Starting phenix.real_space_refine on Mon Aug 25 16:08:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zal_39879/08_2025/8zal_39879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zal_39879/08_2025/8zal_39879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zal_39879/08_2025/8zal_39879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zal_39879/08_2025/8zal_39879.map" model { file = "/net/cci-nas-00/data/ceres_data/8zal_39879/08_2025/8zal_39879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zal_39879/08_2025/8zal_39879.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 86 5.16 5 C 18457 2.51 5 N 5227 2.21 5 O 5776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29546 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2639 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "B" Number of atoms: 2628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2628 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 328} Chain: "C" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2639 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "D" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2639 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "E" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2639 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2639 Classifications: {'peptide': 344} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "G" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3306 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain: "H" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3306 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain: "I" Number of atoms: 3306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3306 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain: "J" Number of atoms: 3805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3805 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 470} Time building chain proxies: 6.92, per 1000 atoms: 0.23 Number of scatterers: 29546 At special positions: 0 Unit cell: (110.09, 111.18, 336.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 86 16.00 O 5776 8.00 N 5227 7.00 C 18457 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: 2.28 Conformation dependent library (CDL) restraints added in 945.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7270 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 24 sheets defined 57.0% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 94 through 152 removed outlier: 3.823A pdb=" N LYS A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Proline residue: A 148 - end of helix Processing helix chain 'A' and resid 156 through 186 removed outlier: 3.704A pdb=" N LEU A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 195 Processing helix chain 'A' and resid 196 through 215 Processing helix chain 'A' and resid 279 through 283 removed outlier: 4.091A pdb=" N ASP A 282 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 279 through 283' Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.508A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 331 " --> pdb=" O GLN A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 331' Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'B' and resid 95 through 152 removed outlier: 3.782A pdb=" N LYS B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Proline residue: B 148 - end of helix removed outlier: 3.533A pdb=" N ASN B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 186 Processing helix chain 'B' and resid 192 through 195 Processing helix chain 'B' and resid 196 through 215 Processing helix chain 'B' and resid 261 through 263 No H-bonds generated for 'chain 'B' and resid 261 through 263' Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.708A pdb=" N GLN B 332 " --> pdb=" O LYS B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 388 Processing helix chain 'C' and resid 94 through 152 removed outlier: 3.810A pdb=" N GLN C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Proline residue: C 148 - end of helix removed outlier: 3.572A pdb=" N ASN C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 186 removed outlier: 3.666A pdb=" N LEU C 160 " --> pdb=" O GLY C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 195 Processing helix chain 'C' and resid 196 through 215 removed outlier: 3.815A pdb=" N GLU C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 removed outlier: 4.360A pdb=" N ALA C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 264' Processing helix chain 'C' and resid 279 through 283 removed outlier: 3.564A pdb=" N ASP C 282 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 283' Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.866A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU C 331 " --> pdb=" O GLN C 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 331' Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'D' and resid 94 through 152 removed outlier: 4.132A pdb=" N LYS D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Proline residue: D 148 - end of helix removed outlier: 3.555A pdb=" N ASN D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 183 removed outlier: 3.758A pdb=" N LEU D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 195 Processing helix chain 'D' and resid 196 through 215 removed outlier: 3.668A pdb=" N ALA D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 266 removed outlier: 4.230A pdb=" N ASN D 265 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET D 266 " --> pdb=" O ILE D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 262 through 266' Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.630A pdb=" N GLU D 331 " --> pdb=" O GLN D 327 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLN D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 388 Processing helix chain 'E' and resid 94 through 145 removed outlier: 3.759A pdb=" N LYS E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR E 143 " --> pdb=" O ALA E 139 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 152 removed outlier: 3.557A pdb=" N ALA E 152 " --> pdb=" O PRO E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 186 Processing helix chain 'E' and resid 196 through 215 Processing helix chain 'E' and resid 262 through 266 removed outlier: 4.117A pdb=" N ASN E 265 " --> pdb=" O GLN E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 removed outlier: 3.891A pdb=" N GLN E 332 " --> pdb=" O LYS E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 Processing helix chain 'F' and resid 94 through 151 removed outlier: 4.316A pdb=" N SER F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) Proline residue: F 148 - end of helix removed outlier: 3.904A pdb=" N ASN F 151 " --> pdb=" O VAL F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 186 removed outlier: 3.612A pdb=" N LEU F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 195 Processing helix chain 'F' and resid 196 through 215 removed outlier: 3.520A pdb=" N ALA F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F 205 " --> pdb=" O GLN F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 266 removed outlier: 4.484A pdb=" N ASN F 265 " --> pdb=" O GLN F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.594A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU F 331 " --> pdb=" O GLN F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 374 through 387 Processing helix chain 'G' and resid 2 through 14 removed outlier: 3.662A pdb=" N GLN G 9 " --> pdb=" O GLN G 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 36 removed outlier: 3.957A pdb=" N ILE G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN G 32 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU G 33 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 147 removed outlier: 3.707A pdb=" N LEU G 117 " --> pdb=" O TYR G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 186 removed outlier: 3.771A pdb=" N VAL G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 201 removed outlier: 3.528A pdb=" N PHE G 201 " --> pdb=" O VAL G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.509A pdb=" N LEU G 212 " --> pdb=" O PRO G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 241 Processing helix chain 'G' and resid 242 through 245 Processing helix chain 'G' and resid 293 through 295 No H-bonds generated for 'chain 'G' and resid 293 through 295' Processing helix chain 'G' and resid 296 through 365 removed outlier: 4.085A pdb=" N LYS G 303 " --> pdb=" O ASN G 299 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER G 353 " --> pdb=" O VAL G 349 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER G 354 " --> pdb=" O SER G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 405 removed outlier: 3.577A pdb=" N VAL G 372 " --> pdb=" O THR G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 417 removed outlier: 3.841A pdb=" N ASN G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 14 removed outlier: 3.992A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 36 removed outlier: 3.863A pdb=" N ILE H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ASN H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 77 through 147 removed outlier: 4.457A pdb=" N TRP H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU H 117 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 187 removed outlier: 3.833A pdb=" N VAL H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE H 185 " --> pdb=" O GLN H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 201 removed outlier: 3.746A pdb=" N PHE H 201 " --> pdb=" O VAL H 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 198 through 201' Processing helix chain 'H' and resid 208 through 220 Processing helix chain 'H' and resid 220 through 242 Processing helix chain 'H' and resid 295 through 365 removed outlier: 4.289A pdb=" N ASN H 299 " --> pdb=" O GLY H 295 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS H 303 " --> pdb=" O ASN H 299 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN H 335 " --> pdb=" O PHE H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 405 removed outlier: 3.696A pdb=" N VAL H 372 " --> pdb=" O THR H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 417 removed outlier: 3.677A pdb=" N ALA H 414 " --> pdb=" O GLN H 410 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU H 415 " --> pdb=" O ASP H 411 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 14 removed outlier: 3.639A pdb=" N LEU I 12 " --> pdb=" O GLN I 8 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 36 removed outlier: 3.595A pdb=" N ARG I 18 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN I 32 " --> pdb=" O PHE I 28 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 77 through 147 removed outlier: 4.288A pdb=" N TRP I 81 " --> pdb=" O ASP I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 187 removed outlier: 3.787A pdb=" N VAL I 154 " --> pdb=" O ALA I 150 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE I 185 " --> pdb=" O GLN I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 201 removed outlier: 3.753A pdb=" N PHE I 201 " --> pdb=" O VAL I 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 201' Processing helix chain 'I' and resid 208 through 217 removed outlier: 3.547A pdb=" N LEU I 212 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 242 Processing helix chain 'I' and resid 243 through 245 No H-bonds generated for 'chain 'I' and resid 243 through 245' Processing helix chain 'I' and resid 298 through 365 removed outlier: 3.832A pdb=" N LYS I 303 " --> pdb=" O ASN I 299 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN I 304 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 405 Processing helix chain 'I' and resid 408 through 417 removed outlier: 3.907A pdb=" N LEU I 412 " --> pdb=" O ASN I 408 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA I 414 " --> pdb=" O GLN I 410 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU I 415 " --> pdb=" O ASP I 411 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN I 417 " --> pdb=" O LEU I 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 44 removed outlier: 4.084A pdb=" N GLN J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL J 27 " --> pdb=" O THR J 23 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 33 " --> pdb=" O ASP J 29 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J 35 " --> pdb=" O THR J 31 " (cutoff:3.500A) Proline residue: J 38 - end of helix Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 52 through 66 removed outlier: 4.270A pdb=" N PHE J 58 " --> pdb=" O VAL J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 76 removed outlier: 3.519A pdb=" N LEU J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG J 75 " --> pdb=" O TRP J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 98 Processing helix chain 'J' and resid 101 through 117 removed outlier: 3.753A pdb=" N GLY J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 131 Processing helix chain 'J' and resid 132 through 134 No H-bonds generated for 'chain 'J' and resid 132 through 134' Processing helix chain 'J' and resid 135 through 165 removed outlier: 3.721A pdb=" N THR J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL J 147 " --> pdb=" O TRP J 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA J 150 " --> pdb=" O THR J 146 " (cutoff:3.500A) Proline residue: J 151 - end of helix Proline residue: J 155 - end of helix Processing helix chain 'J' and resid 173 through 189 removed outlier: 3.693A pdb=" N ILE J 177 " --> pdb=" O ILE J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 223 removed outlier: 3.834A pdb=" N LEU J 206 " --> pdb=" O ASP J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 230 Processing helix chain 'J' and resid 231 through 255 removed outlier: 3.618A pdb=" N LEU J 253 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR J 254 " --> pdb=" O VAL J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 266 removed outlier: 4.031A pdb=" N LEU J 264 " --> pdb=" O ASP J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 289 removed outlier: 3.661A pdb=" N VAL J 289 " --> pdb=" O PHE J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 299 removed outlier: 4.230A pdb=" N GLN J 293 " --> pdb=" O VAL J 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 309 Processing helix chain 'J' and resid 310 through 314 removed outlier: 3.503A pdb=" N VAL J 313 " --> pdb=" O SER J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 316 through 327 Proline residue: J 322 - end of helix Processing helix chain 'J' and resid 328 through 332 removed outlier: 3.734A pdb=" N LEU J 331 " --> pdb=" O ALA J 328 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASP J 332 " --> pdb=" O HIS J 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 328 through 332' Processing helix chain 'J' and resid 333 through 353 Processing helix chain 'J' and resid 360 through 364 Processing helix chain 'J' and resid 365 through 387 removed outlier: 4.273A pdb=" N PHE J 373 " --> pdb=" O PHE J 369 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA J 374 " --> pdb=" O ILE J 370 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE J 378 " --> pdb=" O ALA J 374 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE J 379 " --> pdb=" O VAL J 375 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET J 380 " --> pdb=" O ALA J 376 " (cutoff:3.500A) Proline residue: J 381 - end of helix Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 394 through 434 removed outlier: 3.680A pdb=" N THR J 419 " --> pdb=" O SER J 415 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 453 removed outlier: 3.594A pdb=" N TYR J 447 " --> pdb=" O ALA J 443 " (cutoff:3.500A) Processing helix chain 'J' and resid 456 through 492 removed outlier: 3.669A pdb=" N VAL J 490 " --> pdb=" O GLY J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 493 through 498 removed outlier: 3.743A pdb=" N ALA J 498 " --> pdb=" O VAL J 495 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 5.267A pdb=" N LEU A 292 