352 (mp) REVERT: H 39 ASP cc_start: 0.6769 (p0) cc_final: 0.6477 (p0) REVERT: H 124 LYS cc_start: 0.8941 (pptt) cc_final: 0.8245 (ptmt) REVERT: H 149 MET cc_start: 0.4994 (ppp) cc_final: 0.4715 (ppp) REVERT: H 234 THR cc_start: 0.8691 (p) cc_final: 0.8360 (p) REVERT: H 235 MET cc_start: 0.7962 (mmm) cc_final: 0.7232 (mmt) REVERT: H 295 MET cc_start: 0.7743 (ppp) cc_final: 0.7303 (ppp) REVERT: I 26 LEU cc_start: 0.8900 (mt) cc_final: 0.8657 (mt) REVERT: I 186 ASN cc_start: 0.8031 (m-40) cc_final: 0.7609 (m-40) REVERT: I 203 MET cc_start: 0.5297 (tpt) cc_final: 0.5093 (tpt) REVERT: I 282 TYR cc_start: 0.7988 (m-80) cc_final: 0.7663 (m-80) REVERT: I 286 LEU cc_start: 0.8453 (mt) cc_final: 0.8194 (mt) REVERT: I 347 CYS cc_start: 0.7974 (t) cc_final: 0.7487 (t) REVERT: I 378 LEU cc_start: 0.8002 (mp) cc_final: 0.7744 (mp) REVERT: J 85 GLN cc_start: 0.8091 (mp10) cc_final: 0.7786 (mm-40) REVERT: J 120 ASP cc_start: 0.6931 (t0) cc_final: 0.6555 (t0) REVERT: J 122 VAL cc_start: 0.9141 (t) cc_final: 0.8927 (t) REVERT: J 235 MET cc_start: 0.7909 (mtp) cc_final: 0.7325 (mtm) REVERT: J 241 CYS cc_start: 0.8138 (t) cc_final: 0.7909 (t) REVERT: J 259 MET cc_start: 0.7749 (mmm) cc_final: 0.6773 (mmm) REVERT: J 328 VAL cc_start: 0.8509 (m) cc_final: 0.8140 (m) REVERT: K 14 VAL cc_start: 0.8731 (m) cc_final: 0.8522 (p) REVERT: K 36 MET cc_start: 0.7004 (mmm) cc_final: 0.6323 (tpp) REVERT: K 75 ILE cc_start: 0.6604 (mm) cc_final: 0.6324 (tt) REVERT: K 116 ASP cc_start: 0.7987 (p0) cc_final: 0.7263 (p0) REVERT: K 122 ILE cc_start: 0.8105 (pt) cc_final: 0.7631 (pt) REVERT: K 191 THR cc_start: 0.7613 (p) cc_final: 0.7381 (p) REVERT: K 335 ILE cc_start: 0.7382 (mm) cc_final: 0.7022 (mm) REVERT: K 377 MET cc_start: 0.7596 (tmm) cc_final: 0.7132 (tmm) REVERT: K 386 GLU cc_start: 0.7869 (mp0) cc_final: 0.7578 (mp0) REVERT: L 87 PHE cc_start: 0.7353 (m-80) cc_final: 0.7105 (m-80) REVERT: L 235 MET cc_start: 0.6536 (mtt) cc_final: 0.6216 (mtt) REVERT: L 259 MET cc_start: 0.7713 (mmm) cc_final: 0.7373 (mmm) REVERT: L 269 MET cc_start: 0.6473 (mtm) cc_final: 0.6263 (mtm) REVERT: L 301 MET cc_start: 0.7361 (tpt) cc_final: 0.6944 (tpt) REVERT: M 21 TRP cc_start: 0.7887 (m100) cc_final: 0.7523 (m100) REVERT: M 33 ASP cc_start: 0.5717 (p0) cc_final: 0.5181 (p0) REVERT: M 75 ILE cc_start: 0.8480 (mm) cc_final: 0.8033 (tt) REVERT: M 154 MET cc_start: 0.7588 (ttp) cc_final: 0.6964 (tmm) REVERT: M 191 THR cc_start: 0.8419 (p) cc_final: 0.8090 (p) REVERT: M 209 ILE cc_start: 0.8951 (mp) cc_final: 0.8528 (tt) REVERT: M 213 CYS cc_start: 0.5493 (t) cc_final: 0.4652 (t) REVERT: M 231 ILE cc_start: 0.8574 (mm) cc_final: 0.7812 (mm) REVERT: M 282 TYR cc_start: 0.5338 (t80) cc_final: 0.5025 (t80) REVERT: M 334 THR cc_start: 0.7293 (m) cc_final: 0.7028 (p) REVERT: M 335 ILE cc_start: 0.7814 (mm) cc_final: 0.7594 (mm) REVERT: N 14 ASN cc_start: 0.8404 (m-40) cc_final: 0.7594 (m-40) REVERT: N 258 ASN cc_start: 0.9126 (m-40) cc_final: 0.8367 (t0) REVERT: N 268 PHE cc_start: 0.6869 (m-80) cc_final: 0.5988 (m-80) REVERT: N 295 MET cc_start: 0.7136 (tpp) cc_final: 0.6512 (tmm) REVERT: N 299 LYS cc_start: 0.7807 (tmtt) cc_final: 0.7371 (tmtt) REVERT: N 416 MET cc_start: 0.4328 (tpt) cc_final: 0.3875 (tpt) REVERT: O 74 VAL cc_start: 0.8025 (t) cc_final: 0.7670 (t) REVERT: O 113 GLU cc_start: 0.7618 (mp0) cc_final: 0.6660 (tm-30) REVERT: O 155 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6882 (tm-30) REVERT: O 191 THR cc_start: 0.7929 (p) cc_final: 0.7684 (p) REVERT: O 286 LEU cc_start: 0.6536 (tp) cc_final: 0.6306 (tp) REVERT: O 295 CYS cc_start: 0.8734 (m) cc_final: 0.8406 (m) REVERT: O 347 CYS cc_start: 0.7407 (t) cc_final: 0.7141 (m) REVERT: O 388 TRP cc_start: 0.3812 (m-90) cc_final: 0.3606 (m-90) REVERT: O 413 MET cc_start: 0.6920 (mmm) cc_final: 0.6268 (mmt) REVERT: P 202 TYR cc_start: 0.5721 (m-80) cc_final: 0.5500 (m-10) REVERT: P 296 PHE cc_start: 0.6932 (m-10) cc_final: 0.6525 (m-80) REVERT: P 332 MET cc_start: 0.6834 (mmm) cc_final: 0.6588 (mmm) REVERT: Q 80 THR cc_start: 0.8185 (p) cc_final: 0.7667 (t) REVERT: Q 113 GLU cc_start: 0.8969 (mp0) cc_final: 0.6470 (tm-30) REVERT: Q 120 ASP cc_start: 0.6392 (t70) cc_final: 0.3666 (t70) REVERT: Q 130 THR cc_start: 0.8305 (p) cc_final: 0.8001 (t) REVERT: Q 191 THR cc_start: 0.8096 (p) cc_final: 0.7778 (p) REVERT: Q 217 LEU cc_start: 0.7807 (mm) cc_final: 0.7544 (mm) REVERT: Q 313 MET cc_start: 0.3625 (mmm) cc_final: 0.2733 (tpt) REVERT: Q 318 LEU cc_start: 0.6389 (mt) cc_final: 0.5927 (mt) REVERT: R 6 HIS cc_start: 0.8177 (t-90) cc_final: 0.7896 (t-90) REVERT: R 14 ASN cc_start: 0.8449 (m-40) cc_final: 0.7616 (m110) REVERT: R 295 MET cc_start: 0.8536 (ttt) cc_final: 0.7784 (tpp) REVERT: R 300 ASN cc_start: 0.7982 (m-40) cc_final: 0.7041 (t0) REVERT: R 302 MET cc_start: 0.7387 (mmt) cc_final: 0.7067 (mmm) outliers start: 1 outliers final: 0 residues processed: 1409 average time/residue: 0.5868 time to fit residues: 1402.5477 Evaluate side-chains 1034 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1034 time to evaluate : 5.189 ------------------------------------------------------------------------------- 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: 50.0000 chunk 445 optimal weight: 0.9980 chunk 718 optimal weight: 20.0000 chunk 438 optimal weight: 40.0000 chunk 340 optimal weight: 40.0000 chunk 499 optimal weight: 20.0000 chunk 753 optimal weight: 30.0000 chunk 693 optimal weight: 7.9990 chunk 599 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 463 optimal weight: 50.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- 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 192 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 281 GLN B 337 ASN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 350 ASN F 380 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 349 ASN L 309 HIS M 309 HIS N 300 ASN N 339 ASN ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 380 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS ** R 