Starting phenix.real_space_refine on Tue May 27 07:11:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zal_39879/05_2025/8zal_39879.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zal_39879/05_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_39879/05_2025/8zal_39879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zal_39879/05_2025/8zal_39879.map" model { file = "/net/cci-nas-00/data/ceres_data/8zal_39879/05_2025/8zal_39879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zal_39879/05_2025/8zal_39879.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 16.71, per 1000 atoms: 0.57 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: 6.66 Conformation dependent library (CDL) restraints added in 3.5 seconds 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: 2.96 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: 10.78 Time building geometry restraints manager: 7.84 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: 4.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 60.770 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (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 TRP 0.009 0.001 TRP J 482 HIS 0.004 0.001 HIS J 429 PHE 0.010 0.001 PHE C 258 TYR 0.014 0.001 TYR I 7 ARG 0.016 0.000 ARG B 229 Details of bonding type rmsd hydrogen bonds : bond 0.17584 ( 1864) hydrogen bonds : angle 5.98020 ( 5454) covalent geometry : bond 0.00375 (29983) covalent geometry : angle 0.55462 (40800) *********************** 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 : 3.149 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: 0.8147 (mt) REVERT: A 214 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8015 (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: 0.8083 (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: 0.8183 (mtpp) REVERT: B 140 GLN cc_start: 0.8270 (tp40) cc_final: 0.7665 (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: 0.7845 (t0) REVERT: C 102 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7705 (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: 0.7630 (tp-100) REVERT: C 146 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7754 (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: 0.7348 (tttm) REVERT: D 110 SER cc_start: 0.8627 (t) cc_final: 0.8176 (p) REVERT: D 116 HIS cc_start: 0.8487 (t70) cc_final: 0.8165 (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 244 MET cc_start: 0.8046 (mtp) cc_final: 0.7793 (mtt) REVERT: D 252 MET cc_start: 0.8866 (mtt) cc_final: 0.8644 (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: 0.7820 (t) REVERT: D 371 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7448 (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: 0.7847 (mmmm) REVERT: E 118 LEU cc_start: 0.8236 (mt) cc_final: 0.8015 (mm) REVERT: E 194 GLU cc_start: 0.7370 (mp0) cc_final: 0.7131 (mp0) REVERT: E 217 ARG cc_start: 0.7642 (mtm-85) cc_final: 0.7228 (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: 0.6316 (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: 0.7733 (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: 0.7646 (mp0) REVERT: F 327 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7297 (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: 0.7389 (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: 0.7965 (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: 0.7962 (m-80) REVERT: G 345 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8285 (ttmm) REVERT: G 390 ARG cc_start: 0.7939 (mtt90) cc_final: 0.7721 (mtt-85) REVERT: H 8 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7726 (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: 0.7471 (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: 0.8807 (mm) REVERT: H 162 ASP cc_start: 0.7534 (m-30) cc_final: 0.6854 (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: 0.7659 (p) REVERT: H 350 SER cc_start: 0.8206 (t) cc_final: 0.7981 (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: 0.7380 (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: 0.6961 (mt) REVERT: I 229 SER cc_start: 0.8033 (t) cc_final: 0.7777 (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: 0.8335 (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: 0.7677 (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: 0.7669 (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: 0.7798 (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: 0.7605 (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: 0.7952 (m-10) outliers start: 7 outliers final: 3 residues processed: 1175 average time/residue: 0.4461 time to fit residues: 790.3673 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 : 2.908 ------------------------------------------------------------------------------- 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 320 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 159 optimal weight: 0.1980 chunk 98 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 297 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 265 ASN B 117 GLN B 121 ASN B 173 GLN ** B 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 124 GLN C 179 GLN D 262 GLN D 306 GLN D 353 GLN E 114 GLN E 117 GLN E 124 GLN E 257 ASN F 201 GLN G 5 GLN G 94 GLN G 160 GLN G 225 GLN G 241 GLN G 396 ASN G 397 GLN H 2 ASN H 14 ASN H 103 GLN H 139 GLN H 304 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 26 GLN J 124 GLN J 257 ASN J 403 ASN J 437 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.111448 restraints weight = 45763.658| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.84 r_work: 0.3280 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29983 Z= 0.236 Angle : 0.602 10.071 40800 Z= 0.324 Chirality : 0.044 0.186 4829 Planarity : 0.006 0.103 5352 Dihedral : 4.437 73.213 4153 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.16 % Allowed : 13.23 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.14), residues: 3821 helix: 2.98 (0.11), residues: 1959 sheet: -0.41 (0.24), residues: 500 loop : -1.17 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 482 HIS 0.005 0.001 HIS C 116 PHE 0.019 0.002 PHE J 108 TYR 0.015 0.002 TYR H 48 ARG 0.009 0.001 ARG H 35 Details of bonding type rmsd hydrogen bonds : bond 0.09410 ( 1864) hydrogen bonds : angle 4.75863 ( 5454) covalent geometry : bond 0.00521 (29983) covalent geometry : angle 0.60226 (40800) *********************** 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 1159 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1090 time to evaluate : 3.428 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 126 GLN cc_start: 0.8195 (tp40) cc_final: 0.7911 (tp40) REVERT: A 140 GLN cc_start: 0.8152 (tp40) cc_final: 0.7836 (tp40) REVERT: A 144 ASN cc_start: 0.8442 (m-40) cc_final: 0.8208 (m110) REVERT: A 171 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7624 (tp-100) REVERT: A 188 ILE cc_start: 0.8505 (mm) cc_final: 0.8266 (mt) REVERT: A 242 PRO cc_start: 0.8357 (Cg_endo) cc_final: 0.8105 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7515 (pt0) cc_final: 0.7249 (pt0) REVERT: A 385 VAL cc_start: 0.8534 (p) cc_final: 0.8261 (m) REVERT: A 386 LYS cc_start: 0.8505 (tttt) cc_final: 0.8202 (tttt) REVERT: B 84 LYS cc_start: 0.8555 (mttp) cc_final: 0.8295 (mtpp) REVERT: B 133 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8259 (mtpp) REVERT: B 140 GLN cc_start: 0.8438 (tp40) cc_final: 0.7837 (tp40) REVERT: B 178 ILE cc_start: 0.8721 (mt) cc_final: 0.8498 (mm) REVERT: B 180 GLN cc_start: 0.8089 (mt0) cc_final: 0.7867 (mt0) REVERT: B 279 TYR cc_start: 0.8577 (m-80) cc_final: 0.8327 (m-80) REVERT: C 51 GLU cc_start: 0.6885 (mt-10) cc_final: 0.6612 (mt-10) REVERT: C 54 ASP cc_start: 0.8103 (t0) cc_final: 0.7812 (t0) REVERT: C 62 ILE cc_start: 0.8783 (mp) cc_final: 0.8562 (mt) REVERT: C 81 ASP cc_start: 0.8242 (m-30) cc_final: 0.7061 (m-30) REVERT: C 133 LYS cc_start: 0.8648 (mtpt) cc_final: 0.8427 (mtpt) REVERT: C 140 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7924 (tp-100) REVERT: C 146 ARG cc_start: 0.8315 (mmt-90) cc_final: 0.7904 (mtt-85) REVERT: C 180 GLN cc_start: 0.8401 (mt0) cc_final: 0.8172 (mt0) REVERT: C 205 GLU cc_start: 0.8110 (tp30) cc_final: 0.7638 (tp30) REVERT: C 244 MET cc_start: 0.8749 (ptp) cc_final: 0.8520 (ptm) REVERT: C 284 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7942 (mmmt) REVERT: C 288 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8560 (mtmm) REVERT: C 380 LEU cc_start: 0.8317 (mp) cc_final: 0.8040 (mp) REVERT: D 54 ASP cc_start: 0.8142 (t0) cc_final: 0.7871 (t0) REVERT: D 103 LYS cc_start: 0.7718 (tttm) cc_final: 0.7480 (tttm) REVERT: D 110 SER cc_start: 0.8681 (t) cc_final: 0.8226 (p) REVERT: D 158 GLU cc_start: 0.7539 (tt0) cc_final: 0.7296 (tt0) REVERT: D 252 MET cc_start: 0.8923 (mtt) cc_final: 0.8705 (mtt) REVERT: D 288 LYS cc_start: 0.8381 (ptpt) cc_final: 0.8068 (ptpt) REVERT: D 313 ILE cc_start: 0.8972 (mp) cc_final: 0.8730 (mt) REVERT: D 331 GLU cc_start: 0.7777 (mp0) cc_final: 0.7453 (mp0) REVERT: D 336 ARG cc_start: 0.8663 (mmt90) cc_final: 0.8454 (mmt90) REVERT: D 368 THR cc_start: 0.8371 (m) cc_final: 0.7813 (t) REVERT: D 371 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7517 (mt-10) REVERT: E 62 ILE cc_start: 0.8763 (mm) cc_final: 0.8533 (mm) REVERT: E 78 ASP cc_start: 0.7893 (m-30) cc_final: 0.7511 (p0) REVERT: E 84 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8046 (mmmm) REVERT: E 102 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7112 (mm-30) REVERT: E 194 GLU cc_start: 0.7479 (mp0) cc_final: 0.7205 (mp0) REVERT: E 205 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7839 (mm-30) REVERT: E 217 ARG cc_start: 0.7906 (mtm-85) cc_final: 0.7552 (mtm-85) REVERT: E 266 MET cc_start: 0.8625 (mtt) cc_final: 0.8326 (mtp) REVERT: E 349 ASN cc_start: 0.7886 (t0) cc_final: 0.7659 (t0) REVERT: E 351 ASP cc_start: 0.7863 (p0) cc_final: 0.7502 (p0) REVERT: E 371 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6454 (mm-30) REVERT: E 379 LYS cc_start: 0.8163 (tttt) cc_final: 0.7933 (tttt) REVERT: E 382 ASP cc_start: 0.8337 (t0) cc_final: 0.8069 (t0) REVERT: F 103 LYS cc_start: 0.8147 (tttt) cc_final: 0.7828 (tttt) REVERT: F 105 LYS cc_start: 0.8687 (mttt) cc_final: 0.8478 (mtmm) REVERT: F 171 GLN cc_start: 0.8575 (tp40) cc_final: 0.8331 (tp40) REVERT: F 187 MET cc_start: 0.8313 (mmm) cc_final: 0.8107 (mmm) REVERT: F 194 GLU cc_start: 0.8219 (mp0) cc_final: 0.7889 (mp0) REVERT: F 327 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7339 (mm110) REVERT: F 328 LYS cc_start: 0.8773 (tttt) cc_final: 0.8496 (tttt) REVERT: F 357 ASN cc_start: 0.8504 (p0) cc_final: 0.8276 (p0) REVERT: G 5 GLN cc_start: 0.8063 (mt0) cc_final: 0.7861 (mt0) REVERT: G 56 ASP cc_start: 0.8009 (m-30) cc_final: 0.7796 (m-30) REVERT: G 158 ARG cc_start: 0.7603 (tpt170) cc_final: 0.7354 (tpm170) REVERT: G 183 ARG cc_start: 0.7195 (tmt170) cc_final: 0.6988 (tmt-80) REVERT: G 229 SER cc_start: 0.8222 (t) cc_final: 0.7979 (m) REVERT: G 237 