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG A 322 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 64 removed outlier: 4.100A pdb=" N MET A 244 " --> pdb=" O ILE A 64 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 217 through 219 removed outlier: 3.891A pdb=" N VAL A 90 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU A 89 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 75 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 91 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 52 removed outlier: 5.935A pdb=" N VAL B 289 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU B 324 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 291 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B 254 " --> pdb=" O ILE B 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.989A pdb=" N MET B 244 " --> pdb=" O ILE B 64 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 217 through 219 removed outlier: 3.939A pdb=" N VAL B 90 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU B 89 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL B 75 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 91 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 258 through 259 Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 58 removed outlier: 9.855A pdb=" N THR C 52 " --> pdb=" O LYS C 259 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N LYS C 259 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP C 54 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN C 257 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU C 292 " --> pdb=" O PRO C 320 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C 322 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR C 341 " --> pdb=" O ASP C 54 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP C 54 " --> pdb=" O THR C 341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 62 through 64 removed outlier: 4.098A pdb=" N MET C 244 " --> pdb=" O ILE C 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 217 through 219 removed outlier: 6.836A pdb=" N ILE C 218 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N LEU C 89 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL C 75 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 91 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 365 through 366 removed outlier: 3.662A pdb=" N ALA C 365 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N THR D 91 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL D 75 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU D 89 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL D 90 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 50 removed outlier: 6.906A pdb=" N ARG D 322 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU D 292 " --> pdb=" O PRO D 320 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA D 55 " --> pdb=" O THR D 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 62 through 63 removed outlier: 6.603A pdb=" N ALA D 245 " --> pdb=" O SER D 227 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 58 removed outlier: 9.687A pdb=" N THR E 52 " --> pdb=" O LYS E 259 " (cutoff:3.500A) removed outlier: 9.371A pdb=" N LYS E 259 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASP E 54 " --> pdb=" O ASN E 257 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU E 292 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG E 322 " --> pdb=" O VAL E 290 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR E 341 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASP E 54 " --> pdb=" O THR E 341 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 62 through 64 removed outlier: 4.161A pdb=" N MET E 244 " --> pdb=" O ILE E 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 217 through 219 removed outlier: 6.909A pdb=" N ILE E 218 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS E 74 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E 70 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 49 through 58 removed outlier: 9.513A pdb=" N THR F 52 " --> pdb=" O LYS F 259 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS F 259 " --> pdb=" O THR F 52 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASP F 54 " --> pdb=" O ASN F 257 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE F 258 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY F 291 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU F 324 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL F 289 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL F 283 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR F 276 " --> pdb=" O VAL F 283 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N THR F 341 " --> pdb=" O ASP F 54 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASP F 54 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 62 through 63 Processing sheet with id=AC2, first strand: chain 'F' and resid 217 through 219 removed outlier: 6.774A pdb=" N ILE F 218 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU F 89 " --> pdb=" O VAL F 75 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL F 75 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR F 91 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 41 through 44 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 41 through 44 current: chain 'G' and resid 247 through 256 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 280 through 281 current: chain 'H' and resid 61 through 76 removed outlier: 4.089A pdb=" N THR H 254 " --> pdb=" O LEU H 69 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU H 248 " --> pdb=" O ILE H 75 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 247 through 257 current: chain 'I' and resid 63 through 76 removed outlier: 4.202A pdb=" N THR I 65 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP I 258 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA I 67 " --> pdb=" O ILE I 256 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU I 248 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET I 279 " --> pdb=" O SER I 257 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER I 277 " --> pdb=" O THR I 259 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 192 through 194 Processing sheet with id=AC5, first strand: chain 'H' and resid 192 through 196 removed outlier: 3.625A pdb=" N LYS H 421 " --> pdb=" O ALA H 195 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 192 through 196 1864 hydrogen bonds defined for protein. 5454 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: 5.55 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8978 1.33 - 1.45: 3905 1.45 - 1.57: 16935 1.57 - 1.69: 0 1.69 - 1.81: 165 Bond restraints: 29983 Sorted by residual: bond pdb=" N ASN H 52 " pdb=" CA ASN H 52 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.27e+00 bond pdb=" N ILE F 120 " pdb=" CA ILE F 120 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.26e-02 6.30e+03 9.08e+00 bond pdb=" N ILE B 278 " pdb=" CA ILE B 278 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.32e-02 5.74e+03 8.83e+00 bond pdb=" N SER B 227 " pdb=" CA SER B 227 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.13e-02 7.83e+03 8.81e+00 bond pdb=" N VAL D 289 " pdb=" CA VAL D 289 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.19e-02 7.06e+03 8.31e+00 ... (remaining 29978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 39868 1.62 - 3.23: 768 3.23 - 4.85: 159 4.85 - 6.47: 4 6.47 - 8.08: 1 Bond angle restraints: 40800 Sorted by residual: angle pdb=" C ILE I 292 " pdb=" CA ILE I 292 " pdb=" CB ILE I 292 " ideal model delta sigma weight residual 111.80 105.67 6.13 1.54e+00 4.22e-01 1.58e+01 angle pdb=" N VAL D 290 " pdb=" CA VAL D 290 " pdb=" C VAL D 290 " ideal model delta sigma weight residual 111.56 108.14 3.42 8.60e-01 1.35e+00 1.58e+01 angle pdb=" CA GLY H 45 " pdb=" C GLY H 45 " pdb=" O GLY H 45 " ideal model delta sigma weight residual 121.63 117.47 4.16 1.07e+00 8.73e-01 1.51e+01 angle pdb=" N ILE H 237 " pdb=" CA ILE H 237 " pdb=" C ILE H 237 " ideal model delta sigma weight residual 110.42 106.70 3.72 9.60e-01 1.09e+00 1.50e+01 angle pdb=" CA VAL G 302 " pdb=" C VAL G 302 " pdb=" O VAL G 302 " ideal model delta sigma weight residual 120.95 116.94 4.01 1.04e+00 9.25e-01 1.49e+01 ... (remaining 40795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 17350 17.78 - 35.55: 712 35.55 - 53.33: 174 53.33 - 71.11: 57 71.11 - 88.89: 22 Dihedral angle restraints: 18315 sinusoidal: 7101 harmonic: 11214 Sorted by residual: dihedral pdb=" CD ARG D 336 " pdb=" NE ARG D 336 " pdb=" CZ ARG D 336 " pdb=" NH1 ARG D 336 " ideal model delta sinusoidal sigma weight residual 0.00 69.71 -69.71 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CD ARG J 335 " pdb=" NE ARG J 335 " pdb=" CZ ARG J 335 " pdb=" NH1 ARG J 335 " ideal model delta sinusoidal sigma weight residual 0.00 -67.91 67.91 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" CD ARG B 228 " pdb=" NE ARG B 228 " pdb=" CZ ARG B 228 " pdb=" NH1 ARG B 228 " ideal model delta sinusoidal sigma weight residual 0.00 -54.90 54.90 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 18312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4092 0.054 - 0.108: 584 0.108 - 0.162: 133 0.162 - 0.215: 18 0.215 - 0.269: 2 Chirality restraints: 4829 Sorted by residual: chirality pdb=" CA ILE I 292 " pdb=" N ILE I 292 " pdb=" C ILE I 292 " pdb=" CB ILE I 292 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG H 55 " pdb=" N ARG H 55 " pdb=" C ARG H 55 " pdb=" CB ARG H 55 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA THR B 296 " pdb=" N THR B 296 " pdb=" C THR B 296 " pdb=" CB THR B 296 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 4826 not shown) Planarity restraints: 5352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 335 " 1.024 9.50e-02 1.11e+02 4.59e-01 1.27e+02 pdb=" NE ARG J 335 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG J 335 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG J 335 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG J 335 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 336 " 1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG D 336 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG D 336 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 336 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 336 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 228 " -0.882 9.50e-02 1.11e+02 3.95e-01 9.48e+01 pdb=" NE ARG B 228 " 0.054 2.00e-02 2.50e+03 pdb=" CZ ARG B 228 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 228 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 228 " -0.023 2.00e-02 2.50e+03 ... (remaining 5349 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 406 2.67 - 3.23: 29925 3.23 - 3.79: 44946 3.79 - 4.34: 58854 4.34 - 4.90: 98042 Nonbonded interactions: 232173 Sorted by model distance: nonbonded pdb=" O PHE I 76 " pdb=" OG1 THR I 247 " model vdw 2.119 3.040 nonbonded pdb=" OD2 ASP H 77 " pdb=" OG SER H 79 " model vdw 2.176 3.040 nonbonded pdb=" OG SER D 301 " pdb=" O LEU D 303 " model vdw 2.228 3.040 nonbonded pdb=" O ASN C 79 " pdb=" OG1 THR C 80 " model vdw 2.249 3.040 nonbonded pdb=" O PRO I 191 " pdb=" OG1 THR I 425 " model vdw 2.255 3.040 ... (remaining 232168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 48 through 390) selection = chain 'B' selection = (chain 'C' and resid 48 through 390) selection = (chain 'D' and resid 48 through 390) selection = (chain 'E' and resid 48 through 390) selection = (chain 'F' and resid 48 through 390) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.140 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 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 : 0.004 0.039 29983 Z= 0.228 Angle : 0.555 8.084 40800 Z= 0.359 Chirality : 0.042 0.269 4829 Planarity : 0.014 0.459 5352 Dihedral : 11.702 88.887 11045 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.22 % Allowed : 5.16 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.14), residues: 3821 helix: 2.83 (0.11), residues: 1948 sheet: -0.81 (0.23), residues: 524 loop : -1.20 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 229 TYR 0.014 0.001 TYR I 7 PHE 0.010 0.001 PHE C 258 TRP 0.009 0.001 TRP J 482 HIS 0.004 0.001 HIS J 429 Details of bonding type rmsd covalent geometry : bond 0.00375 (29983) covalent geometry : angle 0.55462 (40800) hydrogen bonds : bond 0.17584 ( 1864) hydrogen bonds : angle 5.98020 ( 5454) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1170 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ILE cc_start: 0.8365 (mm) cc_final: 0.8146 (mt) REVERT: A 214 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8016 (mm-30) REVERT: A 237 ILE cc_start: 0.8176 (mm) cc_final: 0.7925 (tt) REVERT: A 260 GLU cc_start: 0.7395 (pt0) cc_final: 0.7121 (pt0) REVERT: A 385 VAL cc_start: 0.8356 (p) cc_final: 0.8084 (m) REVERT: A 386 LYS cc_start: 0.8448 (tttt) cc_final: 0.8126 (tttt) REVERT: B 84 LYS cc_start: 0.8383 (mttp) cc_final: 0.7856 (mttp) REVERT: B 87 ASP cc_start: 0.7989 (m-30) cc_final: 0.7774 (m-30) REVERT: B 133 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8185 (mtpp) REVERT: B 134 ILE cc_start: 0.8567 (mm) cc_final: 0.8337 (mt) REVERT: B 140 GLN cc_start: 0.8270 (tp40) cc_final: 0.7660 (tp40) REVERT: B 178 ILE cc_start: 0.8612 (mt) cc_final: 0.8407 (mm) REVERT: B 180 GLN cc_start: 0.8075 (mt0) cc_final: 0.7810 (mt0) REVERT: B 214 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 326 ASP cc_start: 0.7713 (t0) cc_final: 0.7490 (t0) REVERT: C 54 ASP cc_start: 0.8135 (t0) cc_final: 0.7844 (t0) REVERT: C 102 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7704 (mm-30) REVERT: C 133 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8235 (mtpt) REVERT: C 140 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7631 (tp-100) REVERT: C 146 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7747 (mtt-85) REVERT: C 171 GLN cc_start: 0.8098 (tp40) cc_final: 0.7853 (tp-100) REVERT: C 180 GLN cc_start: 0.8323 (mt0) cc_final: 0.8097 (mt0) REVERT: C 194 GLU cc_start: 0.7888 (mp0) cc_final: 0.7670 (mp0) REVERT: C 205 GLU cc_start: 0.7779 (tp30) cc_final: 0.7293 (tp30) REVERT: C 244 MET cc_start: 0.8838 (ptp) cc_final: 0.8563 (ptm) REVERT: C 284 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7886 (mmmt) REVERT: D 54 ASP cc_start: 0.8095 (t0) cc_final: 0.7855 (t0) REVERT: D 103 LYS cc_start: 0.7568 (tttm) cc_final: 0.7347 (tttm) REVERT: D 110 SER cc_start: 0.8627 (t) cc_final: 0.8172 (p) REVERT: D 116 HIS cc_start: 0.8487 (t70) cc_final: 0.8167 (t-90) REVERT: D 153 ASN cc_start: 0.7860 (t0) cc_final: 0.7654 (t0) REVERT: D 158 GLU cc_start: 0.7262 (tt0) cc_final: 0.6961 (tt0) REVERT: D 181 TYR cc_start: 0.8588 (t80) cc_final: 0.8334 (t80) REVERT: D 195 ASP cc_start: 0.7817 (t0) cc_final: 0.7404 (t0) REVERT: D 206 VAL cc_start: 0.8362 (t) cc_final: 0.8141 (t) REVERT: D 252 MET cc_start: 0.8866 (mtt) cc_final: 0.8645 (mtt) REVERT: D 288 LYS cc_start: 0.8404 (ptpt) cc_final: 0.8093 (ptpt) REVERT: D 328 LYS cc_start: 0.8378 (tttp) cc_final: 0.8166 (tttp) REVERT: D 331 GLU cc_start: 0.7685 (mp0) cc_final: 0.7330 (mp0) REVERT: D 368 THR cc_start: 0.8350 (m) cc_final: 0.7821 (t) REVERT: D 371 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7446 (mt-10) REVERT: D 379 LYS cc_start: 0.7873 (ttmt) cc_final: 0.7660 (ttmt) REVERT: E 84 LYS cc_start: 0.8277 (mmmm) cc_final: 0.7848 (mmmm) REVERT: E 118 LEU cc_start: 0.8236 (mt) cc_final: 0.8016 (mm) REVERT: E 194 GLU cc_start: 0.7370 (mp0) cc_final: 0.7130 (mp0) REVERT: E 217 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7227 (mtm-85) REVERT: E 266 MET cc_start: 0.8658 (mtt) cc_final: 0.8325 (mtp) REVERT: E 349 ASN cc_start: 0.7814 (t0) cc_final: 0.7559 (t0) REVERT: E 371 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6317 (mm-30) REVERT: E 379 LYS cc_start: 0.8136 (tttt) cc_final: 0.7926 (tttt) REVERT: E 380 LEU cc_start: 0.8113 (mp) cc_final: 0.7850 (mp) REVERT: E 382 ASP cc_start: 0.8166 (t0) cc_final: 0.7929 (t0) REVERT: F 54 ASP cc_start: 