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.8509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 62298 Z= 0.238 Angle : 0.689 11.139 84645 Z= 0.360 Chirality : 0.047 0.300 9216 Planarity : 0.005 0.136 11043 Dihedral : 11.489 176.957 8784 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.03 % Allowed : 0.20 % Favored : 99.77 % 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: 0.47 (0.10), residues: 7632 helix: 0.65 (0.09), residues: 3627 sheet: 0.62 (0.14), residues: 1305 loop : -0.12 (0.13), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.004 TRP A 388 HIS 0.015 0.001 HIS Q 309 PHE 0.031 0.002 PHE M 49 TYR 0.032 0.002 TYR A 24 ARG 0.014 0.001 ARG E 243 ********************** 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 1321 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1319 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: A 21 TRP cc_start: 0.8347 (m100) cc_final: 0.7281 (m100) REVERT: A 36 MET cc_start: 0.7202 (ppp) cc_final: 0.6871 (ptm) REVERT: A 66 VAL cc_start: 0.7836 (t) cc_final: 0.7223 (t) REVERT: A 75 ILE cc_start: 0.8623 (mt) cc_final: 0.7840 (tt) REVERT: A 77 GLU cc_start: 0.7722 (pt0) cc_final: 0.7420 (pt0) REVERT: A 116 ASP cc_start: 0.7866 (p0) cc_final: 0.7639 (p0) REVERT: A 118 VAL cc_start: 0.9030 (t) cc_final: 0.8697 (p) REVERT: A 122 ILE cc_start: 0.8861 (mt) cc_final: 0.8153 (tp) REVERT: A 153 LEU cc_start: 0.8081 (tt) cc_final: 0.7654 (tt) REVERT: A 157 LEU cc_start: 0.7173 (mt) cc_final: 0.6964 (mt) REVERT: A 413 MET cc_start: 0.6077 (mmm) cc_final: 0.5596 (mmt) REVERT: A 433 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6854 (tm-30) REVERT: B 5 VAL cc_start: 0.8939 (t) cc_final: 0.8737 (t) REVERT: B 14 ASN cc_start: 0.8690 (m110) cc_final: 0.8458 (m-40) REVERT: B 55 GLU cc_start: 0.7488 (tm-30) cc_final: 0.7214 (tm-30) REVERT: B 210 TYR cc_start: 0.7167 (m-80) cc_final: 0.6837 (m-80) REVERT: B 234 THR cc_start: 0.9044 (p) cc_final: 0.8189 (t) REVERT: B 235 MET cc_start: 0.8241 (mtt) cc_final: 0.7455 (ttm) REVERT: B 259 MET cc_start: 0.8066 (mmp) cc_final: 0.7026 (mmm) REVERT: B 276 THR cc_start: 0.7434 (p) cc_final: 0.7199 (p) REVERT: B 291 LEU cc_start: 0.8992 (mm) cc_final: 0.8568 (tp) REVERT: B 295 MET cc_start: 0.7816 (tpp) cc_final: 0.7448 (tpp) REVERT: B 302 MET cc_start: 0.7080 (ttp) cc_final: 0.6721 (ttm) REVERT: B 372 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8848 (tttt) REVERT: C 217 LEU cc_start: 0.8301 (tp) cc_final: 0.7787 (tp) REVERT: C 221 ARG cc_start: 0.7952 (mmt180) cc_final: 0.7638 (mmm160) REVERT: C 295 CYS cc_start: 0.8854 (m) cc_final: 0.8465 (m) REVERT: C 315 CYS cc_start: 0.7186 (m) cc_final: 0.6971 (m) REVERT: D 14 ASN cc_start: 0.8213 (m-40) cc_final: 0.7486 (m-40) REVERT: D 16 ILE cc_start: 0.8615 (mt) cc_final: 0.8381 (mt) REVERT: D 122 VAL cc_start: 0.8844 (t) cc_final: 0.8642 (t) REVERT: D 163 ASP cc_start: 0.6451 (p0) cc_final: 0.5992 (p0) REVERT: D 181 VAL cc_start: 0.6295 (m) cc_final: 0.6072 (m) REVERT: D 259 MET cc_start: 0.7237 (mmm) cc_final: 0.6668 (mmm) REVERT: D 293 GLN cc_start: 