ILE cc_start: 0.7868 (mt) cc_final: 0.7517 (mt) REVERT: G 239 GLN cc_start: 0.8248 (tm-30) cc_final: 0.7812 (tp-100) REVERT: G 244 HIS cc_start: 0.7990 (m90) cc_final: 0.7613 (m90) REVERT: G 344 TYR cc_start: 0.8629 (m-10) cc_final: 0.8386 (m-80) REVERT: G 358 MET cc_start: 0.8109 (mmp) cc_final: 0.7828 (mmp) REVERT: G 367 ARG cc_start: 0.7584 (mmm-85) cc_final: 0.7180 (tpp80) REVERT: G 385 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7801 (mm-30) REVERT: G 390 ARG cc_start: 0.8607 (mtt90) cc_final: 0.8376 (mtt-85) REVERT: G 401 LYS cc_start: 0.7941 (tppt) cc_final: 0.7621 (tppt) REVERT: H 11 ARG cc_start: 0.7770 (tpt-90) cc_final: 0.7465 (tpt-90) REVERT: H 41 GLN cc_start: 0.7815 (tt0) cc_final: 0.7610 (tt0) REVERT: H 42 LEU cc_start: 0.8320 (mt) cc_final: 0.7910 (mt) REVERT: H 69 LEU cc_start: 0.7902 (mt) cc_final: 0.7512 (mm) REVERT: H 70 GLN cc_start: 0.7667 (mp10) cc_final: 0.7338 (mp10) REVERT: H 130 LYS cc_start: 0.8487 (tmmt) cc_final: 0.8105 (ttmt) REVERT: H 131 GLU cc_start: 0.8035 (tp30) cc_final: 0.7730 (tp30) REVERT: H 158 ARG cc_start: 0.7693 (tpp-160) cc_final: 0.7412 (tpp-160) REVERT: H 162 ASP cc_start: 0.8056 (m-30) cc_final: 0.7283 (t0) REVERT: H 196 LEU cc_start: 0.8495 (tp) cc_final: 0.8264 (tt) REVERT: H 229 SER cc_start: 0.8502 (m) cc_final: 0.8192 (t) REVERT: H 339 SER cc_start: 0.8199 (m) cc_final: 0.7622 (p) REVERT: H 345 LYS cc_start: 0.8296 (ttmt) cc_final: 0.8043 (ttmm) REVERT: H 346 GLN cc_start: 0.8341 (tp-100) cc_final: 0.8130 (tp40) REVERT: H 350 SER cc_start: 0.8503 (t) cc_final: 0.8141 (m) REVERT: H 391 TYR cc_start: 0.8409 (m-10) cc_final: 0.7964 (m-10) REVERT: I 1 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6703 (tm-30) REVERT: I 2 ASN cc_start: 0.6921 (OUTLIER) cc_final: 0.6345 (m-40) REVERT: I 19 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7364 (ttmm) REVERT: I 33 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7839 (tm-30) REVERT: I 95 ASP cc_start: 0.7678 (t0) cc_final: 0.6460 (t0) REVERT: I 127 GLN cc_start: 0.7899 (tp40) cc_final: 0.7663 (tp40) REVERT: I 136 GLN cc_start: 0.8152 (tp40) cc_final: 0.7923 (tm-30) REVERT: I 156 ASN cc_start: 0.8072 (m-40) cc_final: 0.7835 (m-40) REVERT: I 229 SER cc_start: 0.8466 (t) cc_final: 0.8137 (m) REVERT: I 231 ASP cc_start: 0.7826 (t0) cc_final: 0.7601 (m-30) REVERT: I 234 ARG cc_start: 0.7711 (mtm180) cc_final: 0.7506 (mtm180) REVERT: I 235 GLU cc_start: 0.8508 (tp30) cc_final: 0.8241 (mm-30) REVERT: I 297 MET cc_start: 0.7425 (tmm) cc_final: 0.7158 (tmm) REVERT: I 359 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7129 (tm-30) REVERT: I 372 VAL cc_start: 0.7613 (t) cc_final: 0.7403 (p) REVERT: J 21 LEU cc_start: 0.8399 (mt) cc_final: 0.8174 (mm) REVERT: J 81 LEU cc_start: 0.8547 (tp) cc_final: 0.8347 (tp) REVERT: J 82 PHE cc_start: 0.8280 (t80) cc_final: 0.7764 (t80) REVERT: J 84 TRP cc_start: 0.6272 (t60) cc_final: 0.6028 (t60) REVERT: J 140 LEU cc_start: 0.8570 (tt) cc_final: 0.8308 (mt) REVERT: J 145 MET cc_start: 0.7947 (mtp) cc_final: 0.7740 (mmm) REVERT: J 184 MET cc_start: 0.8091 (mtm) cc_final: 0.7846 (mtm) REVERT: J 248 LEU cc_start: 0.8601 (tp) cc_final: 0.8184 (tp) REVERT: J 252 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8046 (mm-30) REVERT: J 260 VAL cc_start: 0.8368 (t) cc_final: 0.8076 (m) REVERT: J 320 LEU cc_start: 0.7938 (mt) cc_final: 0.7698 (mt) REVERT: J 366 TRP cc_start: 0.7267 (m100) cc_final: 0.6755 (m100) REVERT: J 386 THR cc_start: 0.8603 (m) cc_final: 0.8304 (p) REVERT: J 434 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7535 (mt-10) REVERT: J 464 ILE cc_start: 0.8423 (mt) cc_final: 0.8144 (mm) REVERT: J 466 GLN cc_start: 0.8356 (tp40) cc_final: 0.8155 (tp40) REVERT: J 497 PHE cc_start: 0.8318 (m-80) cc_final: 0.8118 (m-80) outliers start: 69 outliers final: 44 residues processed: 1121 average time/residue: 0.4612 time to fit residues: 779.9513 Evaluate side-chains 1102 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 1056 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR 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 B residue 118 LEU Chi-restraints excluded: chain B residue 266 MET 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 377 VAL Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 147 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 145 ASN Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 169 LEU 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 179 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 8 GLN 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 359 MET Chi-restraints excluded: chain J residue 401 LEU 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 238 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 95 optimal weight: 0.0980 chunk 375 optimal weight: 0.6980 chunk 266 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 356 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 79 ASN A 201 GLN B 153 ASN B 173 GLN B 353 GLN C 171 GLN D 144 ASN D 153 ASN E 114 GLN F 173 GLN G 94 GLN G 244 HIS G 397 GLN H 102 GLN I 70 GLN I 139 GLN I 184 GLN I 304 GLN J 26 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.128184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.112385 restraints weight = 46120.002| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.87 r_work: 0.3299 rms_B_bonded: 2.38 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: 0.7844 moved from start: 0.1987 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= 0.170 Angle : 0.551 12.445 40800 Z= 0.292 Chirality : 0.041 0.158 4829 Planarity : 0.005 0.081 5352 Dihedral : 4.152 74.999 4145 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.72 % Allowed : 15.36 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.14), residues: 3821 helix: 3.23 (0.11), residues: 1972 sheet: -0.30 (0.23), residues: 500 loop : -1.03 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 482 HIS 0.005 0.001 HIS G 244 PHE 0.029 0.001 PHE J 107 TYR 0.012 0.001 TYR H 48 ARG 0.009 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08538 ( 1864) hydrogen bonds : angle 4.47855 ( 5454) covalent geometry : bond 0.00344 (29983) covalent geometry : angle 0.55051 (40800) *********************** 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 1150 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1063 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 TYR cc_start: 0.8649 (t80) cc_final: 0.8310 (t80) REVERT: A 171 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7355 (tp-100) REVERT: A 188 ILE cc_start: 0.8483 (mm) cc_final: 0.8236 (mt) REVERT: A 214 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 242 PRO cc_start: 0.8329 (Cg_endo) cc_final: 0.8084 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7519 (pt0) cc_final: 0.6971 (pt0) REVERT: A 349 ASN cc_start: 0.8565 (t0) cc_final: 0.8299 (t0) REVERT: A 385 VAL cc_start: 0.8532 (p) cc_final: 0.8266 (m) REVERT: A 386 LYS cc_start: 0.8547 (tttt) cc_final: 0.8225 (tttt) REVERT: B 133 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8186 (mtpp) REVERT: B 140 GLN cc_start: 0.8412 (tp40) cc_final: 0.7830 (tp40) REVERT: B 180 GLN cc_start: 0.8102 (mt0) cc_final: 0.7853 (mt0) REVERT: B 201 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7352 (mm110) REVERT: B 277 ASP cc_start: 0.7418 (p0) cc_final: 0.6859 (p0) REVERT: B 279 TYR cc_start: 0.8587 (m-80) cc_final: 0.8308 (m-80) REVERT: C 51 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6682 (mt-10) REVERT: C 54 ASP cc_start: 0.8094 (t0) cc_final: 0.7803 (t0) REVERT: C 81 ASP cc_start: 0.8250 (m-30) cc_final: 0.7345 (m-30) REVERT: C 140 GLN cc_start: 0.8309 (tp-100) cc_final: 0.7751 (tp-100) REVERT: C 146 ARG cc_start: 0.8260 (mmt-90) cc_final: 0.7872 (mtt-85) REVERT: C 180 GLN cc_start: 0.8421 (mt0) cc_final: 0.8182 (mt0) REVERT: C 205 GLU cc_start: 0.8085 (tp30) cc_final: 0.7585 (tp30) REVERT: C 244 MET cc_start: 0.8759 (ptp) cc_final: 0.8540 (ptm) REVERT: C 284 LYS cc_start: 0.8213 (mmmt) cc_final: 0.7958 (mmmt) REVERT: C 288 LYS cc_start: 0.8778 (mtmm) cc_final: 0.8570 (mtmm) REVERT: D 54 ASP cc_start: 0.8125 (t0) cc_final: 0.7879 (t0) REVERT: D 103 LYS cc_start: 0.7633 (tttm) cc_final: 0.7396 (tttm) REVERT: D 110 SER cc_start: 0.8666 (t) cc_final: 0.8212 (p) REVERT: D 288 LYS cc_start: 0.8356 (ptpt) cc_final: 0.8058 (ptpt) REVERT: D 331 GLU cc_start: 0.7810 (mp0) cc_final: 0.7453 (mp0) REVERT: D 353 GLN cc_start: 0.7928 (pm20) cc_final: 0.7361 (pt0) REVERT: D 368 THR cc_start: 0.8313 (m) cc_final: 0.7773 (t) REVERT: D 371 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7543 (mt-10) REVERT: E 78 ASP cc_start: 0.7841 (m-30) cc_final: 0.7417 (p0) REVERT: E 84 LYS cc_start: 0.8420 (mmmm) cc_final: 0.8034 (mmmm) REVERT: E 102 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7045 (mm-30) REVERT: E 194 GLU cc_start: 0.7487 (mp0) cc_final: 0.7173 (mp0) REVERT: E 205 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 217 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7555 (mtm-85) REVERT: E 266 MET cc_start: 0.8600 (mtt) cc_final: 0.8296 (mtp) REVERT: E 328 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7732 (mtmm) REVERT: E 349 ASN cc_start: 0.7862 (t0) cc_final: 0.7609 (t0) REVERT: E 351 ASP cc_start: 0.7848 (p0) cc_final: 0.7491 (p0) REVERT: E 371 GLU cc_start: 0.6819 (mm-30) cc_final: 0.6514 (mm-30) REVERT: E 379 LYS cc_start: 0.8150 (tttt) cc_final: 0.7918 (tttt) REVERT: E 382 ASP cc_start: 0.8362 (t0) cc_final: 0.8083 (t0) REVERT: F 103 LYS cc_start: 0.8103 (tttt) cc_final: 0.7788 (tttt) REVERT: F 171 GLN cc_start: 0.8594 (tp40) cc_final: 0.8272 (tp40) REVERT: F 187 MET cc_start: 0.8277 (mmm) cc_final: 0.8053 (mmm) REVERT: F 194 GLU cc_start: 0.8207 (mp0) cc_final: 0.7854 (mp0) REVERT: F 327 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7424 (mm110) REVERT: F 328 LYS cc_start: 0.8799 (tttt) cc_final: 0.8532 (tttt) REVERT: G 5 GLN cc_start: 0.7999 (mt0) cc_final: 0.7724 (mt0) REVERT: G 30 LYS cc_start: 0.8286 (tttt) cc_final: 0.7999 (tttt) REVERT: G 82 ARG cc_start: 0.7739 (mmt-90) cc_final: 0.7323 (mmt-90) REVERT: G 136 GLN cc_start: 0.8197 (tp40) cc_final: 0.7847 (tp-100) REVERT: G 183 ARG cc_start: 0.7147 (tmt170) cc_final: 0.6811 (tmt-80) REVERT: G 217 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7387 (tm-30) REVERT: G 229 SER cc_start: 0.8237 (t) cc_final: 0.7977 (m) REVERT: G 237 ILE cc_start: 0.7841 (mt) cc_final: 0.7480 (mt) REVERT: G 239 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7950 (tp40) REVERT: G 288 PHE cc_start: 0.7678 (t80) cc_final: 0.7198 (t80) REVERT: G 344 TYR cc_start: 0.8553 (m-10) cc_final: 0.8246 (m-80) REVERT: G 358 MET cc_start: 0.8143 (mmp) cc_final: 0.7939 (mmp) REVERT: G 367 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.7289 (tpp80) REVERT: G 385 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7597 (mm-30) REVERT: G 390 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8399 (mtt-85) REVERT: H 11 ARG cc_start: 0.7737 (tpt-90) cc_final: 0.7450 (tpt-90) REVERT: H 42 LEU cc_start: 0.8330 (mt) cc_final: 0.7903 (mt) REVERT: H 69 LEU cc_start: 0.7856 (mt) cc_final: 0.7392 (mm) REVERT: H 70 GLN cc_start: 0.7732 (mp10) cc_final: 0.7036 (mp10) REVERT: H 130 LYS cc_start: 0.8459 (tmmt) cc_final: 0.8092 (ttmt) REVERT: H 131 GLU cc_start: 0.8013 (tp30) cc_final: 0.7685 (tp30) REVERT: H 158 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7354 (tpp-160) REVERT: H 162 ASP cc_start: 0.8027 (m-30) cc_final: 0.7213 (t0) REVERT: H 196 LEU cc_start: 0.8495 (tp) cc_final: 0.8294 (tt) REVERT: H 229 SER cc_start: 0.8525 (m) cc_final: 0.8249 (t) REVERT: H 328 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7773 (mmt90) REVERT: H 345 LYS cc_start: 0.8249 (ttmt) cc_final: 0.8035 (ttmm) REVERT: H 350 SER cc_start: 0.8468 (t) cc_final: 0.8150 (m) REVERT: H 359 GLU cc_start: 0.8134 (tp30) cc_final: 0.7651 (tp30) REVERT: H 391 TYR cc_start: 0.8397 (m-10) cc_final: 0.7975 (m-10) REVERT: I 2 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6396 (m-40) REVERT: I 33 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7806 (tm-30) REVERT: I 44 LEU cc_start: 0.7255 (tt) cc_final: 0.6471 (mt) REVERT: I 70 GLN cc_start: 0.7625 (mm110) cc_final: 0.7395 (mm110) REVERT: I 99 GLN cc_start: 0.7781 (mp10) cc_final: 0.7535 (mp10) REVERT: I 127 GLN cc_start: 0.7934 (tp40) cc_final: 0.7681 (tp40) REVERT: I 136 GLN cc_start: 0.8193 (tp40) cc_final: 0.7979 (tm-30) REVERT: I 156 ASN cc_start: 0.8037 (m-40) cc_final: 0.7767 (m-40) REVERT: I 213 LEU cc_start: 0.8018 (tt) cc_final: 0.7711 (mt) REVERT: I 215 GLU cc_start: 0.8289 (tp30) cc_final: 0.8072 (tm-30) REVERT: I 231 ASP cc_start: 0.7883 (t0) cc_final: 0.7659 (m-30) REVERT: I 234 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7421 (mtm180) REVERT: I 235 GLU cc_start: 0.8479 (tp30) cc_final: 0.8169 (mm-30) REVERT: I 297 MET cc_start: 0.7331 (tmm) cc_final: 0.6785 (tmm) REVERT: I 306 GLN cc_start: 0.7603 (mm110) cc_final: 0.7396 (mm110) REVERT: I 344 TYR cc_start: 0.8438 (m-10) cc_final: 0.7901 (m-10) REVERT: I 359 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7105 (tm-30) REVERT: J 62 ASN cc_start: 0.8455 (t0) cc_final: 0.8155 (t0) REVERT: J 81 LEU cc_start: 0.8555 (tp) cc_final: 0.8233 (tp) REVERT: J 82 PHE cc_start: 0.8258 (t80) cc_final: 0.7762 (t80) REVERT: J 84 TRP cc_start: 0.6294 (t60) cc_final: 0.6028 (t60) REVERT: J 108 PHE cc_start: 0.7832 (m-10) cc_final: 0.7603 (m-10) REVERT: J 131 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6722 (t80) REVERT: J 184 MET cc_start: 0.8017 (mtm) cc_final: 0.7721 (mtm) REVERT: J 248 LEU cc_start: 0.8605 (tp) cc_final: 0.8274 (tp) REVERT: J 252 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7864 (mm-30) REVERT: J 366 TRP cc_start: 0.7168 (m100) cc_final: 0.6696 (m100) REVERT: J 425 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7607 (tm-30) REVERT: J 434 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: J 466 GLN cc_start: 0.8306 (tp40) cc_final: 0.8106 (tp40) outliers start: 87 outliers final: 55 residues processed: 1100 average time/residue: 0.4528 time to fit residues: 752.0265 Evaluate side-chains 1104 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 1046 time to evaluate : 3.099 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LYS 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 151 ASN Chi-restraints excluded: chain C residue 187 MET 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 D residue 159 GLU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 302 LEU 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 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 H residue 5 GLN Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 306 GLN Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain I residue 2 ASN 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 250 LEU Chi-restraints excluded: chain I residue 337 SER Chi-restraints excluded: chain I residue 338 ILE Chi-restraints excluded: chain I residue 395 ILE Chi-restraints excluded: chain J residue 15 MET 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 285 PHE Chi-restraints excluded: chain J residue 359 MET Chi-restraints excluded: chain J residue 434 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 153 optimal weight: 0.2980 chunk 243 optimal weight: 2.9990 chunk 335 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 287 optimal weight: 7.9990 chunk 368 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS A 144 ASN B 121 ASN D 153 ASN E 61 GLN E 63 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN H 102 GLN J 403 ASN J 437 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.111725 restraints weight = 46062.619| |-----------------------------------------------------------------------------| r_work (start): 0.3422 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: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29983 Z= 0.175 Angle : 0.539 9.898 40800 Z= 0.287 Chirality : 0.041 0.153 4829 Planarity : 0.005 0.077 5352 Dihedral : 4.124 76.458 4145 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.13 % Allowed : 16.61 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.14), residues: 3821 helix: 3.32 (0.11), residues: 1991 sheet: -0.21 (0.24), residues: 492 loop : -1.02 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 482 HIS 0.004 0.001 HIS J 428 PHE 0.022 0.001 PHE J 107 TYR 0.021 0.001 TYR E 333 ARG 0.010 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08352 ( 1864) hydrogen bonds : angle 4.36451 ( 5454) covalent geometry : bond 0.00365 (29983) covalent geometry : angle 0.53943 (40800) *********************** 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 1155 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1055 time to evaluate : 3.237 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: 0.8178 (tp40) cc_final: 0.7719 (tm-30) REVERT: A 143 TYR cc_start: 0.8639 (t80) cc_final: 0.8299 (t80) REVERT: A 144 ASN cc_start: 0.8361 (m-40) cc_final: 0.8110 (m110) REVERT: A 171 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7540 (tp-100) REVERT: A 188 ILE cc_start: 0.8505 (mm) cc_final: 0.8251 (mt) REVERT: A 214 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 242 PRO cc_start: 0.8336 (Cg_endo) cc_final: 0.8096 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7489 (pt0) cc_final: 0.7245 (pt0) REVERT: A 294 MET cc_start: 0.8225 (mmm) cc_final: 0.7779 (mmm) REVERT: A 385 VAL cc_start: 0.8533 (p) cc_final: 0.8265 (m) REVERT: A 386 LYS cc_start: 0.8584 (tttt) cc_final: 0.8265 (tttt) REVERT: B 50 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 133 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8196 (mtpp) REVERT: B 140 GLN cc_start: 0.8421 (tp40) cc_final: 0.8029 (tp40) REVERT: C 51 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6706 (mt-10) REVERT: C 54 ASP cc_start: 0.8065 (t0) cc_final: 0.7808 (t0) REVERT: C 81 ASP cc_start: 0.8228 (m-30) cc_final: 0.7322 (m-30) REVERT: C 140 GLN cc_start: 0.8280 (tp-100) cc_final: 0.7711 (tp-100) REVERT: C 146 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.7903 (mtt-85) REVERT: C 180 GLN cc_start: 0.8431 (mt0) cc_final: 0.8201 (mt0) REVERT: C 205 GLU cc_start: 0.7978 (tp30) cc_final: 0.7462 (tp30) REVERT: C 244 MET cc_start: 0.8751 (ptp) cc_final: 0.8535 (ptm) REVERT: C 284 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7959 (mmmt) REVERT: C 288 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8552 (mtmm) REVERT: C 380 LEU cc_start: 0.8380 (mp) cc_final: 0.8024 (mp) REVERT: D 54 ASP cc_start: 0.8096 (t0) cc_final: 0.7865 (t0) REVERT: D 103 LYS cc_start: 0.7624 (tttm) cc_final: 0.7387 (tttm) REVERT: D 110 SER cc_start: 0.8668 (t) cc_final: 0.8227 (p) REVERT: D 288 LYS cc_start: 0.8351 (ptpt) cc_final: 0.7963 (ptpt) REVERT: D 324 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7632 (tm-30) REVERT: D 331 GLU cc_start: 0.7826 (mp0) cc_final: 0.7235 (mp0) REVERT: D 368 THR cc_start: 0.8372 (m) cc_final: 0.7813 (t) REVERT: D 371 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7539 (mt-10) REVERT: E 78 ASP cc_start: 0.7888 (m-30) cc_final: 0.7333 (p0) REVERT: E 84 LYS cc_start: 0.8423 (mmmm) cc_final: 0.7930 (mmmm) REVERT: E 102 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7024 (mm-30) REVERT: E 194 GLU cc_start: 0.7519 (mp0) cc_final: 0.7217 (mp0) REVERT: E 217 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7530 (mtm-85) REVERT: E 266 MET cc_start: 0.8607 (mtt) cc_final: 0.8304 (mtp) REVERT: E 328 LYS cc_start: 0.8043 (mtmm) cc_final: 0.7787 (mtmm) REVERT: E 341 THR cc_start: 0.8163 (p) cc_final: 0.7802 (p) REVERT: E 349 ASN cc_start: 0.7855 (t0) cc_final: 0.7596 (t0) REVERT: E 351 ASP cc_start: 0.7831 (p0) cc_final: 0.7451 (p0) REVERT: E 371 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6557 (mm-30) REVERT: E 379 LYS cc_start: 0.8195 (tttt) cc_final: 0.7953 (tttt) REVERT: E 382 ASP cc_start: 0.8370 (t0) cc_final: 0.8097 (t0) REVERT: F 87 ASP cc_start: 0.7670 (t0) cc_final: 0.7434 (t0) REVERT: F 171 GLN cc_start: 0.8607 (tp40) cc_final: 0.8379 (tp40) REVERT: F 194 GLU cc_start: 0.8186 (mp0) cc_final: 0.7822 (mp0) REVERT: F 327 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7422 (mm110) REVERT: F 328 LYS cc_start: 0.8788 (tttt) cc_final: 0.8517 (tttt) REVERT: G 5 GLN cc_start: 0.8029 (mt0) cc_final: 0.7723 (mt0) REVERT: G 30 LYS cc_start: 0.8307 (tttt) cc_final: 0.7983 (tttt) REVERT: G 82 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.7204 (mmt-90) REVERT: G 156 ASN cc_start: 0.7905 (t0) cc_final: 0.7596 (t0) REVERT: G 160 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7279 (mp-120) REVERT: G 183 ARG cc_start: 0.7121 (tmt170) cc_final: 0.6809 (tmt-80) REVERT: G 188 ASN cc_start: 0.7991 (m110) cc_final: 0.7536 (m-40) REVERT: G 217 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7408 (tm-30) REVERT: G 229 SER cc_start: 0.8184 (t) cc_final: 0.7933 (m) REVERT: G 237 ILE cc_start: 0.7766 (mt) cc_final: 0.7454 (mt) REVERT: G 239 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8103 (tm-30) REVERT: G 288 PHE cc_start: 0.7678 (t80) cc_final: 0.7084 (t80) REVERT: G 328 ARG cc_start: 0.8189 (mtt-85) cc_final: 0.7926 (mmt-90) REVERT: G 344 TYR cc_start: 0.8586 (m-10) cc_final: 0.8255 (m-80) REVERT: G 358 MET cc_start: 0.8067 (mmp) cc_final: 0.7626 (mmp) REVERT: G 367 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7233 (tpp80) REVERT: G 385 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7532 (mm-30) REVERT: G 390 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8410 (mtt-85) REVERT: H 4 MET cc_start: 0.6861 (tpp) cc_final: 0.6613 (tpp) REVERT: H 11 ARG cc_start: 0.7707 (tpt-90) cc_final: 0.7418 (tpt-90) REVERT: H 42 LEU cc_start: 0.8322 (mt) cc_final: 0.7904 (mt) REVERT: H 69 LEU cc_start: 0.7873 (mt) cc_final: 0.7438 (mm) REVERT: H 70 GLN cc_start: 0.7743 (mp10) cc_final: 0.7068 (mp10) REVERT: H 130 LYS cc_start: 0.8520 (tmmt) cc_final: 0.8131 (ttmt) REVERT: H 131 GLU