0.8682 (t0) cc_final: 0.8090 (t0) REVERT: F 103 LYS cc_start: 0.7940 (tttt) cc_final: 0.7732 (tttt) REVERT: F 105 LYS cc_start: 0.8612 (mttt) cc_final: 0.8383 (mtmm) REVERT: F 194 GLU cc_start: 0.8039 (mp0) cc_final: 0.7647 (mp0) REVERT: F 327 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7298 (mm110) REVERT: F 328 LYS cc_start: 0.8727 (tttt) cc_final: 0.8412 (tttt) REVERT: F 351 ASP cc_start: 0.7683 (m-30) cc_final: 0.7388 (m-30) REVERT: F 357 ASN cc_start: 0.8496 (p0) cc_final: 0.8252 (p0) REVERT: G 137 LEU cc_start: 0.8210 (tp) cc_final: 0.7966 (tt) REVERT: G 239 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7516 (tp-100) REVERT: G 244 HIS cc_start: 0.7243 (m90) cc_final: 0.6982 (m90) REVERT: G 344 TYR cc_start: 0.8186 (m-10) cc_final: 0.7961 (m-80) REVERT: G 345 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8279 (ttmm) REVERT: G 390 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7720 (mtt-85) REVERT: H 8 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7725 (mm-40) REVERT: H 11 ARG cc_start: 0.7270 (tpt-90) cc_final: 0.6951 (tpt-90) REVERT: H 33 GLU cc_start: 0.6873 (pp20) cc_final: 0.6638 (pp20) REVERT: H 42 LEU cc_start: 0.7775 (mt) cc_final: 0.7472 (mt) REVERT: H 130 LYS cc_start: 0.8262 (tmmt) cc_final: 0.7979 (ttmt) REVERT: H 133 ILE cc_start: 0.9032 (mt) cc_final: 0.8808 (mm) REVERT: H 162 ASP cc_start: 0.7534 (m-30) cc_final: 0.6853 (t0) REVERT: H 229 SER cc_start: 0.8291 (m) cc_final: 0.7956 (t) REVERT: H 231 ASP cc_start: 0.6736 (t0) cc_final: 0.6518 (t0) REVERT: H 339 SER cc_start: 0.8000 (m) cc_final: 0.7656 (p) REVERT: H 350 SER cc_start: 0.8206 (t) cc_final: 0.7982 (m) REVERT: H 391 TYR cc_start: 0.7803 (m-10) cc_final: 0.7489 (m-10) REVERT: I 33 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7381 (tm-30) REVERT: I 136 GLN cc_start: 0.7758 (tp40) cc_final: 0.7533 (tp40) REVERT: I 221 LEU cc_start: 0.7247 (mt) cc_final: 0.6973 (mt) REVERT: I 229 SER cc_start: 0.8033 (t) cc_final: 0.7779 (m) REVERT: I 359 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7141 (tm-30) REVERT: J 12 LEU cc_start: 0.8542 (mt) cc_final: 0.8334 (pp) REVERT: J 21 LEU cc_start: 0.8349 (mt) cc_final: 0.8117 (mm) REVERT: J 82 PHE cc_start: 0.8209 (t80) cc_final: 0.7678 (t80) REVERT: J 84 TRP cc_start: 0.5889 (t60) cc_final: 0.5661 (t60) REVERT: J 184 MET cc_start: 0.7943 (mtm) cc_final: 0.7668 (mtm) REVERT: J 248 LEU cc_start: 0.8554 (tp) cc_final: 0.8053 (tt) REVERT: J 260 VAL cc_start: 0.8148 (t) cc_final: 0.7841 (m) REVERT: J 316 ILE cc_start: 0.8165 (mm) cc_final: 0.7945 (mm) REVERT: J 383 THR cc_start: 0.8078 (m) cc_final: 0.7799 (m) REVERT: J 386 THR cc_start: 0.8461 (m) cc_final: 0.8120 (p) REVERT: J 425 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7505 (tm-30) REVERT: J 434 GLU cc_start: 0.7827 (tt0) cc_final: 0.7604 (mt-10) REVERT: J 451 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7301 (mt-10) REVERT: J 487 ILE cc_start: 0.8135 (mt) cc_final: 0.7927 (mm) REVERT: J 497 PHE cc_start: 0.8202 (m-80) cc_final: 0.7953 (m-10) outliers start: 7 outliers final: 3 residues processed: 1175 average time/residue: 0.2016 time to fit residues: 358.8363 Evaluate side-chains 1074 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1071 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain J residue 335 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.1980 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN A 144 ASN A 179 GLN A 201 GLN A 265 ASN B 117 GLN B 121 ASN B 173 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 117 GLN C 124 GLN D 262 GLN D 306 GLN D 353 GLN E 114 GLN E 117 GLN E 124 GLN E 257 ASN G 5 GLN G 94 GLN G 160 GLN G 225 GLN G 241 GLN G 396 ASN G 397 GLN H 14 ASN H 103 GLN H 315 GLN H 320 HIS H 325 GLN I 87 GLN I 102 GLN ** I 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 220 ASN I 301 GLN I 332 ASN J 124 GLN J 257 ASN J 403 ASN J 437 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.128353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112510 restraints weight = 46131.710| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.87 r_work: 0.3302 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29983 Z= 0.179 Angle : 0.562 9.744 40800 Z= 0.300 Chirality : 0.042 0.179 4829 Planarity : 0.005 0.098 5352 Dihedral : 4.240 73.688 4153 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.85 % Allowed : 13.17 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.14), residues: 3821 helix: 3.21 (0.11), residues: 1961 sheet: -0.35 (0.24), residues: 500 loop : -1.06 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 227 TYR 0.018 0.001 TYR J 281 PHE 0.019 0.002 PHE J 108 TRP 0.013 0.001 TRP J 482 HIS 0.004 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00369 (29983) covalent geometry : angle 0.56182 (40800) hydrogen bonds : bond 0.08677 ( 1864) hydrogen bonds : angle 4.62347 ( 5454) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1078 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7899 (t0) cc_final: 0.7688 (t0) REVERT: A 126 GLN cc_start: 0.8123 (tp40) cc_final: 0.7824 (tp40) REVERT: A 140 GLN cc_start: 0.8153 (tp40) cc_final: 0.7888 (tp40) REVERT: A 143 TYR cc_start: 0.8633 (t80) cc_final: 0.8227 (t80) REVERT: A 171 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7483 (tp-100) REVERT: A 188 ILE cc_start: 0.8491 (mm) cc_final: 0.8253 (mt) REVERT: A 214 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7879 (mm-30) REVERT: A 242 PRO cc_start: 0.8339 (Cg_endo) cc_final: 0.8088 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7527 (pt0) cc_final: 0.7249 (pt0) REVERT: A 349 ASN cc_start: 0.8570 (t0) cc_final: 0.8301 (t0) REVERT: A 385 VAL cc_start: 0.8551 (p) cc_final: 0.8277 (m) REVERT: A 386 LYS cc_start: 0.8514 (tttt) cc_final: 0.8202 (tttt) REVERT: B 133 LYS cc_start: 0.8418 (mtpp) cc_final: 0.8184 (mtpp) REVERT: B 134 ILE cc_start: 0.8622 (mm) cc_final: 0.8383 (mt) REVERT: B 140 GLN cc_start: 0.8418 (tp40) cc_final: 0.7826 (tp40) REVERT: B 178 ILE cc_start: 0.8698 (mt) cc_final: 0.8464 (mm) REVERT: B 180 GLN cc_start: 0.8113 (mt0) cc_final: 0.7880 (mt0) REVERT: B 201 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7318 (mm110) REVERT: B 279 TYR cc_start: 0.8576 (m-80) cc_final: 0.8292 (m-80) REVERT: C 51 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6598 (mt-10) REVERT: C 54 ASP cc_start: 0.8098 (t0) cc_final: 0.7811 (t0) REVERT: C 62 ILE cc_start: 0.8768 (mp) cc_final: 0.8547 (mt) REVERT: C 81 ASP cc_start: 0.8234 (m-30) cc_final: 0.7101 (m-30) REVERT: C 102 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7882 (mm-30) REVERT: C 133 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8438 (mtpt) REVERT: C 140 GLN cc_start: 0.8240 (tp-100) cc_final: 0.7655 (tp-100) REVERT: C 146 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7730 (mtt-85) REVERT: C 180 GLN cc_start: 0.8385 (mt0) cc_final: 0.8152 (mt0) REVERT: C 205 GLU cc_start: 0.8010 (tp30) cc_final: 0.7500 (tp30) REVERT: C 244 MET cc_start: 0.8786 (ptp) cc_final: 0.8547 (ptm) REVERT: C 284 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7947 (mmmt) REVERT: C 288 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8543 (mtmm) REVERT: C 380 LEU cc_start: 0.8355 (mp) cc_final: 0.8098 (mp) REVERT: D 54 ASP cc_start: 0.8144 (t0) cc_final: 0.7881 (t0) REVERT: D 103 LYS cc_start: 0.7619 (tttm) cc_final: 0.7391 (tttm) REVERT: D 110 SER cc_start: 0.8656 (t) cc_final: 0.8203 (p) REVERT: D 158 GLU cc_start: 0.7425 (tt0) cc_final: 0.7185 (tt0) REVERT: D 181 TYR cc_start: 0.8659 (t80) cc_final: 0.8379 (t80) REVERT: D 252 MET cc_start: 0.8886 (mtt) cc_final: 0.8678 (mtt) REVERT: D 288 LYS cc_start: 0.8366 (ptpt) cc_final: 0.8069 (ptpt) REVERT: D 313 ILE cc_start: 0.8972 (mp) cc_final: 0.8736 (mt) REVERT: D 331 GLU cc_start: 0.7774 (mp0) cc_final: 0.7424 (mp0) REVERT: D 368 THR cc_start: 0.8330 (m) cc_final: 0.7778 (t) REVERT: D 371 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 62 ILE cc_start: 0.8756 (mm) cc_final: 0.8537 (mm) REVERT: E 78 ASP cc_start: 0.7888 (m-30) cc_final: 0.7486 (p0) REVERT: E 84 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8034 (mmmm) REVERT: E 102 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6993 (mm-30) REVERT: E 118 LEU cc_start: 0.8214 (mt) cc_final: 0.8013 (mm) REVERT: E 194 GLU cc_start: 0.7464 (mp0) cc_final: 0.7183 (mp0) REVERT: E 205 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7829 (mm-30) REVERT: E 217 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7518 (mtm-85) REVERT: E 266 MET cc_start: 0.8597 (mtt) cc_final: 0.8282 (mtp) REVERT: E 349 ASN cc_start: 0.7888 (t0) cc_final: 0.7639 (t0) REVERT: E 351 ASP cc_start: 0.7830 (p0) cc_final: 0.7468 (p0) REVERT: E 371 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6470 (mm-30) REVERT: E 379 LYS cc_start: 0.8131 (tttt) cc_final: 0.7901 (tttt) REVERT: E 382 ASP cc_start: 0.8335 (t0) cc_final: 0.8068 (t0) REVERT: F 51 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7657 (mm-30) REVERT: F 52 THR cc_start: 0.8470 (t) cc_final: 0.8050 (m) REVERT: F 103 LYS cc_start: 0.8118 (tttt) cc_final: 0.7772 (tttt) REVERT: F 105 LYS cc_start: 0.8679 (mttt) cc_final: 0.8464 (mtmm) REVERT: F 171 GLN cc_start: 0.8553 (tp40) cc_final: 0.8308 (tp40) REVERT: F 194 GLU cc_start: 0.8228 (mp0) cc_final: 0.7880 (mp0) REVERT: F 327 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7412 (mm110) REVERT: F 328 LYS cc_start: 0.8763 (tttt) cc_final: 0.8490 (tttt) REVERT: F 357 ASN cc_start: 0.8563 (p0) cc_final: 0.8355 (p0) REVERT: F 360 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7371 (ttm110) REVERT: G 5 GLN cc_start: 0.8030 (mt0) cc_final: 0.7790 (mt0) REVERT: G 136 GLN cc_start: 0.8162 (tp40) cc_final: 0.7841 (tp-100) REVERT: G 158 ARG cc_start: 0.7511 (tpt170) cc_final: 0.7294 (tpm170) REVERT: G 186 THR cc_start: 0.8401 (t) cc_final: 0.8200 (m) REVERT: G 229 SER cc_start: 0.8205 (t) cc_final: 0.7958 (m) REVERT: G 237 ILE cc_start: 0.7849 (mt) cc_final: 0.7491 (mt) REVERT: G 239 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7802 (tp-100) REVERT: G 244 HIS cc_start: 0.8009 (m90) cc_final: 0.7616 (m90) REVERT: G 245 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7958 (tt) REVERT: G 344 TYR cc_start: 0.8608 (m-10) cc_final: 0.8379 (m-80) REVERT: G 385 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7798 (mm-30) REVERT: G 390 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8398 (mtt-85) REVERT: G 401 LYS cc_start: 0.7838 (tppt) cc_final: 0.7624 (tppt) REVERT: H 8 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7981 (mm-40) REVERT: H 11 ARG cc_start: 0.7742 (tpt-90) cc_final: 0.7491 (tpt-90) REVERT: H 41 GLN cc_start: 0.7831 (tt0) cc_final: 0.7619 (tt0) REVERT: H 42 LEU cc_start: 0.8281 (mt) cc_final: 0.7879 (mt) REVERT: H 69 LEU cc_start: 0.7890 (mt) cc_final: 0.7472 (mm) REVERT: H 70 GLN cc_start: 0.7628 (mp10) cc_final: 0.7316 (mp10) REVERT: H 130 LYS cc_start: 0.8465 (tmmt) cc_final: 0.8074 (ttmt) REVERT: H 131 GLU cc_start: 0.8004 (tp30) cc_final: 0.7673 (tp30) REVERT: H 158 ARG cc_start: 0.7637 (tpp-160) cc_final: 0.7365 (tpp-160) REVERT: H 162 ASP cc_start: 0.8021 (m-30) cc_final: 0.7287 (t0) REVERT: H 180 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7776 (mm-30) REVERT: H 229 SER cc_start: 0.8513 (m) cc_final: 0.8230 (t) REVERT: H 231 ASP cc_start: 0.7380 (t0) cc_final: 0.7153 (t0) REVERT: H 278 ASN cc_start: 0.8217 (t0) cc_final: 0.7950 (t0) REVERT: H 320 HIS cc_start: 0.7547 (t70) cc_final: 0.7343 (t-90) REVERT: H 345 LYS cc_start: 0.8268 (ttmt) cc_final: 0.8009 (ttmm) REVERT: H 346 GLN cc_start: 0.8314 (tp-100) cc_final: 0.8112 (tp40) REVERT: H 350 SER cc_start: 0.8485 (t) cc_final: 0.8131 (m) REVERT: H 390 ARG cc_start: 0.8539 (mtt180) cc_final: 0.8225 (mtt180) REVERT: H 391 TYR cc_start: 0.8421 (m-10) cc_final: 0.7912 (m-10) REVERT: I 24 ARG cc_start: 0.8356 (ptm-80) cc_final: 0.8043 (ttp80) REVERT: I 33 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7841 (tm-30) REVERT: I 95 ASP cc_start: 0.7667 (t0) cc_final: 0.6429 (t0) REVERT: I 101 ASP cc_start: 0.7384 (m-30) cc_final: 0.7162 (m-30) REVERT: I 127 GLN cc_start: 0.7907 (tp40) cc_final: 0.7661 (tp40) REVERT: I 136 GLN cc_start: 0.8192 (tp40) cc_final: 0.7983 (tm-30) REVERT: I 156 ASN cc_start: 0.8039 (m-40) cc_final: 0.7807 (m-40) REVERT: I 215 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8186 (tm-30) REVERT: I 229 SER cc_start: 0.8456 (t) cc_final: 0.8136 (m) REVERT: I 231 ASP cc_start: 0.7841 (t0) cc_final: 0.7600 (m-30) REVERT: I 235 GLU cc_start: 0.8444 (tp30) cc_final: 0.8210 (mm-30) REVERT: I 297 MET cc_start: 0.7333 (tmm) cc_final: 0.7108 (tmm) REVERT: I 359 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7114 (tm-30) REVERT: I 404 LEU cc_start: 0.7945 (tp) cc_final: 0.7645 (tt) REVERT: J 81 LEU cc_start: 0.8517 (tp) cc_final: 0.8233 (tp) REVERT: J 82 PHE cc_start: 0.8236 (t80) cc_final: 0.7738 (t80) REVERT: J 84 TRP cc_start: 0.6224 (t60) cc_final: 0.5961 (t60) REVERT: J 140 LEU cc_start: 0.8588 (tt) cc_final: 0.8313 (mt) REVERT: J 146 THR cc_start: 0.8366 (m) cc_final: 0.8120 (t) REVERT: J 184 MET cc_start: 0.8058 (mtm) cc_final: 0.7806 (mtm) REVERT: J 248 LEU cc_start: 0.8575 (tp) cc_final: 0.8167 (tp) REVERT: J 252 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8075 (mm-30) REVERT: J 260 VAL cc_start: 0.8333 (t) cc_final: 0.8047 (m) REVERT: J 320 LEU cc_start: 0.7926 (mt) cc_final: 0.7686 (mt) REVERT: J 366 TRP cc_start: 0.7273 (m100) cc_final: 0.6753 (m100) REVERT: J 386 THR cc_start: 0.8598 (m) cc_final: 0.8302 (p) REVERT: J 406 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7740 (mtm110) REVERT: J 425 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7682 (tm-30) REVERT: J 434 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: J 487 ILE cc_start: 0.8155 (mt) cc_final: 0.7914 (mm) outliers start: 59 outliers final: 35 residues processed: 1102 average time/residue: 0.2057 time to fit residues: 341.0885 Evaluate side-chains 1077 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1040 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 434 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 166 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 60 ASN A 79 ASN A 144 ASN B 121 ASN B 153 ASN B 232 GLN C 61 GLN C 171 GLN D 153 ASN E 114 GLN E 173 GLN F 173 GLN F 201 GLN G 94 GLN G 244 HIS ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 2 ASN H 139 GLN H 304 GLN I 70 GLN I 139 GLN I 184 GLN I 304 GLN J 26 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111085 restraints weight = 46039.819| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.86 r_work: 0.3268 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 29983 Z= 0.243 Angle : 0.591 8.282 40800 Z= 0.319 Chirality : 0.044 0.158 4829 Planarity : 0.005 0.095 5352 Dihedral : 4.317 74.972 4145 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.19 % Allowed : 14.51 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.14), residues: 3821 helix: 3.02 (0.11), residues: 1980 sheet: -0.31 (0.24), residues: 492 loop : -1.13 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 227 TYR 0.014 0.002 TYR D 285 PHE 0.026 0.002 PHE J 108 TRP 0.016 0.002 TRP J 482 HIS 0.005 0.001 HIS G 244 Details of bonding type rmsd covalent geometry : bond 0.00541 (29983) covalent geometry : angle 0.59094 (40800) hydrogen bonds : bond 0.09293 ( 1864) hydrogen bonds : angle 4.62241 ( 5454) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1061 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8181 (tp40) cc_final: 0.7921 (tp40) REVERT: A 144 ASN cc_start: 0.8462 (m-40) cc_final: 0.8230 (m110) REVERT: A 171 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7512 (tp-100) REVERT: A 188 ILE cc_start: 0.8508 (mm) cc_final: 0.8262 (mt) REVERT: A 242 PRO cc_start: 0.8348 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7510 (pt0) cc_final: 0.7263 (pt0) REVERT: A 349 ASN cc_start: 0.8607 (t0) cc_final: 0.8395 (t0) REVERT: A 385 VAL cc_start: 0.8523 (p) cc_final: 0.8264 (m) REVERT: A 386 LYS cc_start: 0.8538 (tttt) cc_final: 0.8220 (tttt) REVERT: B 133 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8239 (mtpp) REVERT: B 134 ILE cc_start: 0.8646 (mm) cc_final: 0.8415 (mt) REVERT: B 140 GLN cc_start: 0.8458 (tp40) cc_final: 0.8042 (tp40) REVERT: B 180 GLN cc_start: 0.8121 (mt0) cc_final: 0.7895 (mt0) REVERT: B 201 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7418 (mm110) REVERT: B 279 TYR cc_start: 0.8576 (m-80) cc_final: 0.8287 (m-80) REVERT: C 51 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6630 (mt-10) REVERT: C 54 ASP cc_start: 0.8105 (t0) cc_final: 0.7825 (t0) REVERT: C 81 ASP cc_start: 0.8266 (m-30) cc_final: 0.7347 (m-30) REVERT: C 140 GLN cc_start: 0.8319 (tp-100) cc_final: 0.7751 (tp-100) REVERT: C 146 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.8102 (mtt-85) REVERT: C 180 GLN cc_start: 0.8452 (mt0) cc_final: 0.8216 (mt0) REVERT: C 205 GLU cc_start: 0.8132 (tp30) cc_final: 0.7625 (tp30) REVERT: C 244 MET cc_start: 0.8738 (ptp) cc_final: 0.8518 (ptm) REVERT: C 284 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7954 (mmmt) REVERT: D 54 ASP cc_start: 0.8126 (t0) cc_final: 0.7897 (t0) REVERT: D 103 LYS cc_start: 0.7720 (tttm) cc_final: 0.7490 (tttm) REVERT: D 110 SER cc_start: 0.8691 (t) cc_final: 0.8235 (p) REVERT: D 288 LYS cc_start: 0.8374 (ptpt) cc_final: 0.8074 (ptpt) REVERT: D 331 GLU cc_start: 0.7819 (mp0) cc_final: 0.7464 (mp0) REVERT: D 368 THR cc_start: 0.8371 (m) cc_final: 0.7816 (t) REVERT: D 371 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 78 ASP cc_start: 0.7909 (m-30) cc_final: 0.7497 (p0) REVERT: E 84 LYS cc_start: 0.8407 (mmmm) cc_final: 0.8058 (mmmm) REVERT: E 102 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7122 (mm-30) REVERT: E 194 GLU cc_start: 0.7504 (mp0) cc_final: 0.7231 (mp0) REVERT: E 205 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7848 (mm-30) REVERT: E 217 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7577 (mtm-85) REVERT: E 266 MET cc_start: 0.8631 (mtt) cc_final: 0.8321 (mtp) REVERT: E 349 ASN cc_start: 0.7859 (t0) cc_final: 0.7604 (t0) REVERT: E 351 ASP cc_start: 0.7864 (p0) cc_final: 0.7493 (p0) REVERT: E 371 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6488 (mm-30) REVERT: E 379 LYS cc_start: 0.8177 (tttt) cc_final: 0.7950 (tttt) REVERT: E 382 ASP cc_start: 0.8378 (t0) cc_final: 0.8088 (t0) REVERT: F 103 LYS cc_start: 0.8153 (tttt) cc_final: 0.7843 (tttt) REVERT: F 105 LYS cc_start: 0.8696 (mttt) cc_final: 0.8483 (mttm) REVERT: F 187 MET cc_start: 0.8313 (mmm) cc_final: 0.8095 (mmm) REVERT: F 194 GLU cc_start: 0.8206 (mp0) cc_final: 0.7856 (mp0) REVERT: F 327 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7391 (mm110) REVERT: F 328 LYS cc_start: 0.8817 (tttt) cc_final: 0.8546 (tttt) REVERT: F 357 ASN cc_start: 0.8578 (p0) cc_final: 0.8369 (p0) REVERT: G 5 GLN cc_start: 0.8047 (mt0) cc_final: 0.7785 (mt0) REVERT: G 30 LYS cc_start: 0.8326 (tttt) cc_final: 0.8115 (tttt) REVERT: G 82 ARG cc_start: 0.7785 (mmt-90) cc_final: 0.7328 (mmt-90) REVERT: G 136 GLN cc_start: 0.8148 (tp40) cc_final: 0.7780 (tp-100) REVERT: G 186 THR cc_start: 0.8509 (t) cc_final: 0.8198 (p) REVERT: G 229 SER cc_start: 0.8208 (t) cc_final: 0.7955 (m) REVERT: G 237 ILE cc_start: 0.7851 (mt) cc_final: 0.7535 (mt) REVERT: G 239 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7941 (tp40) REVERT: G 288 PHE cc_start: 0.7691 (t80) cc_final: 0.7238 (t80) REVERT: G 344 TYR cc_start: 0.8569 (m-10) cc_final: 0.8275 (m-80) REVERT: G 358 MET cc_start: 0.8133 (mmp) cc_final: 0.7888 (mmp) REVERT: G 385 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7782 (mm-30) REVERT: G 390 ARG cc_start: 0.8620 (mtt90) cc_final: 0.8406 (mtt-85) REVERT: G 401 LYS cc_start: 0.7876 (tppt) cc_final: 0.7658 (tppt) REVERT: H 11 ARG cc_start: 0.7795 (tpt-90) cc_final: 0.7508 (tpt-90) REVERT: H 42 LEU cc_start: 0.8346 (mt) cc_final: 0.7924 (mt) REVERT: H 69 LEU cc_start: 0.7865 (mt) cc_final: 0.7450 (mm) REVERT: H 70 GLN cc_start: 0.7750 (mp10) cc_final: 0.7060 (mp10) REVERT: H 130 LYS cc_start: 0.8457 (tmmt) cc_final: 0.8105 (ttmt) REVERT: H 131 GLU cc_start: 0.8055 (tp30) cc_final: 0.7731 (tp30) REVERT: H 158 ARG cc_start: 0.7676 (tpp-160) cc_final: 0.7396 (tpp-160) REVERT: H 162 ASP cc_start: 0.8068 (m-30) cc_final: 0.7228 (t0) REVERT: H 180 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7720 (mm-30) REVERT: H 196 LEU cc_start: 0.8507 (tp) cc_final: 0.8278 (tt) REVERT: H 229 SER cc_start: 0.8539 (m) cc_final: 0.8233 (t) REVERT: H 279 MET cc_start: 0.8020 (mtp) cc_final: 0.7242 (mtp) REVERT: H 345 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8037 (ttmm) REVERT: H 346 GLN cc_start: 0.8339 (tp-100) cc_final: 0.8137 (tp40) REVERT: H 350 SER cc_start: 0.8485 (t) cc_final: 0.8141 (m) REVERT: H 391 TYR cc_start: 0.8437 (m-10) cc_final: 0.8123 (m-10) REVERT: I 19 LYS cc_start: 0.7643 (ttmm) cc_final: 0.7370 (ttmm) REVERT: I 33 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7783 (tm-30) REVERT: I 44 LEU cc_start: 0.7284 (tt) cc_final: 0.6500 (mt) REVERT: I 70 GLN cc_start: 0.7681 (mm110) cc_final: 0.7413 (mm110) REVERT: I 99 GLN cc_start: 0.7801 (mp10) cc_final: 0.7563 (mp10) REVERT: I 127 GLN cc_start: 0.7955 (tp40) cc_final: 0.7697 (tp40) REVERT: I 136 GLN cc_start: 0.8165 (tp40) cc_final: 0.7938 (tm-30) REVERT: I 156 ASN cc_start: 0.8114 (m-40) cc_final: 0.7842 (m-40) REVERT: I 219 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7801 (mtm-85) REVERT: I 229 SER cc_start: 0.8391 (t) cc_final: 0.8084 (m) REVERT: I 235 GLU cc_start: 0.8484 (tp30) cc_final: 0.8192 (mm-30) REVERT: I 297 MET cc_start: 0.7335 (tmm) cc_final: 0.6792 (tmm) REVERT: I 306 GLN cc_start: 0.7666 (mm110) cc_final: 0.7421 (mm110) REVERT: I 359 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7056 (tm-30) REVERT: I 404 LEU cc_start: 0.7991 (tp) cc_final: 0.7785 (tt) REVERT: J 81 LEU cc_start: 0.8533 (tp) cc_final: 0.8257 (tp) REVERT: J 82 PHE cc_start: 0.8282 (t80) cc_final: 0.7785 (t80) REVERT: J 84 TRP cc_start: 0.6258 (t60) cc_final: 0.5982 (t60) REVERT: J 131 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6753 (t80) REVERT: J 146 THR cc_start: 0.8391 (m) cc_final: 0.8155 (t) REVERT: J 184 MET cc_start: 0.8054 (mtm) cc_final: 0.7804 (mtm) REVERT: J 248 LEU cc_start: 0.8610 (tp) cc_final: 0.8147 (tp) REVERT: J 252 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7905 (mm-30) REVERT: J 366 TRP cc_start: 0.7252 (m100) cc_final: 0.6770 (m100) REVERT: J 425 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7688 (tm-30) REVERT: J 434 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7556 (mt-10) REVERT: J 464 ILE cc_start: 0.8417 (mt) cc_final: 0.8126 (mm) REVERT: J 487 ILE cc_start: 0.8190 (mt) cc_final: 0.7954 (mm) outliers start: 102 outliers final: 66 residues processed: 1109 average time/residue: 0.2020 time to fit residues: 339.2070 Evaluate side-chains 1108 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1040 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 153 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 324 VAL Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 187 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 105 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 314 optimal weight: 0.0010 chunk 254 optimal weight: 4.9990 chunk 339 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 121 ASN B 126 GLN D 144 ASN D 153 ASN E 61 GLN E 173 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN H 278 ASN I 73 GLN J 26 GLN J 437 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113367 restraints weight = 45776.223| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.86 r_work: 0.3312 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29983 Z= 0.160 Angle : 0.526 9.743 40800 Z= 0.280 Chirality : 0.040 0.152 4829 Planarity : 0.005 0.069 5352 Dihedral : 4.073 76.617 4145 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.97 % Allowed : 16.95 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.14), residues: 3821 helix: 3.37 (0.11), residues: 1989 sheet: -0.24 (0.23), residues: 492 loop : -0.99 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 227 TYR 0.012 0.001 TYR I 7 PHE 0.024 0.001 PHE J 107 TRP 0.010 0.001 TRP J 143 HIS 0.004 0.001 HIS J 428 Details of bonding type rmsd covalent geometry : bond 0.00320 (29983) covalent geometry : angle 0.52576 (40800) hydrogen bonds : bond 0.08077 ( 1864) hydrogen bonds : angle 4.29723 ( 5454) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1050 time to evaluate : 1.218 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: A 140 GLN cc_start: 0.8160 (tp40) cc_final: 0.7756 (tm-30) REVERT: A 143 TYR cc_start: 0.8601 (t80) cc_final: 0.8252 (t80) REVERT: A 144 ASN cc_start: 0.8348 (m-40) cc_final: 0.8088 (m110) REVERT: A 171 GLN cc_start: 0.7874 (tp-100) cc_final: 0.7556 (tp-100) REVERT: A 188 ILE cc_start: 0.8500 (mm) cc_final: 0.8253 (mt) REVERT: A 214 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7901 (mm-30) REVERT: A 242 PRO cc_start: 0.8328 (Cg_endo) cc_final: 0.8086 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7511 (pt0) cc_final: 0.6969 (pt0) REVERT: A 349 ASN cc_start: 0.8564 (t0) cc_final: 0.8331 (t0) REVERT: A 385 VAL cc_start: 0.8530 (p) cc_final: 0.8260 (m) REVERT: A 386 LYS cc_start: 0.8581 (tttt) cc_final: 0.8263 (tttt) REVERT: B 50 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7113 (mm-30) REVERT: B 133 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8189 (mtpp) REVERT: B 134 ILE cc_start: 0.8625 (mm) cc_final: 0.8391 (mt) REVERT: B 140 GLN cc_start: 0.8424 (tp40) cc_final: 0.8035 (tp40) REVERT: B 277 ASP cc_start: 0.7420 (p0) cc_final: 0.6878 (p0) REVERT: C 51 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6717 (mt-10) REVERT: C 54 ASP cc_start: 0.8070 (t0) cc_final: 0.7807 (t0) REVERT: C 81 ASP cc_start: 0.8234 (m-30) cc_final: 0.7321 (m-30) REVERT: C 140 GLN cc_start: 0.8260 (tp-100) cc_final: 0.7700 (tp-100) REVERT: C 146 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.7827 (mtt-85) REVERT: C 180 GLN cc_start: 0.8434 (mt0) cc_final: 0.8192 (mt0) REVERT: C 205 GLU cc_start: 0.7988 (tp30) cc_final: 0.7464 (tp30) REVERT: C 244 MET cc_start: 0.8753 (ptp) cc_final: 0.8533 (ptm) REVERT: C 284 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7964 (mmmt) REVERT: C 380 LEU cc_start: 0.8336 (mp) cc_final: 0.8042 (mp) REVERT: D 54 ASP cc_start: 0.8089 (t0) cc_final: 0.7851 (t0) REVERT: D 62 ILE cc_start: 0.8590 (tp) cc_final: 0.8273 (pt) REVERT: D 103 LYS cc_start: 0.7589 (tttm) cc_final: 0.7356 (tttm) REVERT: D 110 SER cc_start: 0.8659 (t) cc_final: 0.8199 (p) REVERT: D 222 MET cc_start: 0.7467 (ttp) cc_final: 0.6769 (tpp) REVERT: D 288 LYS cc_start: 0.8349 (ptpt) cc_final: 0.7957 (ptpt) REVERT: D 324 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 331 GLU cc_start: 0.7828 (mp0) cc_final: 0.7230 (mp0) REVERT: D 368 THR cc_start: 0.8290 (m) cc_final: 0.7781 (t) REVERT: D 371 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7550 (mt-10) REVERT: E 78 ASP cc_start: 0.7820 (m-30) cc_final: 0.7235 (p0) REVERT: E 84 LYS cc_start: 0.8430 (mmmm) cc_final: 0.7941 (mmmm) REVERT: E 102 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6999 (mm-30) REVERT: E 194 GLU cc_start: 0.7513 (mp0) cc_final: 0.7211 (mp0) REVERT: E 217 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7531 (mtm-85) REVERT: E 266 MET cc_start: 0.8575 (mtt) cc_final: 0.8277 (mtp) REVERT: E 328 LYS cc_start: 0.8013 (mtmm) cc_final: 0.7744 (mtmm) REVERT: E 341 THR cc_start: 0.8115 (p) cc_final: 0.7845 (p) REVERT: E 379 LYS cc_start: 0.8169 (tttt) cc_final: 0.7931 (tttt) REVERT: E 382 ASP cc_start: 0.8362 (t0) cc_final: 0.8087 (t0) REVERT: F 171 GLN cc_start: 0.8533 (tp40) cc_final: 0.8305 (tp40) REVERT: F 194 GLU cc_start: 0.8214 (mp0) cc_final: 0.7834 (mp0) REVERT: F 244 MET cc_start: 0.8018 (ptm) cc_final: 0.7762 (ptm) REVERT: F 327 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7485 (mm-40) REVERT: F 328 LYS cc_start: 0.8780 (tttt) cc_final: 0.8503 (tttt) REVERT: G 5 GLN cc_start: 0.8029 (mt0) cc_final: 0.7801 (mt0) REVERT: G 30 LYS cc_start: 0.8289 (tttt) cc_final: 0.7971 (tttt) REVERT: G 82 ARG cc_start: 0.7655 (mmt-90) cc_final: 0.7143 (mmt-90) REVERT: G 156 ASN cc_start: 0.7817 (t0) cc_final: 0.7514 (t0) REVERT: G 160 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7315 (mp-120) REVERT: G 186 THR cc_start: 0.8520 (t) cc_final: 0.8241 (p) REVERT: G 188 ASN cc_start: 0.7914 (m110) cc_final: 0.7464 (m-40) REVERT: G 217 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7377 (tm-30) REVERT: G 229 SER cc_start: 0.8218 (t) cc_final: 0.7960 (m) REVERT: G 237 ILE cc_start: 0.7756 (mt) cc_final: 0.7427 (mt) REVERT: G 239 GLN cc_start: 0.8316 (tm-30) cc_final: 0.8088 (tm-30) REVERT: G 288 PHE cc_start: 0.7659 (t80) cc_final: 0.7190 (t80) REVERT: G 328 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7966 (mmt-90) REVERT: G 344 TYR cc_start: 0.8583 (m-10) cc_final: 0.8245 (m-80) REVERT: G 385 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7530 (mm-30) REVERT: G 390 ARG cc_start: 0.8632 (mtt90) cc_final: 0.8413 (mtt-85) REVERT: G 401 LYS cc_start: 0.7706 (tppt) cc_final: 0.7375 (tppt) REVERT: H 5 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7254 (mt0) REVERT: H 11 ARG cc_start: 0.7689 (tpt-90) cc_final: 0.7445 (tpt-90) REVERT: H 42 LEU cc_start: 0.8317 (mt) cc_final: 0.7899 (mt) REVERT: H 69 LEU cc_start: 0.7871 (mt) cc_final: 0.7483 (mm) REVERT: H 70 GLN cc_start: 0.7740 (mp10) cc_final: 0.7066 (mp10) REVERT: H 130 LYS cc_start: 0.8515 (tmmt) cc_final: 0.8111 (ttmt) REVERT: H 131 GLU cc_start: 0.8043 (tp30) cc_final: 0.7719 (tp30) REVERT: H 133 ILE cc_start: 0.8973 (mt) cc_final: 0.8746 (mm) REVERT: H 158 ARG cc_start: 0.7599 (tpp-160) cc_final: 0.7356 (tpp-160) REVERT: H 175 LEU cc_start: 0.8432 (tp) cc_final: 0.8222 (tt) REVERT: H 229 SER cc_start: 0.8489 (m) cc_final: 0.8208 (t) REVERT: H 242 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7333 (t0) REVERT: H 328 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7728 (mmt90) REVERT: H 350 SER cc_start: 0.8451 (t) cc_final: 0.8119 (m) REVERT: H 359 GLU cc_start: 0.8160 (tp30) cc_final: 0.7675 (tp30) REVERT: H 374 ASP cc_start: 0.8066 (m-30) cc_final: 0.7775 (m-30) REVERT: H 391 TYR cc_start: 0.8411 (m-10) cc_final: 0.8070 (m-10) REVERT: H 393 TYR cc_start: 0.8726 (t80) cc_final: 0.8505 (t80) REVERT: I 7 TYR cc_start: 0.8081 (t80) cc_final: 0.7776 (t80) REVERT: I 19 LYS cc_start: 0.7556 (ttmm) cc_final: 0.7251 (ttmm) REVERT: I 24 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.8126 (ptm-80) REVERT: I 33 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7806 (tm-30) REVERT: I 70 GLN cc_start: 0.7602 (mm110) cc_final: 0.7308 (mm110) REVERT: I 89 LYS cc_start: 0.8387 (mttp) cc_final: 0.8081 (mttt) REVERT: I 127 GLN cc_start: 0.7990 (tp40) cc_final: 0.7695 (tp40) REVERT: I 156 ASN cc_start: 0.8002 (m-40) cc_final: 0.7719 (m-40) REVERT: I 213 LEU cc_start: 0.8037 (tt) cc_final: 0.7698 (mt) REVERT: I 229 SER cc_start: 0.8415 (t) cc_final: 0.8122 (m) REVERT: I 235 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: I 297 MET cc_start: 0.7381 (tmm) cc_final: 0.6795 (tmm) REVERT: I 322 SER cc_start: 0.8525 (t) cc_final: 0.8087 (m) REVERT: I 344 TYR cc_start: 0.8435 (m-10) cc_final: 0.7852 (m-10) REVERT: I 359 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7160 (tm-30) REVERT: J 21 LEU cc_start: 0.8428 (mm) cc_final: 0.8147 (mm) REVERT: J 62 ASN cc_start: 0.8411 (t0) cc_final: 0.7993 (t0) REVERT: J 81 LEU cc_start: 0.8486 (tp) cc_final: 0.8228 (tp) REVERT: J 82 PHE cc_start: 0.8247 (t80) cc_final: 0.7758 (t80) REVERT: J 84 TRP cc_start: 0.6298 (t60) cc_final: 0.6028 (t60) REVERT: J 131 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.6723 (t80) REVERT: J 184 MET cc_start: 0.7997 (mtm) cc_final: 0.7646 (mtm) REVERT: J 248 LEU cc_start: 0.8606 (tp) cc_final: 0.8340 (tp) REVERT: J 361 PHE cc_start: 0.8037 (t80) cc_final: 0.7766 (t80) REVERT: J 366 TRP cc_start: 0.7147 (m100) cc_final: 0.6693 (m100) REVERT: J 425 