0.8319 (mm110) cc_final: 0.8057 (mm-40) REVERT: E 116 ASP cc_start: 0.7678 (p0) cc_final: 0.7295 (p0) REVERT: E 122 ILE cc_start: 0.8802 (pt) cc_final: 0.8565 (pt) REVERT: E 210 TYR cc_start: 0.7693 (m-80) cc_final: 0.7305 (m-80) REVERT: E 221 ARG cc_start: 0.6748 (mmt180) cc_final: 0.5191 (mtp85) REVERT: E 280 LYS cc_start: 0.2301 (mmtt) cc_final: 0.1281 (tptt) REVERT: E 377 MET cc_start: 0.7993 (tmm) cc_final: 0.7678 (tmm) REVERT: E 378 LEU cc_start: 0.8348 (mt) cc_final: 0.8109 (mp) REVERT: E 388 TRP cc_start: 0.6029 (m-10) cc_final: 0.5676 (m-90) REVERT: E 433 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6628 (tm-30) REVERT: F 14 ASN cc_start: 0.8937 (m-40) cc_final: 0.8255 (m-40) REVERT: F 24 ILE cc_start: 0.8623 (mm) cc_final: 0.8390 (mm) REVERT: F 116 ASP cc_start: 0.8608 (p0) cc_final: 0.8288 (p0) REVERT: F 202 TYR cc_start: 0.7455 (m-80) cc_final: 0.7246 (m-80) REVERT: F 235 MET cc_start: 0.8343 (mtt) cc_final: 0.7632 (ttm) REVERT: F 265 LEU cc_start: 0.7825 (mt) cc_final: 0.7620 (mp) REVERT: F 327 GLU cc_start: 0.7794 (pt0) cc_final: 0.6657 (pt0) REVERT: F 328 VAL cc_start: 0.8622 (t) cc_final: 0.8251 (p) REVERT: F 373 MET cc_start: 0.8416 (pmm) cc_final: 0.8214 (pmm) REVERT: G 113 GLU cc_start: 0.6847 (pp20) cc_final: 0.6207 (pp20) REVERT: G 129 CYS cc_start: 0.8064 (t) cc_final: 0.7726 (t) REVERT: G 169 PHE cc_start: 0.4865 (m-80) cc_final: 0.4634 (m-10) REVERT: G 254 GLU cc_start: 0.7613 (mp0) cc_final: 0.6894 (mm-30) REVERT: G 315 CYS cc_start: 0.8055 (t) cc_final: 0.7026 (t) REVERT: G 317 LEU cc_start: 0.7467 (mt) cc_final: 0.7266 (mt) REVERT: G 327 ASP cc_start: 0.6517 (p0) cc_final: 0.6296 (p0) REVERT: G 378 LEU cc_start: 0.7178 (mp) cc_final: 0.6453 (mp) REVERT: H 124 LYS cc_start: 0.8740 (pptt) cc_final: 0.7976 (ptmt) REVERT: H 149 MET cc_start: 0.5131 (ppp) cc_final: 0.4896 (ppp) REVERT: H 234 THR cc_start: 0.8691 (p) cc_final: 0.8405 (p) REVERT: H 235 MET cc_start: 0.7759 (mmm) cc_final: 0.6913 (mmt) REVERT: H 295 MET cc_start: 0.7417 (ppp) cc_final: 0.7116 (ppp) REVERT: I 122 ILE cc_start: 0.8075 (pt) cc_final: 0.7513 (pt) REVERT: I 129 CYS cc_start: 0.8727 (t) cc_final: 0.8522 (t) REVERT: I 132 LEU cc_start: 0.7830 (tp) cc_final: 0.7603 (tp) REVERT: I 186 ASN cc_start: 0.8145 (m-40) cc_final: 0.7450 (m-40) REVERT: I 234 ILE cc_start: 0.9004 (mt) cc_final: 0.8741 (mt) REVERT: I 282 TYR cc_start: 0.7992 (m-80) cc_final: 0.7624 (m-80) REVERT: I 302 MET cc_start: 0.6991 (mpp) cc_final: 0.6606 (mtm) REVERT: I 347 CYS cc_start: 0.7975 (t) cc_final: 0.7580 (t) REVERT: J 48 ARG cc_start: 0.7425 (mmt-90) cc_final: 0.7079 (tpp-160) REVERT: J 59 ASN cc_start: 0.4328 (p0) cc_final: 0.3925 (p0) REVERT: J 85 GLN cc_start: 0.8186 (mp10) cc_final: 0.7899 (mm-40) REVERT: J 120 ASP cc_start: 0.7020 (t0) cc_final: 0.6649 (t0) REVERT: J 230 LEU cc_start: 0.8593 (tp) cc_final: 0.8314 (tp) REVERT: J 235 MET cc_start: 0.7999 (mtp) cc_final: 0.7289 (mtm) REVERT: J 241 CYS cc_start: 0.8169 (t) cc_final: 0.7968 (t) REVERT: J 259 MET cc_start: 0.7724 (mmm) cc_final: 0.6664 (mmm) REVERT: J 432 TYR cc_start: 0.3865 (m-10) cc_final: 0.3497 (m-80) REVERT: K 36 MET cc_start: 0.6766 (mmm) cc_final: 0.6300 (tpp) REVERT: K 75 ILE cc_start: 0.6377 (mm) cc_final: 0.5861 (tt) REVERT: K 116 ASP cc_start: 0.8064 (p0) cc_final: 0.7455 (p0) REVERT: K 122 ILE cc_start: 0.8015 (pt) cc_final: 0.7591 (pt) REVERT: K 335 ILE cc_start: 0.7320 (mm) cc_final: 0.7022 (mm) REVERT: K 377 MET cc_start: 0.7743 (tmm) cc_final: 0.7191 (tmm) REVERT: L 116 ASP cc_start: 0.7420 (m-30) cc_final: 0.6932 (m-30) REVERT: L 259 MET cc_start: 0.7912 (mmm) cc_final: 0.7641 (mmm) REVERT: L 267 PHE cc_start: 0.6398 (m-10) cc_final: 0.6149 (m-10) REVERT: L 269 MET cc_start: 0.6715 (mtm) cc_final: 0.6360 (mtm) REVERT: L 301 MET cc_start: 0.7686 (tpt) cc_final: 0.7179 (tpt) REVERT: M 21 TRP cc_start: 0.8034 (m100) cc_final: 0.7664 (m100) REVERT: M 33 ASP cc_start: 0.5863 (p0) cc_final: 0.5328 (p0) REVERT: M 75 ILE cc_start: 0.8362 (mm) cc_final: 0.7810 (tp) REVERT: M 154 MET cc_start: 0.7972 (ttp) cc_final: 0.7413 (tmm) REVERT: M 191 THR cc_start: 0.8453 (p) cc_final: 0.8136 (p) REVERT: M 209 ILE cc_start: 0.9184 (mp) cc_final: 0.8655 (tt) REVERT: M 213 CYS cc_start: 0.6156 (t) cc_final: 0.5393 (t) REVERT: M 231 ILE cc_start: 0.8363 (mm) cc_final: 0.7822 (mm) REVERT: M 234 ILE cc_start: 0.8650 (mt) cc_final: 0.8332 (mm) REVERT: M 313 MET cc_start: 0.7233 (mmm) cc_final: 0.6569 (mmm) REVERT: M 335 ILE cc_start: 0.7942 (mm) cc_final: 0.7725 (mm) REVERT: M 398 MET cc_start: 0.6634 (mmm) cc_final: 0.6425 (mmm) REVERT: N 14 ASN cc_start: 0.8436 (m-40) cc_final: 0.7640 (m-40) REVERT: N 20 PHE cc_start: 0.7403 (t80) cc_final: 0.6445 (t80) REVERT: N 258 ASN cc_start: 0.9113 (m-40) cc_final: 0.8629 (t0) REVERT: N 266 HIS cc_start: 0.7214 (p-80) cc_final: 0.6743 (p-80) REVERT: N 268 PHE cc_start: 0.6880 (m-80) cc_final: 0.5602 (m-10) REVERT: N 416 MET cc_start: 0.4275 (tpt) cc_final: 0.3798 (tpt) REVERT: O 33 ASP cc_start: 0.7647 (p0) cc_final: 0.6746 (p0) REVERT: O 74 VAL cc_start: 0.7896 (t) cc_final: 0.7570 (t) REVERT: O 154 MET cc_start: 0.7372 (tmm) cc_final: 0.7151 (tmm) REVERT: O 191 THR cc_start: 0.7793 (p) cc_final: 0.7370 (p) REVERT: O 337 THR cc_start: 0.7682 (p) cc_final: 0.7471 (p) REVERT: O 339 ARG cc_start: 0.5234 (mpt180) cc_final: 0.5001 (mmt-90) REVERT: O 347 CYS cc_start: 0.7508 (t) cc_final: 0.7176 (m) REVERT: O 413 MET cc_start: 0.6947 (mmm) cc_final: 0.6599 (mmt) REVERT: P 53 TYR cc_start: 0.6968 (m-10) cc_final: 0.6609 (m-10) REVERT: P 252 LEU cc_start: 0.8155 (mt) cc_final: 0.7567 (pt) REVERT: P 325 MET cc_start: 0.8566 (pmm) cc_final: 0.8313 (ptp) REVERT: P 332 MET cc_start: 0.6628 (mmm) cc_final: 0.6252 (mmm) REVERT: Q 80 THR cc_start: 0.7841 (p) cc_final: 0.7140 (t) REVERT: Q 113 GLU cc_start: 0.9139 (mp0) cc_final: 0.6648 (tm-30) REVERT: Q 116 ASP cc_start: 0.7719 (p0) cc_final: 0.7483 (p0) REVERT: Q 130 THR cc_start: 0.8430 (p) cc_final: 0.8100 (t) REVERT: Q 217 LEU cc_start: 0.7883 (mm) cc_final: 0.7514 (mm) REVERT: Q 313 MET cc_start: 