cc_start: 0.8037 (tp30) cc_final: 0.7708 (tp30) REVERT: H 133 ILE cc_start: 0.9018 (mt) cc_final: 0.8784 (mm) REVERT: H 158 ARG cc_start: 0.7629 (tpp-160) cc_final: 0.7364 (tpp-160) REVERT: H 162 ASP cc_start: 0.8060 (m-30) cc_final: 0.7183 (t0) REVERT: H 175 LEU cc_start: 0.8446 (tp) cc_final: 0.8227 (tt) REVERT: H 196 LEU cc_start: 0.8492 (tp) cc_final: 0.8283 (tt) REVERT: H 229 SER cc_start: 0.8478 (m) cc_final: 0.8192 (t) REVERT: H 242 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7338 (t0) REVERT: H 279 MET cc_start: 0.7965 (mtp) cc_final: 0.7251 (mtp) REVERT: H 328 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7758 (mmt90) REVERT: H 350 SER cc_start: 0.8477 (t) cc_final: 0.8163 (m) REVERT: H 359 GLU cc_start: 0.8188 (tp30) cc_final: 0.7698 (tp30) REVERT: H 374 ASP cc_start: 0.8061 (m-30) cc_final: 0.7838 (m-30) REVERT: H 391 TYR cc_start: 0.8412 (m-10) cc_final: 0.8060 (m-10) REVERT: H 393 TYR cc_start: 0.8718 (t80) cc_final: 0.8504 (t80) REVERT: H 409 GLU cc_start: 0.6791 (tp30) cc_final: 0.6459 (tp30) REVERT: I 7 TYR cc_start: 0.8119 (t80) cc_final: 0.7799 (t80) REVERT: I 19 LYS cc_start: 0.7576 (ttmm) cc_final: 0.7321 (ttmm) REVERT: I 33 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7802 (tm-30) REVERT: I 70 GLN cc_start: 0.7622 (mm110) cc_final: 0.7324 (mm110) REVERT: I 127 GLN cc_start: 0.7972 (tp40) cc_final: 0.7676 (tp40) REVERT: I 136 GLN cc_start: 0.8219 (tp40) cc_final: 0.7991 (tm-30) REVERT: I 156 ASN cc_start: 0.8033 (m-40) cc_final: 0.7756 (m-40) REVERT: I 229 SER cc_start: 0.8449 (t) cc_final: 0.8137 (m) REVERT: I 235 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: I 297 MET cc_start: 0.7492 (tmm) cc_final: 0.7147 (tmm) REVERT: I 322 SER cc_start: 0.8549 (t) cc_final: 0.8101 (m) REVERT: I 344 TYR cc_start: 0.8446 (m-10) cc_final: 0.7874 (m-10) REVERT: I 359 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7160 (tm-30) REVERT: J 21 LEU cc_start: 0.8431 (mm) cc_final: 0.8186 (mm) REVERT: J 81 LEU cc_start: 0.8484 (tp) cc_final: 0.8234 (tp) REVERT: J 82 PHE cc_start: 0.8258 (t80) cc_final: 0.7761 (t80) REVERT: J 84 TRP cc_start: 0.6295 (t60) cc_final: 0.6026 (t60) REVERT: J 131 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6743 (t80) REVERT: J 184 MET cc_start: 0.7990 (mtm) cc_final: 0.7716 (mtm) REVERT: J 186 LEU cc_start: 0.8315 (mt) cc_final: 0.8100 (pp) REVERT: J 248 LEU cc_start: 0.8599 (tp) cc_final: 0.8344 (tp) REVERT: J 252 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8021 (mm-30) REVERT: J 366 TRP cc_start: 0.7175 (m100) cc_final: 0.6695 (m100) REVERT: J 406 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7644 (mtp-110) REVERT: J 425 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7736 (tm-30) REVERT: J 434 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7563 (mt-10) REVERT: J 466 GLN cc_start: 0.8273 (tp40) cc_final: 0.8067 (tp40) outliers start: 100 outliers final: 72 residues processed: 1099 average time/residue: 0.4449 time to fit residues: 737.4719 Evaluate side-chains 1115 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1038 time to evaluate : 3.064 ------------------------------------------------------------------------------- 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 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 151 ASN 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 51 GLU Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 LYS Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 167 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 372 ILE 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 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 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 217 GLU Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 306 GLN 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 235 GLU 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 338 ILE Chi-restraints excluded: chain I residue 364 VAL 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 131 TYR Chi-restraints excluded: chain J residue 206 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 434 GLU Chi-restraints excluded: chain J residue 489 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 142 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 375 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 20 optimal weight: 0.0050 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 GLN E 201 GLN G 94 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.128219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112423 restraints weight = 45846.314| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.87 r_work: 0.3308 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29983 Z= 0.163 Angle : 0.537 12.956 40800 Z= 0.282 Chirality : 0.040 0.144 4829 Planarity : 0.005 0.069 5352 Dihedral : 4.056 77.507 4145 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.57 % Allowed : 17.42 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.14), residues: 3821 helix: 3.38 (0.11), residues: 1997 sheet: -0.18 (0.24), residues: 492 loop : -1.01 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 482 HIS 0.003 0.001 HIS J 166 PHE 0.027 0.001 PHE J 108 TYR 0.019 0.001 TYR E 143 ARG 0.012 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08034 ( 1864) hydrogen bonds : angle 4.25741 ( 5454) covalent geometry : bond 0.00334 (29983) covalent geometry : angle 0.53713 (40800) *********************** 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 1167 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1053 time to evaluate : 3.349 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: 0.8188 (tp40) cc_final: 0.7701 (tm-30) REVERT: A 143 TYR cc_start: 0.8617 (t80) cc_final: 0.8266 (t80) REVERT: A 144 ASN cc_start: 0.8338 (m-40) cc_final: 0.8067 (m110) REVERT: A 171 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7449 (tp-100) REVERT: A 188 ILE cc_start: 0.8499 (mm) cc_final: 0.8245 (mt) REVERT: A 214 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 242 PRO cc_start: 0.8338 (Cg_endo) cc_final: 0.8100 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7503 (pt0) cc_final: 0.7259 (pt0) REVERT: A 349 ASN cc_start: 0.8554 (t0) cc_final: 0.8274 (t0) REVERT: A 385 VAL cc_start: 0.8530 (p) cc_final: 0.8259 (m) REVERT: A 386 LYS cc_start: 0.8584 (tttt) cc_final: 0.8264 (tttt) REVERT: B 50 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7120 (mm-30) REVERT: B 133 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8157 (mtpp) REVERT: B 140 GLN cc_start: 0.8442 (tp40) cc_final: 0.8065 (tp40) REVERT: C 51 GLU cc_start: 0.6974 (mt-10) cc_final: 0.6686 (mt-10) REVERT: C 54 ASP cc_start: 0.8047 (t0) cc_final: 0.7799 (t0) REVERT: C 81 ASP cc_start: 0.8236 (m-30) cc_final: 0.7324 (m-30) REVERT: C 140 GLN cc_start: 0.8258 (tp-100) cc_final: 0.7691 (tp-100) REVERT: C 146 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7832 (mtt-85) REVERT: C 180 GLN cc_start: 0.8451 (mt0) cc_final: 0.8237 (mt0) REVERT: C 205 GLU cc_start: 0.7984 (tp30) cc_final: 0.7479 (tp30) REVERT: C 229 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8395 (tmm-80) REVERT: C 244 MET cc_start: 0.8760 (ptp) cc_final: 0.8552 (ptm) REVERT: C 284 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7971 (mmmt) REVERT: D 54 ASP cc_start: 0.8085 (t0) cc_final: 0.7880 (t0) REVERT: D 103 LYS cc_start: 0.7562 (tttm) cc_final: 0.7327 (tttm) REVERT: D 110 SER cc_start: 0.8663 (t) cc_final: 0.8216 (p) REVERT: D 164 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7516 (mtp85) REVERT: D 288 LYS cc_start: 0.8339 (ptpt) cc_final: 0.7970 (ptpt) REVERT: D 324 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7672 (tm-30) REVERT: D 331 GLU cc_start: 0.7811 (mp0) cc_final: 0.7202 (mp0) REVERT: D 368 THR cc_start: 0.8366 (m) cc_final: 0.7831 (t) REVERT: D 371 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7544 (mt-10) REVERT: E 78 ASP cc_start: 0.7825 (m-30) cc_final: 0.7545 (m-30) REVERT: E 81 ASP cc_start: 0.7693 (m-30) cc_final: 0.7443 (m-30) REVERT: E 84 LYS cc_start: 0.8389 (mmmm) cc_final: 0.7943 (mmmm) REVERT: E 102 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6993 (mm-30) REVERT: E 194 GLU cc_start: 0.7534 (mp0) cc_final: 0.7222 (mp0) REVERT: E 217 ARG cc_start: 0.7868 (mtm-85) cc_final: 0.7518 (mtm-85) REVERT: E 222 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7683 (mtm) REVERT: E 266 MET cc_start: 0.8595 (mtt) cc_final: 0.8293 (mtp) REVERT: E 341 THR cc_start: 0.8160 (p) cc_final: 0.7791 (p) REVERT: E 351 ASP cc_start: 0.7792 (p0) cc_final: 0.7586 (p0) REVERT: E 379 LYS cc_start: 0.8201 (tttt) cc_final: 0.7960 (tttt) REVERT: E 382 ASP cc_start: 0.8370 (t0) cc_final: 0.8119 (t0) REVERT: F 87 ASP cc_start: 0.7659 (t0) cc_final: 0.7416 (t0) REVERT: F 140 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8167 (tp-100) REVERT: F 171 GLN cc_start: 0.8631 (tp40) cc_final: 0.8356 (tp40) REVERT: F 194 GLU cc_start: 0.8162 (mp0) cc_final: 0.7800 (mp0) REVERT: F 327 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7442 (mm110) REVERT: F 328 LYS cc_start: 0.8764 (tttt) cc_final: 0.8496 (tttt) REVERT: G 5 GLN cc_start: 0.8040 (mt0) cc_final: 0.7799 (mt0) REVERT: G 82 ARG cc_start: 0.7670 (mmt-90) cc_final: 0.7105 (mmt-90) REVERT: G 156 ASN cc_start: 0.7832 (t0) cc_final: 0.7491 (t0) REVERT: G 160 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7270 (mp-120) REVERT: G 183 ARG cc_start: 0.7235 (tmt170) cc_final: 0.6885 (tmt-80) REVERT: G 188 ASN cc_start: 0.7949 (m110) cc_final: 0.7509 (m-40) REVERT: G 217 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7372 (tm-30) REVERT: G 229 SER cc_start: 0.8222 (t) cc_final: 0.7959 (m) REVERT: G 237 ILE cc_start: 0.7808 (mt) cc_final: 0.7503 (mt) REVERT: G 288 PHE cc_start: 0.7675 (t80) cc_final: 0.7055 (t80) REVERT: G 328 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7932 (mmt-90) REVERT: G 344 TYR cc_start: 0.8588 (m-10) cc_final: 0.8209 (m-80) REVERT: G 358 MET cc_start: 0.8045 (mmp) cc_final: 0.7583 (mmp) REVERT: G 367 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7233 (tpp80) REVERT: G 385 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7483 (mm-30) REVERT: G 390 ARG cc_start: 0.8637 (mtt90) cc_final: 0.8418 (mtt-85) REVERT: H 5 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: H 11 ARG cc_start: 0.7673 (tpt-90) cc_final: 0.7380 (tpt-90) REVERT: H 35 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7603 (ttm-80) REVERT: H 42 LEU cc_start: 0.8332 (mt) cc_final: 0.7907 (mt) REVERT: H 69 LEU cc_start: 0.7883 (mt) cc_final: 0.7504 (mm) REVERT: H 70 GLN cc_start: 0.7779 (mp10) cc_final: 0.7110 (mp10) REVERT: H 130 LYS cc_start: 0.8514 (tmmt) cc_final: 0.8117 (ttmt) REVERT: H 131 GLU cc_start: 0.8048 (tp30) cc_final: 0.7646 (tp30) REVERT: H 133 ILE cc_start: 0.9014 (mt) cc_final: 0.8780 (mm) REVERT: H 135 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7378 (ttm-80) REVERT: H 158 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7355 (tpp-160) REVERT: H 175 LEU cc_start: 0.8523 (tp) cc_final: 0.8317 (tt) REVERT: H 196 LEU cc_start: 0.8479 (tp) cc_final: 0.8258 (tt) REVERT: H 229 SER cc_start: 0.8476 (m) cc_final: 0.8191 (t) REVERT: H 242 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7299 (t0) REVERT: H 328 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7726 (mmt90) REVERT: H 350 SER cc_start: 0.8480 (t) cc_final: 0.8158 (m) REVERT: H 359 GLU cc_start: 0.8187 (tp30) cc_final: 0.7701 (tp30) REVERT: H 374 ASP cc_start: 0.8043 (m-30) cc_final: 0.7743 (m-30) REVERT: H 390 ARG cc_start: 0.8575 (mtt180) cc_final: 0.8348 (mtt180) REVERT: H 391 TYR cc_start: 0.8410 (m-10) cc_final: 0.8105 (m-10) REVERT: H 393 TYR cc_start: 0.8723 (t80) cc_final: 0.8517 (t80) REVERT: I 19 LYS cc_start: 0.7584 (ttmm) cc_final: 0.7296 (ttmm) REVERT: I 33 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7792 (tm-30) REVERT: I 70 GLN cc_start: 0.7563 (mm110) cc_final: 0.7252 (mm110) REVERT: I 127 GLN cc_start: 0.7988 (tp40) cc_final: 0.7719 (tp40) REVERT: I 156 ASN cc_start: 0.7996 (m-40) cc_final: 0.7717 (m-40) REVERT: I 213 LEU cc_start: 0.7959 (tt) cc_final: 0.7682 (mt) REVERT: I 219 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: I 229 SER cc_start: 0.8401 (t) cc_final: 0.8098 (m) REVERT: I 235 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: I 297 MET cc_start: 0.7514 (tmm) cc_final: 0.6886 (tmm) REVERT: I 306 GLN cc_start: 0.7584 (mm110) cc_final: 0.7368 (mm110) REVERT: I 322 SER cc_start: 0.8503 (t) cc_final: 0.8083 (m) REVERT: I 344 TYR cc_start: 0.8447 (m-10) cc_final: 0.7852 (m-10) REVERT: I 359 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7190 (tm-30) REVERT: J 81 LEU cc_start: 0.8475 (tp) cc_final: 0.8208 (tp) REVERT: J 82 PHE cc_start: 0.8251 (t80) cc_final: 0.7735 (t80) REVERT: J 84 TRP cc_start: 0.6296 (t60) cc_final: 0.6016 (t60) REVERT: J 131 TYR cc_start: 0.7012 (OUTLIER) cc_final: 0.6740 (t80) REVERT: J 146 THR cc_start: 0.8347 (m) cc_final: 0.8105 (t) REVERT: J 184 MET cc_start: 0.7992 (mtm) cc_final: 0.7641 (mtm) REVERT: J 186 LEU cc_start: 0.8292 (mt) cc_final: 0.8075 (pp) REVERT: J 248 LEU cc_start: 0.8621 (tp) cc_final: 0.8410 (tt) REVERT: J 361 PHE cc_start: 0.8011 (t80) cc_final: 0.7689 (t80) REVERT: J 366 TRP cc_start: 0.7164 (m100) cc_final: 0.6725 (m100) REVERT: J 406 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7718 (mtp-110) REVERT: J 425 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7594 (tm-30) REVERT: J 434 GLU cc_start: 0.7876 (tt0) cc_final: 0.7577 (mt-10) REVERT: J 466 GLN cc_start: 0.8277 (tp40) cc_final: 0.8068 (tp40) REVERT: J 487 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7982 (mp) outliers start: 114 outliers final: 84 residues processed: 1106 average time/residue: 0.4427 time to fit residues: 743.1006 Evaluate side-chains 1131 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1039 time to evaluate : 3.444 ------------------------------------------------------------------------------- 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 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 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 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 324 GLU Chi-restraints excluded: chain C residue 328 LYS 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 276 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 167 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 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 H residue 5 GLN Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 248 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 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 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 337 SER Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 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 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 487 ILE Chi-restraints excluded: chain J residue 489 LEU Chi-restraints excluded: chain J residue 497 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 0 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 290 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 chunk 327 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 121 ASN B 200 GLN C 317 GLN E 201 GLN E 265 ASN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN H 416 ASN I 320 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.110063 restraints weight = 46083.128| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.86 r_work: 0.3260 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 29983 Z= 0.282 Angle : 0.624 11.136 40800 Z= 0.334 Chirality : 0.045 0.158 4829 Planarity : 0.005 0.082 5352 Dihedral : 4.424 76.995 4145 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.13 % Allowed : 18.39 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.14), residues: 3821 helix: 2.98 (0.11), residues: 1983 sheet: -0.27 (0.23), residues: 486 loop : -1.23 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 76 HIS 0.006 0.001 HIS J 429 PHE 0.029 0.002 PHE J 108 TYR 0.018 0.002 TYR I 7 ARG 0.011 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.09523 ( 1864) hydrogen bonds : angle 4.56445 ( 5454) covalent geometry : bond 0.00635 (29983) covalent geometry : angle 0.62367 (40800) *********************** 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 1209 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1077 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8216 (tp40) cc_final: 0.8010 (tp40) REVERT: A 171 GLN cc_start: 0.7965 (tp-100) cc_final: 0.7624 (tp-100) REVERT: A 188 ILE cc_start: 0.8532 (mm) cc_final: 0.8274 (mt) REVERT: A 194 GLU cc_start: 0.8056 (pm20) cc_final: 0.7791 (pm20) REVERT: A 242 PRO cc_start: 0.8354 (Cg_endo) cc_final: 0.8107 (Cg_exo) REVERT: A 294 MET cc_start: 0.8254 (mmm) cc_final: 0.7769 (mmm) REVERT: A 349 ASN cc_start: 0.8601 (t0) cc_final: 0.8357 (t0) REVERT: A 385 VAL cc_start: 0.8525 (p) cc_final: 0.8268 (m) REVERT: A 386 LYS cc_start: 0.8546 (tttt) cc_final: 0.8299 (tttt) REVERT: B 126 GLN cc_start: 0.8224 (tp-100) cc_final: 0.7884 (tp-100) REVERT: B 133 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8264 (mtpp) REVERT: B 140 GLN cc_start: 0.8496 (tp40) cc_final: 0.8096 (tp40) REVERT: C 51 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6684 (mt-10) REVERT: C 54 ASP cc_start: 0.8081 (t0) cc_final: 0.7805 (t0) REVERT: C 81 ASP cc_start: 0.8266 (m-30) cc_final: 0.7068 (m-30) REVERT: C 140 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7977 (tp-100) REVERT: C 146 ARG cc_start: 0.8470 (mmt-90) cc_final: 0.8260 (mtt-85) REVERT: C 153 ASN cc_start: 0.8505 (t0) cc_final: 0.8030 (t0) REVERT: C 180 GLN cc_start: 0.8465 (mt0) cc_final: 0.8237 (mt0) REVERT: C 205 GLU cc_start: 0.8161 (tp30) cc_final: 0.7650 (tp30) REVERT: C 229 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8416 (tmm-80) REVERT: C 284 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7957 (mmmt) REVERT: D 103 LYS cc_start: 0.7685 (tttm) cc_final: 0.7422 (tttm) REVERT: D 110 SER cc_start: 0.8701 (t) cc_final: 0.8256 (p) REVERT: D 288 LYS cc_start: 0.8374 (ptpt) cc_final: 0.7963 (ptpt) REVERT: D 324 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7677 (tm-30) REVERT: D 331 GLU cc_start: 0.7843 (mp0) cc_final: 0.7223 (mp0) REVERT: D 349 ASN cc_start: 0.8378 (t0) cc_final: 0.8170 (t0) REVERT: D 368 THR cc_start: 0.8498 (m) cc_final: 0.7927 (t) REVERT: D 371 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7590 (mt-10) REVERT: E 78 ASP cc_start: 0.7875 (m-30) cc_final: 0.7222 (p0) REVERT: E 81 ASP cc_start: 0.7755 (m-30) cc_final: 0.7075 (m-30) REVERT: E 84 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8107 (mmmm) REVERT: E 102 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7248 (mm-30) REVERT: E 194 GLU cc_start: 0.7526 (mp0) cc_final: 0.7248 (mp0) REVERT: E 217 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7638 (mtm-85) REVERT: E 266 MET cc_start: 0.8629 (mtt) cc_final: 0.8318 (mtp) REVERT: E 341 THR cc_start: 0.8246 (p) cc_final: 0.7896 (p) REVERT: E 350 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8182 (mtt-85) REVERT: E 379 LYS cc_start: 0.8249 (tttt) cc_final: 0.8001 (tttt) REVERT: E 382 ASP cc_start: 0.8383 (t0) cc_final: 0.8144 (t0) REVERT: F 87 ASP cc_start: 0.7655 (t0) cc_final: 0.7415 (t0) REVERT: F 93 ASP cc_start: 0.8093 (t0) cc_final: 0.7865 (t0) REVERT: F 146 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7608 (mtt90) REVERT: F 171 GLN cc_start: 0.8702 (tp40) cc_final: 0.8433 (tp40) REVERT: F 194 GLU cc_start: 0.8173 (mp0) cc_final: 0.7828 (mp0) REVERT: F 327 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7468 (mm110) REVERT: F 328 LYS cc_start: 0.8800 (tttt) cc_final: 0.8532 (tttt) REVERT: G 5 GLN cc_start: 0.8034 (mt0) cc_final: 0.7803 (mt0) REVERT: G 82 ARG cc_start: 0.7908 (mmt-90) cc_final: 0.7409 (mmt-90) REVERT: G 137 LEU cc_start: 0.8253 (tp) cc_final: 0.7971 (tt) REVERT: G 160 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7356 (mp-120) REVERT: G 183 ARG cc_start: 0.7276 (tmt170) cc_final: 0.6899 (tmt-80) REVERT: G 188 ASN cc_start: 0.7991 (m110) cc_final: 0.7541 (m-40) REVERT: G 217 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7511 (tm-30) REVERT: G 229 SER cc_start: 0.8247 (t) cc_final: 0.7989 (m) REVERT: G 237 ILE cc_start: 0.7797 (mt) cc_final: 0.7511 (mt) REVERT: G 288 PHE cc_start: 0.7765 (t80) cc_final: 0.7564 (t80) REVERT: G 341 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8255 (tp) REVERT: G 344 TYR cc_start: 0.8618 (m-10) cc_final: 0.8252 (m-80) REVERT: G 358 MET cc_start: 0.8005 (mmp) cc_final: 0.7647 (mmp) REVERT: G 385 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7665 (mm-30) REVERT: G 390 ARG cc_start: 0.8619 (mtt90) cc_final: 0.8376 (mtt-85) REVERT: H 11 ARG cc_start: 0.7704 (tpt-90) cc_final: 0.7410 (tpt-90) REVERT: H 42 LEU cc_start: 0.8349 (mt) cc_final: 0.7960 (mt) REVERT: H 69 LEU cc_start: 0.7900 (mt) cc_final: 0.7592 (mm) REVERT: H 70 GLN cc_start: 0.7836 (mp10) cc_final: 0.7205 (mp10) REVERT: H 130 LYS cc_start: 0.8464 (tmmt) cc_final: 0.8071 (ttmt) REVERT: H 131 GLU cc_start: 0.8118 (tp30) cc_final: 0.7691 (tp30) REVERT: H 135 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7475 (ttm-80) REVERT: H 158 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7500 (tpp-160) REVERT: H 164 VAL cc_start: 0.8717 (p) cc_final: 0.8506 (t) REVERT: H 196 LEU cc_start: 0.8462 (tp) cc_final: 0.8248 (tt) REVERT: H 229 SER cc_start: 0.8565 (m) cc_final: 0.8277 (t) REVERT: H 242 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7371 (t0) REVERT: H 328 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7797 (mmt90) REVERT: H 345 LYS cc_start: 0.8287 (ttmt) cc_final: 0.8072 (ttmm) REVERT: H 350 SER cc_start: 0.8497 (t) cc_final: 0.8158 (m) REVERT: H 391 TYR cc_start: 0.8395 (m-10) cc_final: 0.8175 (m-10) REVERT: I 7 TYR cc_start: 0.8193 (t80) cc_final: 0.7868 (t80) REVERT: I 