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7613 (tm-30) REVERT: J 434 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: J 487 ILE cc_start: 0.8127 (mt) cc_final: 0.7878 (mm) REVERT: J 489 LEU cc_start: 0.7968 (mt) cc_final: 0.7606 (mm) outliers start: 95 outliers final: 64 residues processed: 1092 average time/residue: 0.2170 time to fit residues: 359.3465 Evaluate side-chains 1103 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1033 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 359 GLU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 371 ASP Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 235 GLU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 23 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 224 LYS Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 450 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 153 optimal weight: 1.9990 chunk 366 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 294 optimal weight: 0.9990 chunk 311 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 200 optimal weight: 0.0570 chunk 95 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS B 121 ASN B 200 GLN E 173 GLN E 201 GLN F 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN I 299 ASN I 306 GLN J 26 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112654 restraints weight = 45950.433| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.87 r_work: 0.3301 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29983 Z= 0.176 Angle : 0.538 10.414 40800 Z= 0.286 Chirality : 0.041 0.149 4829 Planarity : 0.005 0.071 5352 Dihedral : 4.083 77.453 4145 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.35 % Allowed : 18.14 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.14), residues: 3821 helix: 3.33 (0.11), residues: 1998 sheet: -0.15 (0.24), residues: 486 loop : -1.02 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 227 TYR 0.013 0.001 TYR H 125 PHE 0.022 0.001 PHE J 439 TRP 0.011 0.001 TRP A 76 HIS 0.003 0.001 HIS J 166 Details of bonding type rmsd covalent geometry : bond 0.00368 (29983) covalent geometry : angle 0.53760 (40800) hydrogen bonds : bond 0.08236 ( 1864) hydrogen bonds : angle 4.28248 ( 5454) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1049 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8183 (tp40) cc_final: 0.7787 (tm-30) REVERT: A 143 TYR cc_start: 0.8654 (t80) cc_final: 0.8325 (t80) REVERT: A 144 ASN cc_start: 0.8375 (m-40) cc_final: 0.8140 (m110) REVERT: A 171 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7568 (tp-100) REVERT: A 188 ILE cc_start: 0.8510 (mm) cc_final: 0.8254 (mt) REVERT: A 242 PRO cc_start: 0.8336 (Cg_endo) cc_final: 0.8097 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7517 (pt0) cc_final: 0.7285 (pt0) REVERT: A 349 ASN cc_start: 0.8598 (t0) cc_final: 0.8351 (t0) REVERT: A 385 VAL cc_start: 0.8523 (p) cc_final: 0.8254 (m) REVERT: A 386 LYS cc_start: 0.8588 (tttt) cc_final: 0.8270 (tttt) REVERT: B 50 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7130 (mm-30) REVERT: B 133 LYS cc_start: 0.8420 (mtpp) cc_final: 0.8187 (mtpp) REVERT: B 134 ILE cc_start: 0.8619 (mm) cc_final: 0.8377 (mt) REVERT: B 140 GLN cc_start: 0.8467 (tp40) cc_final: 0.8074 (tp40) REVERT: B 279 TYR cc_start: 0.8591 (m-80) cc_final: 0.8375 (m-80) REVERT: C 51 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6711 (mt-10) REVERT: C 54 ASP cc_start: 0.8045 (t0) cc_final: 0.7783 (t0) REVERT: C 81 ASP cc_start: 0.8246 (m-30) cc_final: 0.7322 (m-30) REVERT: C 140 GLN cc_start: 0.8276 (tp-100) cc_final: 0.7710 (tp-100) REVERT: C 146 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.7943 (mtt-85) REVERT: C 153 ASN cc_start: 0.8525 (t0) cc_final: 0.8084 (t0) REVERT: C 180 GLN cc_start: 0.8442 (mt0) cc_final: 0.8211 (mt0) REVERT: C 205 GLU cc_start: 0.8082 (tp30) cc_final: 0.7575 (tp30) REVERT: C 229 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8385 (tmm-80) REVERT: C 244 MET cc_start: 0.8758 (ptp) cc_final: 0.8552 (ptm) REVERT: C 284 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7957 (mmmt) REVERT: C 380 LEU cc_start: 0.8329 (mp) cc_final: 0.8112 (mp) REVERT: D 54 ASP cc_start: 0.8100 (t0) cc_final: 0.7882 (t0) REVERT: D 103 LYS cc_start: 0.7610 (tttm) cc_final: 0.7374 (tttm) REVERT: D 110 SER cc_start: 0.8671 (t) cc_final: 0.8221 (p) REVERT: D 288 LYS cc_start: 0.8364 (ptpt) cc_final: 0.7980 (ptpt) REVERT: D 324 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7688 (tm-30) REVERT: D 331 GLU cc_start: 0.7824 (mp0) cc_final: 0.7210 (mp0) REVERT: D 368 THR cc_start: 0.8382 (m) cc_final: 0.7843 (t) REVERT: D 371 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7554 (mt-10) REVERT: E 78 ASP cc_start: 0.7846 (m-30) cc_final: 0.7192 (p0) REVERT: E 81 ASP cc_start: 0.7699 (m-30) cc_final: 0.7003 (m-30) REVERT: E 84 LYS cc_start: 0.8401 (mmmm) cc_final: 0.7990 (mmmm) REVERT: E 102 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7028 (mm-30) REVERT: E 173 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: E 194 GLU cc_start: 0.7524 (mp0) cc_final: 0.7237 (mp0) REVERT: E 217 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7533 (mtm-85) REVERT: E 266 MET cc_start: 0.8593 (mtt) cc_final: 0.8274 (mtp) REVERT: E 328 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7773 (mtmm) REVERT: E 351 ASP cc_start: 0.8013 (p0) cc_final: 0.7783 (p0) REVERT: E 379 LYS cc_start: 0.8204 (tttt) cc_final: 0.7946 (tttt) REVERT: E 382 ASP cc_start: 0.8350 (t0) cc_final: 0.8093 (t0) REVERT: F 87 ASP cc_start: 0.7654 (t0) cc_final: 0.7418 (t0) REVERT: F 93 ASP cc_start: 0.7914 (t0) cc_final: 0.7640 (t0) REVERT: F 171 GLN cc_start: 0.8580 (tp40) cc_final: 0.8277 (tp40) REVERT: F 194 GLU cc_start: 0.8198 (mp0) cc_final: 0.7827 (mp0) REVERT: F 327 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7426 (mm110) REVERT: F 328 LYS cc_start: 0.8777 (tttt) cc_final: 0.8516 (tttt) REVERT: G 5 GLN cc_start: 0.8054 (mt0) cc_final: 0.7807 (mt0) REVERT: G 82 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7100 (mmt-90) REVERT: G 156 ASN cc_start: 0.7847 (t0) cc_final: 0.7520 (t0) REVERT: G 160 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7309 (mp-120) REVERT: G 186 THR cc_start: 0.8539 (t) cc_final: 0.8248 (p) REVERT: G 188 ASN cc_start: 0.7916 (m110) cc_final: 0.7442 (m-40) REVERT: G 217 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7449 (tm-30) REVERT: G 229 SER cc_start: 0.8209 (t) cc_final: 0.7947 (m) REVERT: G 237 ILE cc_start: 0.7813 (mt) cc_final: 0.7516 (mt) REVERT: G 288 PHE cc_start: 0.7669 (t80) cc_final: 0.7088 (t80) REVERT: G 328 ARG cc_start: 0.8218 (mtt-85) cc_final: 0.7983 (mmt-90) REVERT: G 344 TYR cc_start: 0.8579 (m-10) cc_final: 0.8203 (m-80) REVERT: G 385 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7486 (mm-30) REVERT: G 390 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8409 (mtt-85) REVERT: G 401 LYS cc_start: 0.7662 (tppt) cc_final: 0.7374 (tppt) REVERT: H 11 ARG cc_start: 0.7698 (tpt-90) cc_final: 0.7432 (tpt-90) REVERT: H 24 ARG cc_start: 0.8276 (ttt90) cc_final: 0.8055 (ttt90) REVERT: H 35 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7636 (ttm-80) REVERT: H 42 LEU cc_start: 0.8340 (mt) cc_final: 0.7934 (mt) REVERT: H 69 LEU cc_start: 0.7884 (mt) cc_final: 0.7536 (mm) REVERT: H 70 GLN cc_start: 0.7777 (mp10) cc_final: 0.7105 (mp10) REVERT: H 130 LYS cc_start: 0.8518 (tmmt) cc_final: 0.8101 (ttmt) REVERT: H 131 GLU cc_start: 0.8048 (tp30) cc_final: 0.7641 (tp30) REVERT: H 135 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7405 (ttm-80) REVERT: H 158 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7362 (tpp-160) REVERT: H 164 VAL cc_start: 0.8711 (p) cc_final: 0.8463 (t) REVERT: H 175 LEU cc_start: 0.8527 (tp) cc_final: 0.8317 (tt) REVERT: H 229 SER cc_start: 0.8478 (m) cc_final: 0.8192 (t) REVERT: H 242 ASP cc_start: 0.7580 (OUTLIER) cc_final: 0.7291 (t0) REVERT: H 326 THR cc_start: 0.8033 (m) cc_final: 0.7522 (p) REVERT: H 328 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7756 (mmt90) REVERT: H 350 SER cc_start: 0.8490 (t) cc_final: 0.8165 (m) REVERT: H 359 GLU cc_start: 0.8207 (tp30) cc_final: 0.7709 (tp30) REVERT: H 374 ASP cc_start: 0.8112 (m-30) cc_final: 0.7812 (m-30) REVERT: H 391 TYR cc_start: 0.8415 (m-10) cc_final: 0.8104 (m-10) REVERT: H 393 TYR cc_start: 0.8718 (t80) cc_final: 0.8461 (t80) REVERT: I 19 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7257 (ttmm) REVERT: I 24 ARG cc_start: 0.8410 (ptm-80) cc_final: 0.8142 (ptm-80) REVERT: I 33 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7797 (tm-30) REVERT: I 44 LEU cc_start: 0.7266 (tt) cc_final: 0.6474 (mt) REVERT: I 52 ASN cc_start: 0.7079 (m-40) cc_final: 0.6868 (m-40) REVERT: I 70 GLN cc_start: 0.7605 (mm110) cc_final: 0.7282 (mm110) REVERT: I 127 GLN cc_start: 0.7972 (tp40) cc_final: 0.7708 (tp40) REVERT: I 156 ASN cc_start: 0.8008 (m-40) cc_final: 0.7735 (m-40) REVERT: I 215 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7595 (tm-30) REVERT: I 229 SER cc_start: 0.8445 (t) cc_final: 0.8137 (m) REVERT: I 235 GLU cc_start: 0.8427 (tp30) cc_final: 0.8145 (mm-30) REVERT: I 297 MET cc_start: 0.7474 (tmm) cc_final: 0.6819 (tmm) REVERT: I 306 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7374 (mm110) REVERT: I 322 SER cc_start: 0.8524 (t) cc_final: 0.8085 (m) REVERT: I 344 TYR cc_start: 0.8440 (m-10) cc_final: 0.7839 (m-10) REVERT: I 359 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7192 (tm-30) REVERT: J 81 LEU cc_start: 0.8487 (tp) cc_final: 0.8230 (tp) REVERT: J 82 PHE cc_start: 0.8255 (t80) cc_final: 0.7783 (t80) REVERT: J 84 TRP cc_start: 0.6309 (t60) cc_final: 0.6023 (t60) REVERT: J 131 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6803 (t80) REVERT: J 140 LEU cc_start: 0.8730 (mt) cc_final: 0.8529 (mm) REVERT: J 184 MET cc_start: 0.8020 (mtm) cc_final: 0.7658 (mtm) REVERT: J 248 LEU cc_start: 0.8603 (tp) cc_final: 0.8278 (tp) REVERT: J 252 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7995 (mm-30) REVERT: J 361 PHE cc_start: 0.8002 (t80) cc_final: 0.7696 (t80) REVERT: J 366 TRP cc_start: 0.7181 (m100) cc_final: 0.6734 (m100) REVERT: J 386 THR cc_start: 0.8719 (m) cc_final: 0.8376 (p) REVERT: J 425 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7624 (tm-30) REVERT: J 434 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7573 (mt-10) REVERT: J 487 ILE cc_start: 0.8120 (mt) cc_final: 0.7905 (mm) outliers start: 107 outliers final: 81 residues processed: 1097 average time/residue: 0.2276 time to fit residues: 378.1462 Evaluate side-chains 1126 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1039 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 173 GLN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 206 LEU Chi-restraints excluded: chain J residue 224 LYS Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 434 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 352 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 320 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 151 ASN B 121 ASN B 200 GLN E 63 GLN E 201 GLN E 265 ASN F 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN H 416 ASN I 320 HIS J 26 GLN ** J 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110647 restraints weight = 45693.214| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.85 r_work: 0.3274 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29983 Z= 0.246 Angle : 0.593 11.133 40800 Z= 0.318 Chirality : 0.044 0.153 4829 Planarity : 0.005 0.078 5352 Dihedral : 4.308 77.186 4145 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.07 % Allowed : 18.20 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.14), residues: 3821 helix: 3.02 (0.11), residues: 2010 sheet: -0.25 (0.23), residues: 486 loop : -1.19 (0.16), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 227 TYR 0.017 0.002 TYR I 7 PHE 0.024 0.002 PHE I 288 TRP 0.015 0.002 TRP A 76 HIS 0.006 0.001 HIS J 429 Details of bonding type rmsd covalent geometry : bond 0.00549 (29983) covalent geometry : angle 0.59314 (40800) hydrogen bonds : bond 0.09132 ( 1864) hydrogen bonds : angle 4.46650 ( 5454) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1063 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7624 (tp-100) REVERT: A 188 ILE cc_start: 0.8528 (mm) cc_final: 0.8267 (mt) REVERT: A 194 GLU cc_start: 0.8053 (pm20) cc_final: 0.7796 (pm20) REVERT: A 242 PRO cc_start: 0.8359 (Cg_endo) cc_final: 0.8111 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7513 (pt0) cc_final: 0.7281 (pt0) REVERT: A 385 VAL cc_start: 0.8512 (p) cc_final: 0.8251 (m) REVERT: A 386 LYS cc_start: 0.8580 (tttt) cc_final: 0.8266 (tttt) REVERT: B 133 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8198 (mtpp) REVERT: B 134 ILE cc_start: 0.8647 (mm) cc_final: 0.8411 (mt) REVERT: B 279 TYR cc_start: 0.8590 (m-80) cc_final: 0.8346 (m-80) REVERT: C 51 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6678 (mt-10) REVERT: C 54 ASP cc_start: 0.8025 (t0) cc_final: 0.7755 (t0) REVERT: C 81 ASP cc_start: 0.8249 (m-30) cc_final: 0.7808 (m-30) REVERT: C 140 GLN cc_start: 0.8314 (tp-100) cc_final: 0.7944 (tp-100) REVERT: C 146 ARG cc_start: 0.8413 (mmt-90) cc_final: 0.8169 (mtt-85) REVERT: C 180 GLN cc_start: 0.8436 (mt0) cc_final: 0.8209 (mt0) REVERT: C 205 GLU cc_start: 0.8043 (tp30) cc_final: 0.7523 (tp30) REVERT: C 229 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8419 (tmm-80) REVERT: C 284 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7964 (mmmt) REVERT: C 380 LEU cc_start: 0.8396 (mp) cc_final: 0.8172 (mp) REVERT: D 54 ASP cc_start: 0.8097 (t0) cc_final: 0.7884 (t0) REVERT: D 103 LYS cc_start: 0.7652 (tttm) cc_final: 0.7397 (tttm) REVERT: D 110 SER cc_start: 0.8687 (t) cc_final: 0.8232 (p) REVERT: D 288 LYS cc_start: 0.8380 (ptpt) cc_final: 0.7992 (ptpt) REVERT: D 324 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7714 (tm-30) REVERT: D 331 GLU cc_start: 0.7838 (mp0) cc_final: 0.7216 (mp0) REVERT: D 368 THR cc_start: 0.8425 (m) cc_final: 0.7863 (t) REVERT: D 371 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 78 ASP cc_start: 0.7868 (m-30) cc_final: 0.7218 (p0) REVERT: E 81 ASP cc_start: 0.7729 (m-30) cc_final: 0.7158 (m-30) REVERT: E 84 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8015 (mmmm) REVERT: E 102 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7164 (mm-30) REVERT: E 194 GLU cc_start: 0.7518 (mp0) cc_final: 0.7249 (mp0) REVERT: E 217 ARG cc_start: 0.7946 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: E 222 MET cc_start: 0.8190 (mmm) cc_final: 0.7920 (mmm) REVERT: E 266 MET cc_start: 0.8613 (mtt) cc_final: 0.8299 (mtp) REVERT: E 351 ASP cc_start: 0.8009 (p0) cc_final: 0.7764 (p0) REVERT: E 379 LYS cc_start: 0.8219 (tttt) cc_final: 0.7976 (tttt) REVERT: E 382 ASP cc_start: 0.8366 (t0) cc_final: 0.8112 (t0) REVERT: F 87 ASP cc_start: 0.7664 (t0) cc_final: 0.7427 (t0) REVERT: F 93 ASP cc_start: 0.7995 (t0) cc_final: 0.7783 (t0) REVERT: F 146 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7368 (mtt90) REVERT: F 194 GLU cc_start: 0.8205 (mp0) cc_final: 0.7850 (mp0) REVERT: F 327 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7463 (mm110) REVERT: F 328 LYS cc_start: 0.8804 (tttt) cc_final: 0.8538 (tttt) REVERT: G 5 GLN cc_start: 0.8029 (mt0) cc_final: 0.7804 (mt0) REVERT: G 30 LYS cc_start: 0.8294 (tttt) cc_final: 0.7898 (tttt) REVERT: G 82 ARG cc_start: 0.7834 (mmt-90) cc_final: 0.7311 (mmt-90) REVERT: G 160 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7312 (mp-120) REVERT: G 186 THR cc_start: 0.8577 (t) cc_final: 0.8336 (p) REVERT: G 188 ASN cc_start: 0.7923 (m110) cc_final: 0.7455 (m-40) REVERT: G 217 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7468 (tm-30) REVERT: G 229 SER cc_start: 0.8230 (t) cc_final: 0.7973 (m) REVERT: G 237 ILE cc_start: 0.7803 (mt) cc_final: 0.7503 (mt) REVERT: G 341 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8273 (tp) REVERT: G 344 TYR cc_start: 0.8599 (m-10) cc_final: 0.8244 (m-80) REVERT: G 385 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7669 (mm-30) REVERT: G 390 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8382 (mtt-85) REVERT: G 401 LYS cc_start: 0.7721 (tppt) cc_final: 0.7392 (tppt) REVERT: H 11 ARG cc_start: 0.7718 (tpt-90) cc_final: 0.7447 (tpt-90) REVERT: H 24 ARG cc_start: 0.8286 (ttt90) cc_final: 0.8075 (ttt90) REVERT: H 42 LEU cc_start: 0.8329 (mt) cc_final: 0.7929 (mt) REVERT: H 69 LEU cc_start: 0.7904 (mt) cc_final: 0.7605 (mm) REVERT: H 70 GLN cc_start: 0.7833 (mp10) cc_final: 0.7215 (mp10) REVERT: H 73 GLN cc_start: 0.7928 (tp40) cc_final: 0.7580 (tm-30) REVERT: H 130 LYS cc_start: 0.8510 (tmmt) cc_final: 0.8122 (ttmt) REVERT: H 131 GLU cc_start: 0.8101 (tp30) cc_final: 0.7668 (tp30) REVERT: H 135 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7487 (ttm-80) REVERT: H 158 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7500 (tpp-160) REVERT: H 164 VAL cc_start: 0.8713 (p) cc_final: 0.8496 (t) REVERT: H 229 SER cc_start: 0.8557 (m) cc_final: 0.8277 (t) REVERT: H 242 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7349 (t0) REVERT: H 326 THR cc_start: 0.8114 (m) cc_final: 0.7493 (p) REVERT: H 328 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7772 (mmt90) REVERT: H 345 LYS cc_start: 0.8239 (ttmt) cc_final: 0.8008 (ttmm) REVERT: H 350 SER cc_start: 0.8502 (t) cc_final: 0.8164 (m) REVERT: H 374 ASP cc_start: 0.8180 (m-30) cc_final: 0.7908 (m-30) REVERT: H 390 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8211 (mtt180) REVERT: H 391 TYR cc_start: 0.8394 (m-10) cc_final: 0.8190 (m-10) REVERT: I 7 TYR cc_start: 0.8140 (t80) cc_final: 0.7821 (t80) REVERT: I 18 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7469 (mtp-110) REVERT: I 19 LYS cc_start: 0.7626 (ttmm) cc_final: 0.7261 (ttmm) REVERT: I 24 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8119 (ttp80) REVERT: I 33 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7815 (tm-30) REVERT: I 70 GLN cc_start: 0.7611 (mm110) cc_final: 0.7315 (mm110) REVERT: I 127 GLN cc_start: 0.7979 (tp40) cc_final: 0.7728 (tp40) REVERT: I 156 ASN cc_start: 0.8063 (m-40) cc_final: 0.7825 (m-40) REVERT: I 213 LEU cc_start: 0.7968 (tt) cc_final: 0.7692 (mt) REVERT: I 219 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7548 (mtm-85) REVERT: I 229 SER cc_start: 0.8427 (t) cc_final: 0.8098 (m) REVERT: I 235 GLU cc_start: 0.8519 (tp30) cc_final: 0.8204 (mm-30) REVERT: I 297 MET cc_start: 0.7632 (tmm) cc_final: 0.7023 (tmm) REVERT: I 344 TYR cc_start: 0.8441 (m-10) cc_final: 0.7854 (m-10) REVERT: I 359 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7132 (tm-30) REVERT: J 62 ASN cc_start: 0.8520 (t0) cc_final: 0.8227 (t0) REVERT: J 81 LEU cc_start: 0.8539 (tp) cc_final: 0.8329 (tp) REVERT: J 82 PHE cc_start: 0.8294 (t80) cc_final: 0.7671 (t80) REVERT: J 84 TRP cc_start: 0.6333 (t60) cc_final: 0.6114 (t60) REVERT: J 85 SER cc_start: 0.8583 (m) cc_final: 0.8192 (p) REVERT: J 128 LEU cc_start: 0.8407 (mt) cc_final: 0.8196 (mt) REVERT: J 131 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6838 (t80) REVERT: J 140 LEU cc_start: 0.8739 (mt) cc_final: 0.8531 (mm) REVERT: J 183 LEU cc_start: 0.8615 (tt) cc_final: 0.8046 (mm) REVERT: J 184 MET cc_start: 0.7948 (mtm) cc_final: 0.7602 (mtm) REVERT: J 186 LEU cc_start: 0.8370 (mt) cc_final: 0.8140 (pp) REVERT: J 248 LEU cc_start: 0.8638 (tp) cc_final: 0.8172 (tp) REVERT: J 252 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7901 (mm-30) REVERT: J 361 PHE cc_start: 0.7965 (t80) cc_final: 0.7692 (t80) REVERT: J 366 TRP cc_start: 0.7173 (m100) cc_final: 0.6722 (m100) REVERT: J 386 THR cc_start: 0.8695 (m) cc_final: 0.8402 (m) REVERT: J 406 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7676 (mtp-110) REVERT: J 425 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7836 (tm-30) REVERT: J 434 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: J 464 ILE cc_start: 0.8439 (mt) cc_final: 0.8159 (mm) outliers start: 130 outliers final: 105 residues processed: 1121 average time/residue: 0.2255 time to fit residues: 383.3006 Evaluate side-chains 1160 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1048 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 173 GLN Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 372 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 127 GLN Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 320 HIS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 341 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 224 LYS Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 497 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 131 optimal weight: 0.6980 chunk 233 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 chunk 361 optimal weight: 0.0020 chunk 350 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 209 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 overall best weight: 0.4866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 151 ASN B 121 ASN E 63 GLN E 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN G 397 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN H 99 GLN I 52 ASN I 320 HIS ** J 431 GLN ** 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 = 0.3669 r_free = 0.3669 target = 0.129103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113352 restraints weight = 45803.565| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.87 r_work: 0.3314 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29983 Z= 0.153 Angle : 0.536 11.687 40800 Z= 0.281 Chirality : 0.040 0.144 4829 Planarity : 0.005 0.059 5352 Dihedral : 4.036 77.973 4145 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.44 % Allowed : 19.92 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.14), residues: 3821 helix: 3.37 (0.11), residues: 1998 sheet: -0.17 (0.24), residues: 486 loop : -1.02 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 227 TYR 0.019 0.001 TYR H 125 PHE 0.028 0.001 PHE I 288 TRP 0.010 0.001 TRP J 350 HIS 0.030 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00302 (29983) covalent geometry : angle 0.53589 (40800) hydrogen bonds : bond 0.07895 ( 1864) hydrogen bonds : angle 4.18911 ( 5454) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1052 time to evaluate : 1.175 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: A 140 GLN cc_start: 0.8251 (tp40) cc_final: 0.7788 (tm-30) REVERT: A 144 ASN cc_start: 0.8337 (m-40) cc_final: 0.8127 (m110) REVERT: A 171 GLN cc_start: 0.7911 (tp-100) cc_final: 0.7308 (tp-100) REVERT: A 188 ILE cc_start: 0.8504 (mm) cc_final: 0.8265 (mt) REVERT: A 214 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 242 PRO cc_start: 0.8338 (Cg_endo) cc_final: 0.8093 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7502 (pt0) cc_final: 0.6931 (pt0) REVERT: A 349 ASN cc_start: 0.8515 (t0) cc_final: 0.8233 (t0) REVERT: A 385 VAL cc_start: 0.8514 (p) cc_final: 0.8249 (m) REVERT: A 386 LYS cc_start: 0.8585 (tttt) cc_final: 0.8263 (tttt) REVERT: B 50 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 133 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8170 (mtpp) REVERT: B 134 ILE cc_start: 0.8615 (mm) cc_final: 0.8370 (mt) REVERT: B 277 ASP cc_start: 0.7389 (p0) cc_final: 0.6812 (p0) REVERT: B 279 TYR cc_start: 0.8602 (m-80) cc_final: 0.8354 (m-80) REVERT: B 350 ARG cc_start: 0.8860 (ptp-170) cc_final: 0.8634 (ptp-170) REVERT: C 51 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6671 (mt-10) REVERT: C 54 ASP cc_start: 0.8003 (t0) cc_final: 0.7726 (t0) REVERT: C 81 ASP cc_start: 0.8240 (m-30) cc_final: 0.7301 (m-30) REVERT: C 140 GLN cc_start: 0.8263 (tp-100) cc_final: 0.7693 (tp-100) REVERT: C 146 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7883 (mtt-85) REVERT: C 153 ASN cc_start: 0.8510 (t0) cc_final: 0.8093 (t0) REVERT: C 180 GLN cc_start: 0.8447 (mt0) cc_final: 0.8216 (mt0) REVERT: C 205 GLU cc_start: 0.8014 (tp30) cc_final: 0.7498 (tp30) REVERT: C 229 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8395 (tmm-80) REVERT: C 284 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7951 (mmmt) REVERT: C 358 LYS cc_start: 0.7812 (tmtt) cc_final: 0.7427 (tmtt) REVERT: C 380 LEU cc_start: 0.8325 (mp) cc_final: 0.8082 (mp) REVERT: D 54 ASP cc_start: 0.8077 (t0) cc_final: 0.7852 (t0) REVERT: D 103 LYS cc_start: 0.7556 (tttm) cc_final: 0.7326 (tttm) REVERT: D 110 SER cc_start: 0.8662 (t) cc_final: 0.8218 (p) REVERT: D 288 LYS cc_start: 0.8353 (ptpt) cc_final: 0.7977 (ptpt) REVERT: D 324 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7729 (tm-30) REVERT: D 331 GLU cc_start: 0.7796 (mp0) cc_final: 0.7184 (mp0) REVERT: D 368 THR cc_start: 0.8326 (m) cc_final: 0.7803 (t) REVERT: D 371 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7546 (mt-10) REVERT: E 78 ASP cc_start: 0.7778 (m-30) cc_final: 0.7293 (p0) REVERT: E 84 LYS cc_start: 0.8382 (mmmm) cc_final: 0.8009 (mmmm) REVERT: E 102 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6994 (mm-30) REVERT: E 194 GLU cc_start: 0.7501 (mp0) cc_final: 0.7229 (mp0) REVERT: E 217 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: E 266 MET cc_start: 0.8576 (mtt) cc_final: 0.8268 (mtp) REVERT: E 328 LYS cc_start: 0.8020 (mtmm) cc_final: 0.7780 (mtmm) REVERT: E 351 ASP cc_start: 0.7976 (p0) cc_final: 0.7729 (p0) REVERT: E 379 LYS cc_start: 0.8170 (tttt) cc_final: 0.7923 (tttt) REVERT: E 382 ASP cc_start: 0.8323 (t0) cc_final: 0.8075 (t0) REVERT: F 87 ASP cc_start: 0.7635 (t0) cc_final: 0.7423 (t0) REVERT: F 93 ASP cc_start: 0.7895 (t0) cc_final: 0.7686 (t0) REVERT: F 140 GLN cc_start: 0.8405 (tp-100) cc_final: 0.8180 (tp-100) REVERT: F 146 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.6952 (mtt90) REVERT: F 171 GLN cc_start: 0.8523 (tp40) cc_final: 0.8322 (tp40) REVERT: F 194 GLU cc_start: 0.8165 (mp0) cc_final: 0.7799 (mp0) REVERT: F 327 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7434 (mm110) REVERT: F 328 LYS cc_start: 0.8767 (tttt) cc_final: 0.8500 (tttt) REVERT: G 5 GLN cc_start: 0.7977 (mt0) cc_final: 0.7739 (mt0) REVERT: G 30 LYS cc_start: 0.8287 (tttt) cc_final: 0.7874 (tttt) REVERT: G 96 VAL cc_start: 0.8321 (t) cc_final: 0.8061 (m) REVERT: G 156 ASN cc_start: 0.7784 (t0) cc_final: 0.7445 (t0) REVERT: G 160 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7261 (mp-120) REVERT: G 186 THR cc_start: 0.8564 (t) cc_final: 0.8312 (p) REVERT: G 188 ASN cc_start: 0.7898 (m110) cc_final: 0.7429 (m-40) REVERT: G 217 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7354 (tm-30) REVERT: G 229 SER cc_start: 0.8183 (t) cc_final: 0.7923 (m) REVERT: G 237 ILE cc_start: 0.7775 (mt) cc_final: 0.7495 (mt) REVERT: G 288 PHE cc_start: 0.7556 (t80) cc_final: 0.7128 (t80) REVERT: G 341 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8233 (tp) REVERT: G 344 TYR cc_start: 0.8579 (m-10) cc_final: 0.8223 (m-80) REVERT: G 385 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7556 (mm-30) REVERT: G 390 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8403 (mtt-85) REVERT: G 401 LYS cc_start: 0.7557 (tppt) cc_final: 0.7311 (tppt) REVERT: H 5 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: H 11 ARG cc_start: 0.7643 (tpt-90) cc_final: 0.7389 (tpt-90) REVERT: H 24 ARG cc_start: 0.8250 (ttt90) cc_final: 0.8004 (ttt90) REVERT: H 42 LEU cc_start: 0.8296 (mt) cc_final: 0.7881 (mt) REVERT: H 69 LEU cc_start: 0.7881 (mt) cc_final: 0.7609 (mm) REVERT: H 70 GLN cc_start: 0.7848 (mp10) cc_final: 0.7198 (mp10) REVERT: H 73 GLN cc_start: 0.7868 (tp40) cc_final: 0.7551 (tm-30) REVERT: H 130 LYS cc_start: 0.8464 (tmmt) cc_final: 0.8058 (ttmt) REVERT: H 131 GLU cc_start: 0.8057 (tp30) cc_final: 0.7622 (tp30) REVERT: H 135 ARG cc_start: 0.7884 (ttm-80) cc_final: 0.7422 (ttm-80) REVERT: H 158 ARG cc_start: 0.7618 (tpp-160) cc_final: 0.7359 (tpp-160) REVERT: H 164 VAL cc_start: 0.8713 (p) cc_final: 0.8475 (t) REVERT: H 175 LEU cc_start: 0.8524 (tp) cc_final: 0.8317 (tt) REVERT: H 225 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7322 (tp40) REVERT: H 229 SER cc_start: 0.8474 (m) cc_final: 0.8188 (t) REVERT: H 234 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7416 (tmm-80) REVERT: H 242 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7267 (t0) REVERT: H 254 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7215 (m) REVERT: H 326 THR cc_start: 0.8038 (m) cc_final: 0.7474 (p) REVERT: H 328 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7858 (mmt90) REVERT: H 350 SER cc_start: 0.8476 (t) cc_final: 0.8149 (m) REVERT: H 374 ASP cc_start: 0.8074 (m-30) cc_final: 0.7808 (m-30) REVERT: H 390 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8334 (mtt180) REVERT: H 391 TYR cc_start: 0.8406 (m-10) cc_final: 0.8106 (m-10) REVERT: I 7 TYR cc_start: 0.8055 (t80) cc_final: 0.7758 (t80) REVERT: I 19 LYS cc_start: 0.7561 (ttmm) cc_final: 0.7222 (ttmm) REVERT: I 24 ARG cc_start: 0.8401 (ptm-80) cc_final: 0.8128 (ptm-80) REVERT: I 44 LEU cc_start: 0.7267 (tt) cc_final: 0.6507 (mt) REVERT: I 70 GLN cc_start: 0.7497 (mm110) cc_final: 0.7235 (mm110) REVERT: I 127 GLN cc_start: 0.8007 (tp40) cc_final: 0.7670 (tp40) REVERT: I 156 ASN cc_start: 0.7967 (m-40) cc_final: 0.7732 (m-40) REVERT: I 213 LEU cc_start: 0.7966 (tt) cc_final: 0.7661 (mt) REVERT: I 219 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7535 (mtm-85) REVERT: I 229 SER cc_start: 0.8408 (t) cc_final: 0.8090 (m) REVERT: I 235 GLU cc_start: 0.8419 (tp30) cc_final: 0.8124 (mm-30) REVERT: I 297 MET cc_start: 0.7572 (tmm) cc_final: 0.7178 (tmm) REVERT: I 306 GLN cc_start: 0.7526 (mm110) cc_final: 0.7317 (mm110) REVERT: I 322 SER cc_start: 0.8383 (t) cc_final: 0.7932 (m) REVERT: I 344 TYR cc_start: 0.8441 (m-10) cc_final: 0.7834 (m-10) REVERT: I 359 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7180 (tm-30) REVERT: J 81 LEU cc_start: 0.8471 (tp) cc_final: 0.8188 (tp) REVERT: J 82 PHE cc_start: 0.8233 (t80) cc_final: 0.7750 (t80) REVERT: J 84 TRP cc_start: 0.6322 (t60) cc_final: 0.6026 (t60) REVERT: J 128 LEU cc_start: 0.8415 (mt) cc_final: 0.8200 (mt) REVERT: J 131 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6740 (t80) REVERT: J 184 MET cc_start: 0.7974 (mtm) cc_final: 0.7628 (mtm) REVERT: J 186 LEU cc_start: 0.8283 (mt) cc_final: 0.8071 (pp) REVERT: J 248 LEU cc_start: 0.8632 (tp) cc_final: 0.8244 (tp) REVERT: J 252 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7902 (mm-30) REVERT: J 335 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7243 (mtt-85) REVERT: J 361 PHE cc_start: 0.7953 (t80) cc_final: 0.7716 (t80) REVERT: J 366 TRP cc_start: 0.7150 (m100) cc_final: 0.6711 (m100) REVERT: J 425 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7604 (tm-30) REVERT: J 434 GLU cc_start: 0.7874 (tt0) cc_final: 0.7581 (mt-10) outliers start: 110 outliers final: 79 residues processed: 1099 average time/residue: 0.2125 time to fit residues: 354.3003 Evaluate side-chains 1129 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 1041 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 320 HIS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 383 THR Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 497 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 300 optimal weight: 2.9990 chunk 282 optimal weight: 0.7980 chunk 52 optimal weight: 0.0070 chunk 139 optimal weight: 1.9990 chunk 291 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 325 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 327 GLN F 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 306 GLN I 320 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112499 restraints weight = 45930.062| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.87 r_work: 0.3297 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 29983 Z= 0.184 Angle : 0.561 12.059 40800 Z= 0.295 Chirality : 0.041 0.151 4829 Planarity : 0.005 0.065 5352 Dihedral : 4.100 78.164 4145 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.53 % Allowed : 20.24 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.14), residues: 3821 helix: 3.31 (0.11), residues: 1999 sheet: -0.16 (0.24), residues: 486 loop : -1.06 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 227 TYR 0.023 0.001 