0.3531 (mmm) cc_final: 0.2952 (tpt) REVERT: Q 318 LEU cc_start: 0.6497 (mt) cc_final: 0.5936 (mt) REVERT: R 5 VAL cc_start: 0.7371 (t) cc_final: 0.7133 (t) REVERT: R 6 HIS cc_start: 0.8264 (t-90) cc_final: 0.7978 (t-90) REVERT: R 14 ASN cc_start: 0.8427 (m-40) cc_final: 0.7755 (m110) REVERT: R 130 ASP cc_start: 0.6566 (t70) cc_final: 0.6335 (t70) REVERT: R 235 MET cc_start: 0.7771 (mtp) cc_final: 0.7505 (mtt) REVERT: R 300 ASN cc_start: 0.7808 (m-40) cc_final: 0.7202 (t0) REVERT: R 302 MET cc_start: 0.7591 (mmt) cc_final: 0.7313 (mmm) REVERT: R 377 PHE cc_start: 0.6268 (t80) cc_final: 0.5888 (t80) outliers start: 2 outliers final: 0 residues processed: 1319 average time/residue: 0.5917 time to fit residues: 1329.4353 Evaluate side-chains 1011 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1011 time to evaluate : 5.159 ------------------------------------------------------------------------------- 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: 6.9990 chunk 476 optimal weight: 8.9990 chunk 638 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 553 optimal weight: 8.9990 chunk 88 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 600 optimal weight: 30.0000 chunk 251 optimal weight: 10.0000 chunk 616 optimal weight: 7.9990 chunk 76 optimal weight: 0.0060 overall best weight: 6.6004 ------------------------------------------------------------------------------- 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 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 380 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS I 256 GLN I 309 HIS ** J 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 ASN ** N 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 107 HIS ** P 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 136 GLN R 192 HIS ** R 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.088680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.073866 restraints weight = 184181.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.076991 restraints weight = 110245.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.079221 restraints weight = 71832.240| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.8702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62298 Z= 0.202 Angle : 0.671 11.460 84645 Z= 0.347 Chirality : 0.047 0.359 9216 Planarity : 0.005 0.077 11043 Dihedral : 11.374 177.902 8784 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.03 % Allowed : 0.26 % Favored : 99.71 % 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: 0.47 (0.10), residues: 7632 helix: 0.72 (0.09), residues: 3609 sheet: 0.59 (0.14), residues: 1296 loop : -0.19 (0.13), residues: 2727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP A 388 HIS 0.009 0.001 HIS B 309 PHE 0.033 0.002 PHE M 49 TYR 0.034 0.002 TYR A 24 ARG 0.011 0.001 ARG A 121 =============================================================================== Job complete usr+sys time: 21055.33 seconds wall clock time: 363 minutes 39.63 seconds (21819.63 seconds total)