11 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7571 (ttp80) REVERT: I 33 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7811 (tm-30) REVERT: I 70 GLN cc_start: 0.7543 (mm110) cc_final: 0.7293 (mm110) REVERT: I 127 GLN cc_start: 0.8015 (tp40) cc_final: 0.7694 (tp40) REVERT: I 156 ASN cc_start: 0.8116 (m-40) cc_final: 0.7877 (m-40) REVERT: I 213 LEU cc_start: 0.7993 (tt) cc_final: 0.7716 (mt) REVERT: I 219 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7493 (mtm-85) REVERT: I 229 SER cc_start: 0.8492 (t) cc_final: 0.8167 (m) REVERT: I 235 GLU cc_start: 0.8508 (tp30) cc_final: 0.8200 (mm-30) REVERT: I 297 MET cc_start: 0.7599 (tmm) cc_final: 0.7047 (tmm) REVERT: I 306 GLN cc_start: 0.7659 (mm110) cc_final: 0.7436 (mm110) REVERT: I 344 TYR cc_start: 0.8447 (m-10) cc_final: 0.7870 (m-10) REVERT: I 359 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7106 (tm-30) REVERT: I 372 VAL cc_start: 0.7740 (t) cc_final: 0.7520 (p) REVERT: J 81 LEU cc_start: 0.8540 (tp) cc_final: 0.8325 (tp) REVERT: J 82 PHE cc_start: 0.8303 (t80) cc_final: 0.7671 (t80) REVERT: J 84 TRP cc_start: 0.6343 (t60) cc_final: 0.6127 (t60) REVERT: J 85 SER cc_start: 0.8619 (m) cc_final: 0.8234 (p) REVERT: J 108 PHE cc_start: 0.7652 (m-10) cc_final: 0.7430 (m-10) REVERT: J 131 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.6798 (t80) REVERT: J 146 THR cc_start: 0.8384 (m) cc_final: 0.8154 (t) REVERT: J 183 LEU cc_start: 0.8606 (tt) cc_final: 0.8019 (mm) REVERT: J 184 MET cc_start: 0.7925 (mtm) cc_final: 0.7582 (mtm) REVERT: J 186 LEU cc_start: 0.8387 (mt) cc_final: 0.8140 (pp) REVERT: J 248 LEU cc_start: 0.8642 (tp) cc_final: 0.8126 (tp) REVERT: J 252 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7895 (mm-30) REVERT: J 361 PHE cc_start: 0.7966 (t80) cc_final: 0.7681 (t80) REVERT: J 366 TRP cc_start: 0.7189 (m100) cc_final: 0.6737 (m100) REVERT: J 386 THR cc_start: 0.8698 (m) cc_final: 0.8399 (m) REVERT: J 425 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7649 (tm-30) REVERT: J 434 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7613 (mt-10) REVERT: J 464 ILE cc_start: 0.8437 (mt) cc_final: 0.8170 (mm) REVERT: J 466 GLN cc_start: 0.8405 (tp40) cc_final: 0.8181 (tp40) outliers start: 132 outliers final: 102 residues processed: 1137 average time/residue: 0.4567 time to fit residues: 790.4640 Evaluate side-chains 1169 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1059 time to evaluate : 3.762 ------------------------------------------------------------------------------- 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 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 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 354 VAL 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 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 131 VAL Chi-restraints excluded: chain E residue 350 ARG 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 167 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain F residue 302 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 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 205 LYS Chi-restraints excluded: chain G residue 222 SER 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 24 ARG 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 217 GLU Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain H residue 242 ASP Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 248 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 209 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 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 341 ILE Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 395 ILE 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 23 THR Chi-restraints excluded: chain J residue 37 ILE 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 262 LEU Chi-restraints excluded: chain J residue 271 THR 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 403 ASN Chi-restraints excluded: chain J residue 434 GLU Chi-restraints excluded: chain J residue 489 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 271 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 343 optimal weight: 0.9990 chunk 317 optimal weight: 3.9990 chunk 332 optimal weight: 0.7980 chunk 272 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 G 94 GLN G 346 GLN G 397 GLN H 41 GLN H 99 GLN I 320 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.127148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111257 restraints weight = 46089.224| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.92 r_work: 0.3263 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 29983 Z= 0.232 Angle : 0.601 11.419 40800 Z= 0.319 Chirality : 0.043 0.160 4829 Planarity : 0.005 0.071 5352 Dihedral : 4.364 76.850 4145 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.47 % Allowed : 19.08 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.14), residues: 3821 helix: 3.04 (0.11), residues: 1983 sheet: -0.31 (0.23), residues: 486 loop : -1.22 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 210 HIS 0.022 0.001 HIS I 320 PHE 0.030 0.002 PHE I 288 TYR 0.020 0.002 TYR H 125 ARG 0.013 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.09144 ( 1864) hydrogen bonds : angle 4.49252 ( 5454) covalent geometry : bond 0.00513 (29983) covalent geometry : angle 0.60129 (40800) *********************** 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 1202 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1059 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8271 (tp40) cc_final: 0.7770 (tm-30) REVERT: A 144 ASN cc_start: 0.8460 (m-40) cc_final: 0.8196 (m110) REVERT: A 171 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7434 (tp-100) REVERT: A 188 ILE cc_start: 0.8494 (mm) cc_final: 0.8241 (mt) REVERT: A 242 PRO cc_start: 0.8367 (Cg_endo) cc_final: 0.8124 (Cg_exo) REVERT: A 349 ASN cc_start: 0.8603 (t0) cc_final: 0.8335 (t0) REVERT: A 385 VAL cc_start: 0.8485 (p) cc_final: 0.8223 (m) REVERT: B 133 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8211 (mtpp) REVERT: B 140 GLN cc_start: 0.8465 (tp40) cc_final: 0.8049 (tp40) REVERT: B 277 ASP cc_start: 0.7359 (p0) cc_final: 0.7112 (p0) REVERT: B 350 ARG cc_start: 0.8896 (ptp-170) cc_final: 0.8673 (ptp-170) REVERT: C 51 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6689 (mt-10) REVERT: C 54 ASP cc_start: 0.8040 (t0) cc_final: 0.7745 (t0) REVERT: C 81 ASP cc_start: 0.8240 (m-30) cc_final: 0.7002 (m-30) REVERT: C 140 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7954 (tp-100) REVERT: C 146 ARG cc_start: 0.8385 (mmt-90) cc_final: 0.8181 (mtt-85) REVERT: C 180 GLN cc_start: 0.8451 (mt0) cc_final: 0.8237 (mt0) REVERT: C 205 GLU cc_start: 0.8137 (tp30) cc_final: 0.7610 (tp30) REVERT: C 229 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8407 (tmm-80) REVERT: C 284 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7966 (mmmt) REVERT: D 103 LYS cc_start: 0.7646 (tttm) cc_final: 0.7394 (tttm) REVERT: D 110 SER cc_start: 0.8655 (t) cc_final: 0.8195 (p) REVERT: D 288 LYS cc_start: 0.8394 (ptpt) cc_final: 0.7963 (ptpt) REVERT: D 324 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 331 GLU cc_start: 0.7788 (mp0) cc_final: 0.7166 (mp0) REVERT: D 349 ASN cc_start: 0.8340 (t0) cc_final: 0.8112 (t0) REVERT: D 368 THR cc_start: 0.8419 (m) cc_final: 0.7867 (t) REVERT: D 371 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7555 (mt-10) REVERT: E 78 ASP cc_start: 0.7847 (m-30) cc_final: 0.7178 (p0) REVERT: E 81 ASP cc_start: 0.7753 (m-30) cc_final: 0.7130 (m-30) REVERT: E 84 LYS cc_start: 0.8434 (mmmm) cc_final: 0.8056 (mmmm) REVERT: E 102 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7244 (mm-30) REVERT: E 194 GLU cc_start: 0.7555 (mp0) cc_final: 0.7266 (mp0) REVERT: E 217 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: E 266 MET cc_start: 0.8635 (mtt) cc_final: 0.8316 (mtp) REVERT: E 341 THR cc_start: 0.8202 (p) cc_final: 0.7837 (p) REVERT: E 379 LYS cc_start: 0.8172 (tttt) cc_final: 0.7921 (tttt) REVERT: E 382 ASP cc_start: 0.8321 (t0) cc_final: 0.8063 (t0) REVERT: F 87 ASP cc_start: 0.7652 (t0) cc_final: 0.7419 (t0) REVERT: F 93 ASP cc_start: 0.8089 (t0) cc_final: 0.7867 (t0) REVERT: F 146 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7400 (mtt90) REVERT: F 171 GLN cc_start: 0.8675 (tp40) cc_final: 0.8385 (tp40) REVERT: F 194 GLU cc_start: 0.8162 (mp0) cc_final: 0.7794 (mp0) REVERT: F 327 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7457 (mm110) REVERT: F 328 LYS cc_start: 0.8803 (tttt) cc_final: 0.8520 (tttt) REVERT: G 5 GLN cc_start: 0.8032 (mt0) cc_final: 0.7783 (mt0) REVERT: G 30 LYS cc_start: 0.8314 (tttt) cc_final: 0.7888 (tttt) REVERT: G 82 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7445 (mmt-90) REVERT: G 137 LEU cc_start: 0.8250 (tp) cc_final: 0.7968 (tt) REVERT: G 143 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7672 (mtp85) REVERT: G 160 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7315 (mp-120) REVERT: G 188 ASN cc_start: 0.7986 (m110) cc_final: 0.7519 (m-40) REVERT: G 217 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7457 (tm-30) REVERT: G 229 SER cc_start: 0.8264 (t) cc_final: 0.8003 (m) REVERT: G 237 ILE cc_start: 0.7835 (mt) cc_final: 0.7550 (mt) REVERT: G 341 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8207 (tp) REVERT: G 344 TYR cc_start: 0.8630 (m-10) cc_final: 0.8272 (m-80) REVERT: G 358 MET cc_start: 0.8041 (mmp) cc_final: 0.7701 (mmp) REVERT: G 385 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7685 (mm-30) REVERT: G 390 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8351 (mtt-85) REVERT: H 11 ARG cc_start: 0.7667 (tpt-90) cc_final: 0.7379 (tpt-90) REVERT: H 42 LEU cc_start: 0.8300 (mt) cc_final: 0.7900 (mt) REVERT: H 69 LEU cc_start: 0.7889 (mt) cc_final: 0.7595 (mm) REVERT: H 70 GLN cc_start: 0.7892 (mp10) cc_final: 0.7216 (mp10) REVERT: H 130 LYS cc_start: 0.8474 (tmmt) cc_final: 0.8070 (ttmt) REVERT: H 131 GLU cc_start: 0.8045 (tp30) cc_final: 0.7601 (tp30) REVERT: H 135 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.7433 (ttm-80) REVERT: H 158 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7451 (tpp-160) REVERT: H 164 VAL cc_start: 0.8658 (p) cc_final: 0.8452 (t) REVERT: H 196 LEU cc_start: 0.8451 (tp) cc_final: 0.8241 (tt) REVERT: H 225 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7455 (tp40) REVERT: H 229 SER cc_start: 0.8525 (m) cc_final: 0.8227 (t) REVERT: H 242 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7420 (t0) REVERT: H 254 THR cc_start: 0.7542 (OUTLIER) cc_final: 0.7228 (m) REVERT: H 328 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7793 (mmt90) REVERT: H 345 LYS cc_start: 0.8258 (ttmt) cc_final: 0.8026 (ttmm) REVERT: H 350 SER cc_start: 0.8420 (t) cc_final: 0.8082 (m) REVERT: H 391 TYR cc_start: 0.8438 (m-10) cc_final: 0.8210 (m-10) REVERT: I 11 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7481 (ttp80) REVERT: I 19 LYS cc_start: 