TYR E 143 PHE 0.032 0.002 PHE I 288 TRP 0.011 0.001 TRP J 482 HIS 0.021 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00393 (29983) covalent geometry : angle 0.56129 (40800) hydrogen bonds : bond 0.08260 ( 1864) hydrogen bonds : angle 4.25381 ( 5454) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1055 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8209 (tp40) cc_final: 0.7772 (tm-30) REVERT: A 143 TYR cc_start: 0.8664 (t80) cc_final: 0.8314 (t80) REVERT: A 144 ASN cc_start: 0.8365 (m-40) cc_final: 0.8145 (m110) REVERT: A 171 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7520 (tp-100) REVERT: A 188 ILE cc_start: 0.8523 (mm) cc_final: 0.8275 (mt) REVERT: A 242 PRO cc_start: 0.8345 (Cg_endo) cc_final: 0.8097 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7501 (pt0) cc_final: 0.7260 (pt0) REVERT: A 349 ASN cc_start: 0.8553 (t0) cc_final: 0.8306 (t0) REVERT: A 355 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6510 (mp) REVERT: A 385 VAL cc_start: 0.8525 (p) cc_final: 0.8266 (m) REVERT: A 386 LYS cc_start: 0.8583 (tttt) cc_final: 0.8267 (tttt) REVERT: B 50 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7072 (mm-30) REVERT: B 133 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8183 (mtpp) REVERT: B 134 ILE cc_start: 0.8612 (mm) cc_final: 0.8370 (mt) REVERT: B 350 ARG cc_start: 0.8868 (ptp-170) cc_final: 0.8640 (ptp-170) REVERT: C 51 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6671 (mt-10) REVERT: C 54 ASP cc_start: 0.8032 (t0) cc_final: 0.7762 (t0) REVERT: C 81 ASP cc_start: 0.8251 (m-30) cc_final: 0.7302 (m-30) REVERT: C 140 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7708 (tp-100) REVERT: C 146 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8030 (mtt-85) REVERT: C 180 GLN cc_start: 0.8429 (mt0) cc_final: 0.8209 (mt0) REVERT: C 205 GLU cc_start: 0.8114 (tp30) cc_final: 0.7616 (tp30) REVERT: C 229 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8387 (tmm-80) REVERT: C 284 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7943 (mmmt) REVERT: C 380 LEU cc_start: 0.8398 (mp) cc_final: 0.8156 (mp) REVERT: D 103 LYS cc_start: 0.7522 (tttm) cc_final: 0.7277 (tttm) REVERT: D 110 SER cc_start: 0.8652 (t) cc_final: 0.8203 (p) REVERT: D 288 LYS cc_start: 0.8359 (ptpt) cc_final: 0.7975 (ptpt) REVERT: D 324 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7721 (tm-30) REVERT: D 328 LYS cc_start: 0.8325 (tttp) cc_final: 0.8125 (tttp) REVERT: D 331 GLU cc_start: 0.7824 (mp0) cc_final: 0.7234 (mp0) REVERT: D 368 THR cc_start: 0.8381 (m) cc_final: 0.7864 (t) REVERT: D 371 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7553 (mt-10) REVERT: E 78 ASP cc_start: 0.7778 (m-30) cc_final: 0.7185 (p0) REVERT: E 84 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8045 (mmmm) REVERT: E 102 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7052 (mm-30) REVERT: E 194 GLU cc_start: 0.7531 (mp0) cc_final: 0.7262 (mp0) REVERT: E 217 ARG cc_start: 0.7931 (mtm-85) cc_final: 0.7599 (mtm-85) REVERT: E 222 MET cc_start: 0.8200 (mmm) cc_final: 0.7919 (mmm) REVERT: E 266 MET cc_start: 0.8595 (mtt) cc_final: 0.8286 (mtp) REVERT: E 341 THR cc_start: 0.8108 (p) cc_final: 0.7747 (p) REVERT: E 351 ASP cc_start: 0.7971 (p0) cc_final: 0.7725 (p0) REVERT: E 379 LYS cc_start: 0.8190 (tttt) cc_final: 0.7941 (tttt) REVERT: E 382 ASP cc_start: 0.8370 (t0) cc_final: 0.8139 (t0) REVERT: F 87 ASP cc_start: 0.7631 (t0) cc_final: 0.7398 (t0) REVERT: F 140 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8201 (tp-100) REVERT: F 146 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7130 (mtt90) REVERT: F 171 GLN cc_start: 0.8543 (tp40) cc_final: 0.8310 (tp40) REVERT: F 194 GLU cc_start: 0.8171 (mp0) cc_final: 0.7814 (mp0) REVERT: F 327 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7468 (mm110) REVERT: F 328 LYS cc_start: 0.8763 (tttt) cc_final: 0.8493 (tttt) REVERT: G 5 GLN cc_start: 0.7986 (mt0) cc_final: 0.7751 (mt0) REVERT: G 30 LYS cc_start: 0.8320 (tttt) cc_final: 0.7923 (tttt) REVERT: G 156 ASN cc_start: 0.7837 (t0) cc_final: 0.7473 (t0) REVERT: G 160 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7285 (mp-120) REVERT: G 186 THR cc_start: 0.8520 (t) cc_final: 0.8266 (p) REVERT: G 188 ASN cc_start: 0.7936 (m110) cc_final: 0.7461 (m-40) REVERT: G 217 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7430 (tm-30) REVERT: G 229 SER cc_start: 0.8192 (t) cc_final: 0.7931 (m) REVERT: G 237 ILE cc_start: 0.7791 (mt) cc_final: 0.7514 (mt) REVERT: G 248 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7221 (pt) REVERT: G 288 PHE cc_start: 0.7599 (t80) cc_final: 0.7086 (t80) REVERT: G 341 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (tp) REVERT: G 344 TYR cc_start: 0.8580 (m-10) cc_final: 0.8181 (m-80) REVERT: G 358 MET cc_start: 0.8059 (mmp) cc_final: 0.7726 (mmp) REVERT: G 367 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7604 (tpp80) REVERT: G 385 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7502 (mm-30) REVERT: G 390 ARG cc_start: 0.8626 (mtt90) cc_final: 0.8376 (mtt-85) REVERT: G 401 LYS cc_start: 0.7604 (tppt) cc_final: 0.7381 (tppt) REVERT: H 11 ARG cc_start: 0.7659 (tpt-90) cc_final: 0.7379 (tpt-90) REVERT: H 24 ARG cc_start: 0.8269 (ttt90) cc_final: 0.8033 (ttt90) REVERT: H 42 LEU cc_start: 0.8310 (mt) cc_final: 0.7887 (mt) REVERT: H 70 GLN cc_start: 0.7858 (mp10) cc_final: 0.7538 (mp10) REVERT: H 73 GLN cc_start: 0.7870 (tp40) cc_final: 0.7544 (tm-30) REVERT: H 130 LYS cc_start: 0.8504 (tmmt) cc_final: 0.8098 (ttmt) REVERT: H 131 GLU cc_start: 0.8076 (tp30) cc_final: 0.7629 (tp30) REVERT: H 135 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7468 (ttm-80) REVERT: H 158 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7422 (tpp-160) REVERT: H 164 VAL cc_start: 0.8706 (p) cc_final: 0.8478 (t) REVERT: H 175 LEU cc_start: 0.8531 (tp) cc_final: 0.8329 (tt) REVERT: H 225 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7426 (tp40) REVERT: H 229 SER cc_start: 0.8493 (m) cc_final: 0.8180 (t) REVERT: H 234 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7432 (tmm-80) REVERT: H 242 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7319 (t0) REVERT: H 254 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7264 (m) REVERT: H 326 THR cc_start: 0.8074 (m) cc_final: 0.7479 (p) REVERT: H 328 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7776 (mmt90) REVERT: H 350 SER cc_start: 0.8522 (t) cc_final: 0.8179 (m) REVERT: H 374 ASP cc_start: 0.8134 (m-30) cc_final: 0.7875 (m-30) REVERT: H 390 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8304 (mtt180) REVERT: H 391 TYR cc_start: 0.8409 (m-10) cc_final: 0.8153 (m-10) REVERT: I 7 TYR cc_start: 0.8125 (t80) cc_final: 0.7822 (t80) REVERT: I 18 ARG cc_start: 0.7590 (mtp180) cc_final: 0.7365 (mtp-110) REVERT: I 19 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7207 (ttmm) REVERT: I 44 LEU cc_start: 0.7286 (tt) cc_final: 0.6527 (mt) REVERT: I 70 GLN cc_start: 0.7503 (mm110) cc_final: 0.7245 (mm110) REVERT: I 127 GLN cc_start: 0.8021 (tp40) cc_final: 0.7750 (tp40) REVERT: I 156 ASN cc_start: 0.8013 (m-40) cc_final: 0.7784 (m-40) REVERT: I 213 LEU cc_start: 0.7998 (tt) cc_final: 0.7670 (mt) REVERT: I 215 GLU cc_start: 0.8445 (tm-30) cc_final: 0.7841 (tm-30) REVERT: I 219 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7613 (mtm-85) REVERT: I 229 SER cc_start: 0.8387 (t) cc_final: 0.8055 (m) REVERT: I 235 GLU cc_start: 0.8434 (tp30) cc_final: 0.8150 (mm-30) REVERT: I 297 MET cc_start: 0.7534 (tmm) cc_final: 0.7162 (tmm) REVERT: I 306 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7328 (mm110) REVERT: I 344 TYR cc_start: 0.8436 (m-10) cc_final: 0.7829 (m-10) REVERT: I 359 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7192 (tm-30) REVERT: J 81 LEU cc_start: 0.8463 (tp) cc_final: 0.8162 (tp) REVERT: J 82 PHE cc_start: 0.8267 (t80) cc_final: 0.7763 (t80) REVERT: J 84 TRP cc_start: 0.6332 (t60) cc_final: 0.6027 (t60) REVERT: J 131 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6727 (t80) REVERT: J 184 MET cc_start: 0.7918 (mtm) cc_final: 0.7572 (mtm) REVERT: J 186 LEU cc_start: 0.8311 (mt) cc_final: 0.8102 (pp) REVERT: J 248 LEU cc_start: 0.8633 (tp) cc_final: 0.8182 (tp) REVERT: J 252 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7955 (mm-30) REVERT: J 361 PHE cc_start: 0.7950 (t80) cc_final: 0.7706 (t80) REVERT: J 366 TRP cc_start: 0.7130 (m100) cc_final: 0.6682 (m100) REVERT: J 383 THR cc_start: 0.8039 (m) cc_final: 0.7654 (p) REVERT: J 425 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7629 (tm-30) REVERT: J 434 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7665 (mt-10) outliers start: 113 outliers final: 94 residues processed: 1104 average time/residue: 0.1994 time to fit residues: 334.4735 Evaluate side-chains 1154 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1048 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 250 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 290 LEU Chi-restraints excluded: chain I residue 320 HIS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 450 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 497 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 210 optimal weight: 0.7980 chunk 258 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 260 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN F 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN H 87 GLN H 99 GLN H 142 GLN I 320 HIS J 129 ASN J 166 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.112134 restraints weight = 45777.490| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.87 r_work: 0.3301 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29983 Z= 0.173 Angle : 0.560 12.389 40800 Z= 0.293 Chirality : 0.041 0.192 4829 Planarity : 0.005 0.063 5352 Dihedral : 4.085 78.389 4145 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.57 % Allowed : 20.71 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.14), residues: 3821 helix: 3.33 (0.11), residues: 1998 sheet: -0.13 (0.24), residues: 486 loop : -1.05 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 227 TYR 0.024 0.001 TYR E 143 PHE 0.033 0.001 PHE I 288 TRP 0.010 0.001 TRP J 482 HIS 0.020 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00365 (29983) covalent geometry : angle 0.56036 (40800) hydrogen bonds : bond 0.08105 ( 1864) hydrogen bonds : angle 4.22459 ( 5454) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1055 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8240 (tp40) cc_final: 0.7768 (tm-30) REVERT: A 144 ASN cc_start: 0.8375 (m-40) cc_final: 0.8160 (m110) REVERT: A 171 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7491 (tp-100) REVERT: A 188 ILE cc_start: 0.8521 (mm) cc_final: 0.8274 (mt) REVERT: A 242 PRO cc_start: 0.8347 (Cg_endo) cc_final: 0.8101 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7506 (pt0) cc_final: 0.7266 (pt0) REVERT: A 349 ASN cc_start: 0.8591 (t0) cc_final: 0.8323 (t0) REVERT: A 385 VAL cc_start: 0.8524 (p) cc_final: 0.8262 (m) REVERT: A 386 LYS cc_start: 0.8586 (tttt) cc_final: 0.8269 (tttt) REVERT: B 50 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 133 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8185 (mtpp) REVERT: B 134 ILE cc_start: 0.8607 (mm) cc_final: 0.8367 (mt) REVERT: B 350 ARG cc_start: 0.8881 (ptp-170) cc_final: 0.8658 (ptp-170) REVERT: C 51 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6661 (mt-10) REVERT: C 54 ASP cc_start: 0.8033 (t0) cc_final: 0.7754 (t0) REVERT: C 81 ASP cc_start: 0.8259 (m-30) cc_final: 0.7313 (m-30) REVERT: C 140 GLN cc_start: 0.8290 (tp-100) cc_final: 0.7729 (tp-100) REVERT: C 146 ARG cc_start: 0.8271 (mmt-90) cc_final: 0.8012 (mtt-85) REVERT: C 180 GLN cc_start: 0.8423 (mt0) cc_final: 0.8199 (mt0) REVERT: C 205 GLU cc_start: 0.8088 (tp30) cc_final: 0.7606 (tp30) REVERT: C 229 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8391 (tmm-80) REVERT: C 284 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7941 (mmmt) REVERT: C 380 LEU cc_start: 0.8393 (mp) cc_final: 0.8141 (mp) REVERT: D 98 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7918 (mtm-85) REVERT: D 103 LYS cc_start: 0.7492 (tttm) cc_final: 0.7254 (tttm) REVERT: D 110 SER cc_start: 0.8648 (t) cc_final: 0.8205 (p) REVERT: D 222 MET cc_start: 0.8030 (ptm) cc_final: 0.7733 (ptm) REVERT: D 288 LYS cc_start: 0.8370 (ptpt) cc_final: 0.7969 (ptpt) REVERT: D 324 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 331 GLU cc_start: 0.7826 (mp0) cc_final: 0.7233 (mp0) REVERT: D 368 THR cc_start: 0.8337 (m) cc_final: 0.7824 (t) REVERT: D 371 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7579 (mt-10) REVERT: E 78 ASP cc_start: 0.7818 (m-30) cc_final: 0.7414 (p0) REVERT: E 84 LYS cc_start: 0.8373 (mmmm) cc_final: 0.8047 (mmmm) REVERT: E 102 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7038 (mm-30) REVERT: E 194 GLU cc_start: 0.7531 (mp0) cc_final: 0.7249 (mp0) REVERT: E 217 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7600 (mtm-85) REVERT: E 222 MET cc_start: 0.8229 (mmm) cc_final: 0.7943 (mmm) REVERT: E 266 MET cc_start: 0.8593 (mtt) cc_final: 0.8290 (mtp) REVERT: E 341 THR cc_start: 0.8100 (p) cc_final: 0.7728 (p) REVERT: E 351 ASP cc_start: 0.7980 (p0) cc_final: 0.7746 (p0) REVERT: E 379 LYS cc_start: 0.8157 (tttt) cc_final: 0.7917 (tttt) REVERT: E 382 ASP cc_start: 0.8349 (t0) cc_final: 0.8131 (t0) REVERT: F 87 ASP cc_start: 0.7627 (t0) cc_final: 0.7397 (t0) REVERT: F 140 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8175 (tp-100) REVERT: F 146 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7136 (mtt90) REVERT: F 171 GLN cc_start: 0.8559 (tp40) cc_final: 0.8308 (tp40) REVERT: F 194 GLU cc_start: 0.8187 (mp0) cc_final: 0.7826 (mp0) REVERT: F 327 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7448 (mm110) REVERT: F 328 LYS cc_start: 0.8772 (tttt) cc_final: 0.8503 (tttt) REVERT: G 5 GLN cc_start: 0.8017 (mt0) cc_final: 0.7676 (mt0) REVERT: G 30 LYS cc_start: 0.8283 (tttt) cc_final: 0.7880 (tttt) REVERT: G 96 VAL cc_start: 0.8324 (t) cc_final: 0.8066 (m) REVERT: G 156 ASN cc_start: 0.7809 (t0) cc_final: 0.7463 (t0) REVERT: G 160 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7267 (mp-120) REVERT: G 186 THR cc_start: 0.8528 (t) cc_final: 0.8279 (p) REVERT: G 188 ASN cc_start: 0.7928 (m110) cc_final: 0.7453 (m-40) REVERT: G 217 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7377 (tm-30) REVERT: G 229 SER cc_start: 0.8198 (t) cc_final: 0.7935 (m) REVERT: G 234 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7705 (ttp-170) REVERT: G 237 ILE cc_start: 0.7780 (mt) cc_final: 0.7510 (mt) REVERT: G 248 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7223 (pt) REVERT: G 288 PHE cc_start: 0.7626 (t80) cc_final: 0.7019 (t80) REVERT: G 341 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8220 (tp) REVERT: G 344 TYR cc_start: 0.8585 (m-10) cc_final: 0.8211 (m-80) REVERT: G 358 MET cc_start: 0.8046 (mmp) cc_final: 0.7709 (mmp) REVERT: G 367 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7568 (tpp80) REVERT: G 385 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7481 (mm-30) REVERT: G 390 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8383 (mtt-85) REVERT: H 5 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: H 11 ARG cc_start: 0.7688 (tpt-90) cc_final: 0.7420 (tpt-90) REVERT: H 24 ARG cc_start: 0.8256 (ttt90) cc_final: 0.8013 (ttt90) REVERT: H 42 LEU cc_start: 0.8180 (mt) cc_final: 0.7796 (mt) REVERT: H 70 GLN cc_start: 0.7855 (mp10) cc_final: 0.7545 (mp10) REVERT: H 73 GLN cc_start: 0.7859 (tp40) cc_final: 0.7544 (tm-30) REVERT: H 130 LYS cc_start: 0.8489 (tmmt) cc_final: 0.8079 (ttmt) REVERT: H 131 GLU cc_start: 0.8061 (tp30) cc_final: 0.7610 (tp30) REVERT: H 135 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7422 (ttm-80) REVERT: H 158 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7350 (tpp-160) REVERT: H 164 VAL cc_start: 0.8708 (p) cc_final: 0.8481 (t) REVERT: H 175 LEU cc_start: 0.8532 (tp) cc_final: 0.8324 (tt) REVERT: H 225 