0.7676 (ttmm) cc_final: 0.7382 (ttmm) REVERT: I 33 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7814 (tm-30) REVERT: I 44 LEU cc_start: 0.7288 (tt) cc_final: 0.6471 (mp) REVERT: I 70 GLN cc_start: 0.7520 (mm110) cc_final: 0.7272 (mm110) REVERT: I 99 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7645 (mp10) REVERT: I 127 GLN cc_start: 0.7966 (tp40) cc_final: 0.7705 (tp40) REVERT: I 156 ASN cc_start: 0.8042 (m-40) cc_final: 0.7808 (m-40) REVERT: I 215 GLU cc_start: 0.8293 (tp30) cc_final: 0.8040 (tp30) REVERT: I 219 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7448 (mtm-85) REVERT: I 229 SER cc_start: 0.8418 (t) cc_final: 0.8087 (m) REVERT: I 235 GLU cc_start: 0.8500 (tp30) cc_final: 0.8221 (mm-30) REVERT: I 297 MET cc_start: 0.7703 (tmm) cc_final: 0.7118 (tmm) REVERT: I 306 GLN cc_start: 0.7630 (mm110) cc_final: 0.7397 (mm110) REVERT: I 344 TYR cc_start: 0.8448 (m-10) cc_final: 0.7865 (m-10) REVERT: I 359 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7111 (tm-30) REVERT: J 21 LEU cc_start: 0.8466 (mm) cc_final: 0.8228 (mm) REVERT: J 81 LEU cc_start: 0.8534 (tp) cc_final: 0.8275 (tp) REVERT: J 82 PHE cc_start: 0.8289 (t80) cc_final: 0.7741 (t80) REVERT: J 84 TRP cc_start: 0.6314 (t60) cc_final: 0.6026 (t60) REVERT: J 108 PHE cc_start: 0.7673 (m-10) cc_final: 0.7409 (m-10) REVERT: J 131 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6779 (t80) REVERT: J 146 THR cc_start: 0.8351 (m) cc_final: 0.8147 (t) REVERT: J 184 MET cc_start: 0.8056 (mtm) cc_final: 0.7705 (mtm) REVERT: J 248 LEU cc_start: 0.8616 (tp) cc_final: 0.8121 (tp) REVERT: J 252 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7921 (mm-30) REVERT: J 361 PHE cc_start: 0.7949 (t80) cc_final: 0.7685 (t80) REVERT: J 366 TRP cc_start: 0.7093 (m100) cc_final: 0.6644 (m100) REVERT: J 386 THR cc_start: 0.8674 (m) cc_final: 0.8368 (m) REVERT: J 425 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7547 (tm-30) REVERT: J 434 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: J 464 ILE cc_start: 0.8407 (mt) cc_final: 0.8131 (mm) REVERT: J 466 GLN cc_start: 0.8385 (tp40) cc_final: 0.8148 (tp40) outliers start: 143 outliers final: 114 residues processed: 1121 average time/residue: 0.4575 time to fit residues: 778.8041 Evaluate side-chains 1178 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1055 time to evaluate : 3.027 ------------------------------------------------------------------------------- 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 347 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 255 ASP 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 354 VAL 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 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 106 THR 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 D residue 290 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 222 MET 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 146 ARG Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 294 MET 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 F residue 372 ILE 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 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 205 LYS Chi-restraints excluded: chain G residue 222 SER 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 24 ARG Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 224 LEU 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 248 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 306 GLN 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 231 ASP 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 341 ILE Chi-restraints excluded: chain I residue 364 VAL 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 37 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 131 TYR Chi-restraints excluded: chain J residue 140 LEU 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 403 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 85 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 247 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 342 optimal weight: 1.9990 chunk 304 optimal weight: 0.9980 chunk 354 optimal weight: 0.3980 chunk 0 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 339 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 ASN D 61 GLN G 346 GLN G 397 GLN H 41 GLN I 320 HIS J 129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.129884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113613 restraints weight = 46156.894| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.94 r_work: 0.3279 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29983 Z= 0.184 Angle : 0.579 11.994 40800 Z= 0.304 Chirality : 0.042 0.170 4829 Planarity : 0.005 0.066 5352 Dihedral : 4.224 77.255 4145 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.94 % Allowed : 19.92 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.14), residues: 3821 helix: 3.20 (0.11), residues: 1997 sheet: -0.25 (0.23), residues: 486 loop : -1.16 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 482 HIS 0.024 0.001 HIS I 320 PHE 0.034 0.002 PHE I 288 TYR 0.021 0.001 TYR H 125 ARG 0.013 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08536 ( 1864) hydrogen bonds : angle 4.36845 ( 5454) covalent geometry : bond 0.00392 (29983) covalent geometry : angle 0.57900 (40800) *********************** 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 1184 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 1058 time to evaluate : 3.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8260 (tp40) cc_final: 0.7731 (tm-30) REVERT: A 143 TYR cc_start: 0.8672 (t80) cc_final: 0.8375 (t80) REVERT: A 144 ASN cc_start: 0.8413 (m-40) cc_final: 0.8081 (m110) REVERT: A 171 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7512 (tp-100) REVERT: A 188 ILE cc_start: 0.8494 (mm) cc_final: 0.8248 (mt) REVERT: A 242 PRO cc_start: 0.8352 (Cg_endo) cc_final: 0.8109 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7472 (pt0) cc_final: 0.7208 (pt0) REVERT: A 349 ASN cc_start: 0.8593 (t0) cc_final: 0.8319 (t0) REVERT: A 385 VAL cc_start: 0.8482 (p) cc_final: 0.8220 (m) REVERT: B 50 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 133 LYS cc_start: 0.8408 (mtpp) cc_final: 0.8161 (mtpp) REVERT: B 140 GLN cc_start: 0.8430 (tp40) cc_final: 0.7829 (tp40) REVERT: B 350 ARG cc_start: 0.8891 (ptp-170) cc_final: 0.8680 (ptp-170) REVERT: C 51 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6695 (mt-10) REVERT: C 54 ASP cc_start: 0.8043 (t0) cc_final: 0.7759 (t0) REVERT: C 81 ASP cc_start: 0.8247 (m-30) cc_final: 0.7827 (m-30) REVERT: C 140 GLN cc_start: 0.8323 (tp-100) cc_final: 0.7756 (tp-100) REVERT: C 146 ARG cc_start: 0.8332 (mmt-90) cc_final: 0.8104 (mtt-85) REVERT: C 153 ASN cc_start: 0.8494 (t0) cc_final: 0.8052 (t0) REVERT: C 180 GLN cc_start: 0.8434 (mt0) cc_final: 0.8220 (mt0) REVERT: C 205 GLU cc_start: 0.8027 (tp30) cc_final: 0.7486 (tp30) REVERT: C 229 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8408 (tmm-80) REVERT: C 284 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7951 (mmmt) REVERT: D 103 LYS cc_start: 0.7667 (tttm) cc_final: 0.7420 (tttm) REVERT: D 110 SER cc_start: 0.8643 (t) cc_final: 0.8182 (p) REVERT: D 288 LYS cc_start: 0.8375 (ptpt) cc_final: 0.7964 (ptpt) REVERT: D 324 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7712 (tm-30) REVERT: D 331 GLU cc_start: 0.7781 (mp0) cc_final: 0.7159 (mp0) REVERT: D 349 ASN cc_start: 0.8325 (t0) cc_final: 0.8092 (t0) REVERT: D 368 THR cc_start: 0.8407 (m) cc_final: 0.7862 (t) REVERT: D 371 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7580 (mt-10) REVERT: E 78 ASP cc_start: 0.7849 (m-30) cc_final: 0.7316 (p0) REVERT: E 84 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8047 (mmmm) REVERT: E 102 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7158 (mm-30) REVERT: E 194 GLU cc_start: 0.7573 (mp0) cc_final: 0.7282 (mp0) REVERT: E 217 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: E 266 MET cc_start: 0.8616 (mtt) cc_final: 0.8301 (mtp) REVERT: E 341 THR cc_start: 0.8165 (p) cc_final: 0.7790 (p) REVERT: E 379 LYS cc_start: 0.8154 (tttt) cc_final: 0.7906 (tttt) REVERT: E 382 ASP cc_start: 0.8303 (t0) cc_final: 0.8060 (t0) REVERT: F 87 ASP cc_start: 0.7667 (t0) cc_final: 0.7426 (t0) REVERT: F 140 GLN cc_start: 0.8358 (tp-100) cc_final: 0.8120 (tp-100) REVERT: F 146 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7195 (mtt90) REVERT: F 171 GLN cc_start: 0.8663 (tp40) cc_final: 0.8363 (tp40) REVERT: F 194 GLU cc_start: 0.8154 (mp0) cc_final: 0.7773 (mp0) REVERT: F 327 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7461 (mm110) REVERT: F 328 LYS cc_start: 0.8815 (tttt) cc_final: 0.8525 (tttt) REVERT: G 5 GLN cc_start: 0.8020 (mt0) cc_final: 0.7695 (mt0) REVERT: G 30 LYS cc_start: 0.8322 (tttt) cc_final: 0.7883 (tttt) REVERT: G 137 LEU cc_start: 0.8227 (tp) cc_final: 0.7959 (tt) REVERT: G 160 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7352 (mp-120) REVERT: G 188 ASN cc_start: 0.7989 (m110) cc_final: 0.7519 (m-40) REVERT: G 217 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7361 (tm-30) REVERT: G 229 SER cc_start: 0.8247 (t) cc_final: 0.7985 (m) REVERT: G 237 ILE cc_start: 0.7774 (mt) cc_final: 0.7493 (mt) REVERT: G 248 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7208 (pt) REVERT: G 341 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8132 (tp) REVERT: G 344 TYR cc_start: 0.8627 (m-10) cc_final: 0.8312 (m-80) REVERT: G 358 MET cc_start: 0.8055 (mmp) cc_final: 0.7816 (mmp) REVERT: G 385 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7634 (mt-10) REVERT: G 390 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8381 (mtt-85) REVERT: H 11 ARG cc_start: 0.7647 (tpt-90) cc_final: 0.7348 (tpt-90) REVERT: H 29 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7848 (tm-30) REVERT: H 42 LEU cc_start: 0.8283 (mt) cc_final: 0.7873 (mt) REVERT: H 70 GLN cc_start: 0.7880 (mp10) cc_final: 0.7543 (mp10) REVERT: H 130 LYS cc_start: 0.8438 (tmmt) cc_final: 0.8024 (ttmt) REVERT: H 131 GLU cc_start: 0.8039 (tp30) cc_final: 0.7592 (tp30) REVERT: H 135 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7421 (ttm-80) REVERT: H 158 ARG cc_start: 0.7681 (tpp-160) cc_final: 0.7403 (tpp-160) REVERT: H 164 VAL cc_start: 0.8656 (p) cc_final: 0.8428 (t) REVERT: H 225 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (tp40) REVERT: H 229 SER cc_start: 0.8479 (m) cc_final: 0.8194 (t) REVERT: H 242 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.7409 (t0) REVERT: H 254 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7258 (m) REVERT: H 328 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7761 (mmt90) REVERT: H 350 SER cc_start: 0.8430 (t) cc_final: 0.8067 (m) REVERT: H 359 GLU cc_start: 0.8164 (tp30) cc_final: 0.7667 (tp30) REVERT: H 390 ARG cc_start: 0.8594 (mtt180) cc_final: 0.8330 (mtt180) REVERT: H 391 TYR cc_start: 0.8450 (m-10) cc_final: 0.8173 (m-10) REVERT: I 7 TYR cc_start: 