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7418 (tp40) REVERT: H 229 SER cc_start: 0.8488 (m) cc_final: 0.8203 (t) REVERT: H 234 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7426 (tmm-80) REVERT: H 242 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7291 (t0) REVERT: H 254 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.7248 (m) REVERT: H 326 THR cc_start: 0.8069 (m) cc_final: 0.7485 (p) REVERT: H 328 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7853 (mmt90) REVERT: H 350 SER cc_start: 0.8498 (t) cc_final: 0.8166 (m) REVERT: H 374 ASP cc_start: 0.8138 (m-30) cc_final: 0.7861 (m-30) REVERT: H 391 TYR cc_start: 0.8415 (m-10) cc_final: 0.8154 (m-10) REVERT: I 7 TYR cc_start: 0.8089 (t80) cc_final: 0.7792 (t80) REVERT: I 18 ARG cc_start: 0.7575 (mtp180) cc_final: 0.7341 (mtp-110) REVERT: I 19 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7213 (ttmm) REVERT: I 70 GLN cc_start: 0.7480 (mm110) cc_final: 0.7230 (mm110) REVERT: I 127 GLN cc_start: 0.8023 (tp40) cc_final: 0.7745 (tp40) REVERT: I 156 ASN cc_start: 0.7997 (m-40) cc_final: 0.7770 (m-40) REVERT: I 213 LEU cc_start: 0.8000 (tt) cc_final: 0.7663 (mt) REVERT: I 215 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8032 (tp30) REVERT: I 219 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7520 (mtm-85) REVERT: I 229 SER cc_start: 0.8383 (t) cc_final: 0.8051 (m) REVERT: I 235 GLU cc_start: 0.8432 (tp30) cc_final: 0.8145 (mm-30) REVERT: I 297 MET cc_start: 0.7569 (tmm) cc_final: 0.7275 (tmm) REVERT: I 306 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7359 (mm110) REVERT: I 317 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7417 (tm-30) REVERT: I 344 TYR cc_start: 0.8444 (m-10) cc_final: 0.7841 (m-10) REVERT: I 346 GLN cc_start: 0.8352 (tp40) cc_final: 0.7981 (tm-30) REVERT: I 359 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7197 (tm-30) REVERT: J 81 LEU cc_start: 0.8461 (tp) cc_final: 0.8170 (tp) REVERT: J 82 PHE cc_start: 0.8256 (t80) cc_final: 0.7759 (t80) REVERT: J 84 TRP cc_start: 0.6332 (t60) cc_final: 0.6028 (t60) REVERT: J 131 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6738 (t80) REVERT: J 184 MET cc_start: 0.7972 (mtm) cc_final: 0.7616 (mtm) REVERT: J 186 LEU cc_start: 0.8289 (mt) cc_final: 0.8076 (pp) REVERT: J 242 VAL cc_start: 0.8488 (m) cc_final: 0.8177 (p) REVERT: J 248 LEU cc_start: 0.8602 (tp) cc_final: 0.8294 (tt) REVERT: J 366 TRP cc_start: 0.7154 (m100) cc_final: 0.6698 (m100) REVERT: J 383 THR cc_start: 0.8040 (m) cc_final: 0.7694 (p) REVERT: J 425 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7645 (tm-30) REVERT: J 434 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7680 (mt-10) outliers start: 114 outliers final: 96 residues processed: 1106 average time/residue: 0.1992 time to fit residues: 334.3689 Evaluate side-chains 1154 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1046 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 386 LYS Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 23 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 320 HIS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain I residue 419 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 224 LYS Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 450 LEU Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 497 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 305 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 330 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 195 optimal weight: 0.0770 chunk 296 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 350 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 200 GLN B 327 GLN F 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN H 142 GLN I 320 HIS J 26 GLN J 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111910 restraints weight = 45753.279| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.87 r_work: 0.3291 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29983 Z= 0.198 Angle : 0.588 12.855 40800 Z= 0.308 Chirality : 0.042 0.168 4829 Planarity : 0.005 0.068 5352 Dihedral : 4.158 78.315 4145 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.69 % Allowed : 20.71 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.14), residues: 3821 helix: 3.24 (0.11), residues: 2000 sheet: -0.17 (0.24), residues: 486 loop : -1.08 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 217 TYR 0.025 0.001 TYR E 143 PHE 0.034 0.002 PHE I 288 TRP 0.012 0.001 TRP E 210 HIS 0.023 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00430 (29983) covalent geometry : angle 0.58793 (40800) hydrogen bonds : bond 0.08400 ( 1864) hydrogen bonds : angle 4.28300 ( 5454) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7642 Ramachandran restraints generated. 3821 Oldfield, 0 Emsley, 3821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1048 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8211 (tp40) cc_final: 0.7800 (tm-30) REVERT: A 143 TYR cc_start: 0.8690 (t80) cc_final: 0.8345 (t80) REVERT: A 171 GLN cc_start: 0.7860 (tp-100) cc_final: 0.7510 (tp-100) REVERT: A 188 ILE cc_start: 0.8528 (mm) cc_final: 0.8281 (mt) REVERT: A 242 PRO cc_start: 0.8349 (Cg_endo) cc_final: 0.8101 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7510 (pt0) cc_final: 0.7270 (pt0) REVERT: A 349 ASN cc_start: 0.8592 (t0) cc_final: 0.8361 (t0) REVERT: A 355 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6534 (mp) REVERT: A 385 VAL cc_start: 0.8519 (p) cc_final: 0.8261 (m) REVERT: A 386 LYS cc_start: 0.8596 (tttt) cc_final: 0.8280 (tttt) REVERT: B 50 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 133 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8189 (mtpp) REVERT: B 134 ILE cc_start: 0.8618 (mm) cc_final: 0.8382 (mt) REVERT: B 350 ARG cc_start: 0.8894 (ptp-170) cc_final: 0.8672 (ptp-170) REVERT: C 51 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6679 (mt-10) REVERT: C 54 ASP cc_start: 0.8032 (t0) cc_final: 0.7749 (t0) REVERT: C 81 ASP cc_start: 0.8239 (m-30) cc_final: 0.7810 (m-30) REVERT: C 140 GLN cc_start: 0.8295 (tp-100) cc_final: 0.7731 (tp-100) REVERT: C 146 ARG cc_start: 0.8322 (mmt-90) cc_final: 0.8080 (mtt-85) REVERT: C 180 GLN cc_start: 0.8422 (mt0) cc_final: 0.8199 (mt0) REVERT: C 205 GLU cc_start: 0.8088 (tp30) cc_final: 0.7610 (tp30) REVERT: C 229 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (tmm-80) REVERT: C 284 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7943 (mmmt) REVERT: C 380 LEU cc_start: 0.8395 (mp) cc_final: 0.8146 (mp) REVERT: D 103 LYS cc_start: 0.7531 (tttm) cc_final: 0.7290 (tttm) REVERT: D 110 SER cc_start: 0.8656 (t) cc_final: 0.8212 (p) REVERT: D 222 MET cc_start: 0.8015 (ptm) cc_final: 0.7717 (ptm) REVERT: D 288 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7951 (ptpt) REVERT: D 324 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 331 GLU cc_start: 0.7832 (mp0) cc_final: 0.7223 (mp0) REVERT: D 368 THR cc_start: 0.8372 (m) cc_final: 0.7861 (t) REVERT: D 371 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7566 (mt-10) REVERT: E 78 ASP cc_start: 0.7809 (m-30) cc_final: 0.7396 (p0) REVERT: E 84 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8060 (mmmm) REVERT: E 102 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7088 (mm-30) REVERT: E 194 GLU cc_start: 0.7553 (mp0) cc_final: 0.7266 (mp0) REVERT: E 217 ARG cc_start: 0.7935 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: E 222 MET cc_start: 0.8233 (mmm) cc_final: 0.7959 (mmm) REVERT: E 266 MET cc_start: 0.8590 (mtt) cc_final: 0.8280 (mtp) REVERT: E 341 THR cc_start: 0.8192 (p) cc_final: 0.7827 (p) REVERT: E 351 ASP cc_start: 0.7991 (p0) cc_final: 0.7761 (p0) REVERT: E 379 LYS cc_start: 0.8174 (tttt) cc_final: 0.7932 (tttt) REVERT: E 382 ASP cc_start: 0.8350 (t0) cc_final: 0.8143 (t0) REVERT: F 87 ASP cc_start: 0.7604 (t0) cc_final: 0.7374 (t0) REVERT: F 140 GLN cc_start: 0.8417 (tp-100) cc_final: 0.8197 (tp-100) REVERT: F 146 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7203 (mtt90) REVERT: F 171 GLN cc_start: 0.8594 (tp40) cc_final: 0.8321 (tp40) REVERT: F 194 GLU cc_start: 0.8191 (mp0) cc_final: 0.7822 (mp0) REVERT: F 327 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7481 (mm110) REVERT: F 328 LYS cc_start: 0.8776 (tttt) cc_final: 0.8504 (tttt) REVERT: G 5 GLN cc_start: 0.8019 (mt0) cc_final: 0.7691 (mt0) REVERT: G 30 LYS cc_start: 0.8303 (tttt) cc_final: 0.7907 (tttt) REVERT: G 98 TYR cc_start: 0.8400 (t80) cc_final: 0.8055 (t80) REVERT: G 156 ASN cc_start: 0.7864 (t0) cc_final: 0.7518 (t0) REVERT: G 160 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7288 (mp-120) REVERT: G 186 THR cc_start: 0.8540 (t) cc_final: 0.8294 (p) REVERT: G 188 ASN cc_start: 0.7931 (m110) cc_final: 0.7447 (m-40) REVERT: G 217 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7444 (tm-30) REVERT: G 229 SER cc_start: 0.8195 (t) cc_final: 0.7930 (m) REVERT: G 234 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7701 (ttp-170) REVERT: G 237 ILE cc_start: 0.7781 (mt) cc_final: 0.7508 (mt) REVERT: G 248 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7191 (pt) REVERT: G 288 PHE cc_start: 0.7654 (t80) cc_final: 0.7207 (t80) REVERT: G 341 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8242 (tp) REVERT: G 344 TYR cc_start: 0.8589 (m-10) cc_final: 0.8221 (m-80) REVERT: G 358 MET cc_start: 0.8029 (mmp) cc_final: 0.7684 (mmp) REVERT: G 367 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7562 (tpp80) REVERT: G 385 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7525 (mm-30) REVERT: G 390 ARG cc_start: 0.8630 (mtt90) cc_final: 0.8387 (mtt-85) REVERT: H 5 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7273 (mt0) REVERT: H 11 ARG cc_start: 0.7662 (tpt-90) cc_final: 0.7384 (tpt-90) REVERT: H 24 ARG cc_start: 0.8251 (ttt90) cc_final: 0.8037 (ttt90) REVERT: H 42 LEU cc_start: 0.8177 (mt) cc_final: 0.7774 (mt) REVERT: H 70 GLN cc_start: 0.7857 (mp10) cc_final: 0.7545 (mp10) REVERT: H 73 GLN cc_start: 0.7866 (tp40) cc_final: 0.7526 (tm-30) REVERT: H 130 LYS cc_start: 0.8491 (tmmt) cc_final: 0.8083 (ttmt) REVERT: H 131 GLU cc_start: 0.8076 (tp30) cc_final: 0.7616 (tp30) REVERT: H 135 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7450 (ttm-80) REVERT: H 158 ARG cc_start: 0.7635 (tpp-160) cc_final: 0.7357 (tpp-160) REVERT: H 164 VAL cc_start: 0.8701 (p) cc_final: 0.8475 (t) REVERT: H 175 LEU cc_start: 0.8533 (tp) cc_final: 0.8329 (tt) REVERT: H 225 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7421 (tp40) REVERT: H 229 SER cc_start: 0.8492 (m) cc_final: 0.8185 (t) REVERT: H 234 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7496 (tmm-80) REVERT: H 242 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7298 (t0) REVERT: H 254 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7212 (m) REVERT: H 326 THR cc_start: 0.8085 (m) cc_final: 0.7488 (p) REVERT: H 328 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7728 (mmt90) REVERT: H 350 SER cc_start: 0.8502 (t) cc_final: 0.8161 (m) REVERT: H 374 ASP cc_start: 0.8159 (m-30) cc_final: 0.7908 (m-30) REVERT: H 390 ARG cc_start: 0.8553 (mtt180) cc_final: 0.8306 (mtt180) REVERT: H 391 TYR cc_start: 0.8420 (m-10) cc_final: 0.8158 (m-10) REVERT: I 7 TYR cc_start: 0.8110 (t80) cc_final: 0.7847 (t80) REVERT: I 19 LYS cc_start: 0.7567 (ttmm) cc_final: 0.7202 (ttmm) REVERT: I 44 LEU cc_start: 0.7313 (tt) cc_final: 0.6566 (mt) REVERT: I 70 GLN cc_start: 0.7504 (mm110) cc_final: 0.7239 (mm110) REVERT: I 127 GLN cc_start: 0.8024 (tp40) cc_final: 0.7732 (tp40) REVERT: I 156 ASN cc_start: 0.8037 (m-40) cc_final: 0.7806 (m-40) REVERT: I 204 ASP cc_start: 0.6617 (t70) cc_final: 0.6285 (t0) REVERT: I 215 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8007 (tp30) REVERT: I 219 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7514 (mtm-85) REVERT: I 229 SER cc_start: 0.8406 (t) cc_final: 0.8071 (m) REVERT: I 235 GLU cc_start: 0.8454 (tp30) cc_final: 0.8169 (mm-30) REVERT: I 297 MET cc_start: 0.7622 (tmm) cc_final: 0.7361 (tmm) REVERT: I 306 GLN cc_start: 0.7585 (mm-40) cc_final: 0.7380 (mm110) REVERT: I 317 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7519 (tm-30) REVERT: I 344 TYR cc_start: 0.8436 (m-10) cc_final: 0.7838 (m-10) REVERT: I 346 GLN cc_start: 0.8357 (tp40) cc_final: 0.7989 (tm-30) REVERT: I 359 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7171 (tm-30) REVERT: J 81 LEU cc_start: 0.8498 (tp) cc_final: 0.8214 (tp) REVERT: J 82 PHE cc_start: 0.8275 (t80) cc_final: 0.7752 (t80) REVERT: J 84 TRP cc_start: 0.6326 (t60) cc_final: 0.6021 (t60) REVERT: J 131 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6757 (t80) REVERT: J 184 MET cc_start: 0.7903 (mtm) cc_final: 0.7538 (mtm) REVERT: J 366 TRP cc_start: 0.7173 (m100) cc_final: 0.6714 (m100) REVERT: J 383 THR cc_start: 0.8090 (m) cc_final: 0.7752 (p) REVERT: J 425 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7639 (tm-30) REVERT: J 434 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7665 (mt-10) outliers start: 118 outliers final: 94 residues processed: 1103 average time/residue: 0.2117 time to fit residues: 354.5598 Evaluate side-chains 1149 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1042 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 138 LYS Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain F residue 340 SER Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 236 GLN Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 290 LEU Chi-restraints excluded: chain G residue 341 ILE Chi-restraints excluded: chain G residue 367 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 192 GLU Chi-restraints excluded: chain H residue 225 GLN Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 369 ILE Chi-restraints excluded: chain H residue 407 LEU Chi-restraints excluded: chain I residue 8 GLN Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 133 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 189 TYR Chi-restraints excluded: chain I residue 209 VAL Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 249 ASP Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 259 THR Chi-restraints excluded: chain I residue 320 HIS Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain I residue 412 LEU Chi-restraints excluded: chain I residue 419 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 13 VAL Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 285 PHE Chi-restraints excluded: chain J residue 297 GLU Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 450 LEU Chi-restraints excluded: chain J residue 489 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 44 optimal weight: 0.0770 chunk 89 optimal weight: 0.8980 chunk 226 optimal weight: 1.9990 chunk 369 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 331 optimal weight: 0.9990 chunk 275 optimal weight: 0.0870 chunk 170 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN F 173 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 99 GLN I 320 HIS J 26 GLN J 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112859 restraints weight = 46010.157| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.89 r_work: 0.3311 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29983 Z= 0.159 Angle : 0.567 13.002 40800 Z= 0.294 Chirality : 0.040 0.178 4829 Planarity : 0.005 0.061 5352 Dihedral : 4.046 78.728 4145 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.41 % Allowed : 20.99 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.20 (0.14), residues: 3821 helix: 3.38 (0.11), residues: 1997 sheet: -0.13 (0.24), residues: 486 loop : -1.03 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 217 TYR 0.023 0.001 TYR H 125 PHE 0.032 0.001 PHE I 288 TRP 0.011 0.001 TRP J 350 HIS 0.023 0.001 HIS I 320 Details of bonding type rmsd covalent geometry : bond 0.00324 (29983) covalent geometry : angle 0.56656 (40800) hydrogen bonds : bond 0.07829 ( 1864) hydrogen bonds : angle 4.16705 ( 5454) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9260.23 seconds wall clock time: 158 minutes 32.61 seconds (9512.61 seconds total)