0.8158 (t80) cc_final: 0.7839 (t80) REVERT: I 19 LYS cc_start: 0.7637 (ttmm) cc_final: 0.7326 (ttmm) REVERT: I 33 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7828 (tm-30) REVERT: I 44 LEU cc_start: 0.7264 (tt) cc_final: 0.6496 (mp) REVERT: I 70 GLN cc_start: 0.7520 (mm110) cc_final: 0.7272 (mm110) REVERT: I 127 GLN cc_start: 0.7978 (tp40) cc_final: 0.7708 (tp40) REVERT: I 156 ASN cc_start: 0.7999 (m-40) cc_final: 0.7763 (m-40) REVERT: I 213 LEU cc_start: 0.7982 (tt) cc_final: 0.7705 (mt) REVERT: I 219 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7430 (mtm-85) REVERT: I 229 SER cc_start: 0.8378 (t) cc_final: 0.8061 (m) REVERT: I 235 GLU cc_start: 0.8459 (tp30) cc_final: 0.8166 (mm-30) REVERT: I 297 MET cc_start: 0.7722 (tmm) cc_final: 0.7174 (tmm) REVERT: I 344 TYR cc_start: 0.8456 (m-10) cc_final: 0.7862 (m-10) REVERT: I 359 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7146 (tm-30) REVERT: J 81 LEU cc_start: 0.8503 (tp) cc_final: 0.8224 (tp) REVERT: J 82 PHE cc_start: 0.8251 (t80) cc_final: 0.7713 (t80) REVERT: J 84 TRP cc_start: 0.6356 (t60) cc_final: 0.6058 (t60) REVERT: J 131 TYR cc_start: 0.7051 (OUTLIER) cc_final: 0.6760 (t80) REVERT: J 184 MET cc_start: 0.8005 (mtm) cc_final: 0.7655 (mtm) REVERT: J 186 LEU cc_start: 0.8358 (mt) cc_final: 0.8120 (pp) REVERT: J 248 LEU cc_start: 0.8593 (tp) cc_final: 0.8296 (tt) REVERT: J 366 TRP cc_start: 0.7157 (m100) cc_final: 0.6696 (m100) REVERT: J 425 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7693 (tm-30) REVERT: J 434 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7627 (mt-10) REVERT: J 466 GLN cc_start: 0.8347 (tp40) cc_final: 0.8121 (tp40) REVERT: J 487 ILE cc_start: 0.8164 (mt) cc_final: 0.7920 (mm) outliers start: 126 outliers final: 103 residues processed: 1118 average time/residue: 0.4366 time to fit residues: 740.2031 Evaluate side-chains 1160 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1047 time to evaluate : 3.383 ------------------------------------------------------------------------------- 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 286 THR 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 147 VAL 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 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 276 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 332 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 167 VAL Chi-restraints excluded: chain F residue 192 LYS 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 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 160 GLN Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 204 ASP Chi-restraints excluded: chain G residue 222 SER 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 341 ILE Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 48 TYR Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 224 LEU 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 248 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 258 ASP Chi-restraints excluded: chain H residue 306 GLN 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 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 23 THR 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 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 403 ASN 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 365 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 134 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 351 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN G 397 GLN H 41 GLN I 320 HIS J 129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.112124 restraints weight = 45957.195| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.90 r_work: 0.3280 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29983 Z= 0.199 Angle : 0.600 12.560 40800 Z= 0.315 Chirality : 0.042 0.154 4829 Planarity : 0.005 0.067 5352 Dihedral : 4.238 77.458 4145 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.04 % Allowed : 20.11 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.14), residues: 3821 helix: 3.16 (0.11), residues: 1997 sheet: -0.26 (0.23), residues: 486 loop : -1.16 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 143 HIS 0.018 0.001 HIS I 320 PHE 0.034 0.002 PHE I 288 TYR 0.023 0.001 TYR H 125 ARG 0.014 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08611 ( 1864) hydrogen bonds : angle 4.39209 ( 5454) covalent geometry : bond 0.00430 (29983) covalent geometry : angle 0.60020 (40800) *********************** 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 1182 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 1053 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8279 (tp40) cc_final: 0.7785 (tm-30) REVERT: A 143 TYR cc_start: 0.8668 (t80) cc_final: 0.8368 (t80) REVERT: A 144 ASN cc_start: 0.8407 (m-40) cc_final: 0.8197 (m110) REVERT: A 171 GLN cc_start: 0.7850 (tp-100) cc_final: 0.7500 (tp-100) REVERT: A 188 ILE cc_start: 0.8505 (mm) cc_final: 0.8259 (mt) REVERT: A 242 PRO cc_start: 0.8356 (Cg_endo) cc_final: 0.8109 (Cg_exo) REVERT: A 260 GLU cc_start: 0.7484 (pt0) cc_final: 0.6951 (pt0) REVERT: A 349 ASN cc_start: 0.8608 (t0) cc_final: 0.8337 (t0) REVERT: A 355 LEU cc_start: 0.6733 (OUTLIER) cc_final: 0.6512 (mp) REVERT: A 385 VAL cc_start: 0.8478 (p) cc_final: 0.8216 (m) REVERT: A 386 LYS cc_start: 0.8552 (tttt) cc_final: 0.8230 (tttt) REVERT: B 50 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7087 (mm-30) REVERT: B 133 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8166 (mtpp) REVERT: B 140 GLN cc_start: 0.8419 (tp40) cc_final: 0.7817 (tp40) REVERT: B 277 ASP cc_start: 0.7373 (p0) cc_final: 0.7049 (p0) REVERT: B 350 ARG cc_start: 0.8894 (ptp-170) cc_final: 0.8684 (ptp-170) REVERT: C 51 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6695 (mt-10) REVERT: C 54 ASP cc_start: 0.8043 (t0) cc_final: 0.7758 (t0) REVERT: C 81 ASP cc_start: 0.8253 (m-30) cc_final: 0.7816 (m-30) REVERT: C 140 GLN cc_start: 0.8322 (tp-100) cc_final: 0.7764 (tp-100) REVERT: C 146 ARG cc_start: 0.8344 (mmt-90) cc_final: 0.8127 (mtt-85) REVERT: C 153 ASN cc_start: 0.8497 (t0) cc_final: 0.8031 (t0) REVERT: C 180 GLN cc_start: 0.8436 (mt0) cc_final: 0.8224 (mt0) REVERT: C 205 GLU cc_start: 0.8004 (tp30) cc_final: 0.7468 (tp30) REVERT: C 229 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8412 (tmm-80) REVERT: C 284 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7940 (mmmt) REVERT: D 103 LYS cc_start: 0.7588 (tttm) cc_final: 0.7339 (tttm) REVERT: D 110 SER cc_start: 0.8635 (t) cc_final: 0.8174 (p) REVERT: D 288 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7944 (ptpt) REVERT: D 324 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7717 (tm-30) REVERT: D 328 LYS cc_start: 0.8365 (tttp) cc_final: 0.8165 (tttp) REVERT: D 331 GLU cc_start: 0.7750 (mp0) cc_final: 0.7153 (mp0) REVERT: D 349 ASN cc_start: 0.8323 (t0) cc_final: 0.8103 (t0) REVERT: D 368 THR cc_start: 0.8414 (m) cc_final: 0.7863 (t) REVERT: D 371 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7561 (mt-10) REVERT: E 78 ASP cc_start: 0.7844 (m-30) cc_final: 0.7603 (m-30) REVERT: E 84 LYS cc_start: 0.8402 (mmmm) cc_final: 0.8057 (mmmm) REVERT: E 102 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7144 (mm-30) REVERT: E 194 GLU cc_start: 0.7567 (mp0) cc_final: 0.7272 (mp0) REVERT: E 217 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7617 (mtm-85) REVERT: E 266 MET cc_start: 0.8605 (mtt) cc_final: 0.8292 (mtp) REVERT: E 341 THR cc_start: 0.8197 (p) cc_final: 0.7882 (p) REVERT: E 379 LYS cc_start: 0.8136 (tttt) cc_final: 0.7878 (tttt) REVERT: E 382 ASP cc_start: 0.8317 (t0) cc_final: 0.8084 (t0) REVERT: F 87 ASP cc_start: 0.7652 (t0) cc_final: 0.7412 (t0) REVERT: F 140 GLN cc_start: 0.8355 (tp-100) cc_final: 0.8113 (tp-100) REVERT: F 146 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7203 (mtt90) REVERT: F 171 GLN cc_start: 0.8668 (tp40) cc_final: 0.8366 (tp40) REVERT: F 194 GLU cc_start: 0.8157 (mp0) cc_final: 0.7773 (mp0) REVERT: F 327 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7433 (mm110) REVERT: F 328 LYS cc_start: 0.8832 (tttt) cc_final: 0.8531 (tttt) REVERT: G 5 GLN cc_start: 0.7997 (mt0) cc_final: 0.7663 (mt0) REVERT: G 30 LYS cc_start: 0.8294 (tttt) cc_final: 0.7860 (tttt) REVERT: G 82 ARG cc_start: 0.7860 (mmt-90) cc_final: 0.7493 (mmt-90) REVERT: G 137 LEU cc_start: 0.8236 (tp) cc_final: 0.7967 (tt) REVERT: G 143 ARG cc_start: 0.8119 (mtp85) cc_final: 0.7612 (mtp85) REVERT: G 160 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7336 (mp-120) REVERT: G 188 ASN cc_start: 0.7994 (m110) cc_final: 0.7508 (m-40) REVERT: G 217 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7370 (tm-30) REVERT: G 229 SER cc_start: 0.8227 (t) cc_final: 0.7964 (m) REVERT: G 237 ILE cc_start: 0.7772 (mt) cc_final: 0.7487 (mt) REVERT: G 248 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7205 (pt) REVERT: G 288 PHE cc_start: 0.7628 (t80) cc_final: 0.7192 (t80) REVERT: G 341 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8131 (tp) REVERT: G 344 TYR cc_start: 0.8612 (m-10) cc_final: 0.8216 (m-80) REVERT: G 385 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7514 (mm-30) REVERT: G 390 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8375 (mtt-85) REVERT: H 11 ARG cc_start: 0.7637 (tpt-90) cc_final: 0.7343 (tpt-90) REVERT: H 29 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 30 LYS cc_start: 0.8831 (tppp) cc_final: 0.8360 (tptm) REVERT: H 42 LEU cc_start: 0.8253 (mt) cc_final: 0.7852 (mt) REVERT: H 70 GLN cc_start: 0.7881 (mp10) cc_final: 0.7549 (mp10) REVERT: H 130 LYS cc_start: 0.8428 (tmmt) cc_final: 0.8013 (ttmt) REVERT: H 131 GLU cc_start: 0.8036 (tp30) cc_final: 0.7576 (tp30) REVERT: H 135 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7417 (ttm-80) REVERT: H 158 ARG cc_start: 0.7652 (tpp-160) cc_final: 0.7378 (tpp-160) REVERT: H 164 VAL cc_start: 0.8637 (p) cc_final: 0.8434 (t) REVERT: H 175 LEU cc_start: 0.8395 (tp) cc_final: 0.8188 (tt) REVERT: H 225 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7424 (tp40) REVERT: H 227 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7408 (ttm-80) REVERT: H 229 SER cc_start: 0.8453 (m) cc_final: 0.8165 (t) REVERT: H 242 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7406 (t0) REVERT: H 254 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7238 (m) REVERT: H 328 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7721 (mmt90) REVERT: H 350 SER cc_start: 0.8477 (t) cc_final: 0.8115 (m) REVERT: H 359 GLU cc_start: 0.8127 (tp30) cc_final: 0.7660 (tp30) REVERT: H 390 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8326 (mtt180) REVERT: H 391 TYR cc_start: 0.8440 (m-10) cc_final: 0.8162 (m-10) REVERT: H 393 TYR cc_start: 0.8708 (t80) cc_final: 0.8485 (t80) REVERT: I 7 TYR cc_start: 0.8172 (t80) cc_final: 0.7843 (t80) REVERT: I 19 LYS cc_start: 0.7642 (ttmm) cc_final: 0.7313 (ttmm) REVERT: I 44 LEU cc_start: 0.7259 (tt) cc_final: 0.6529 (mp) REVERT: I 70 GLN cc_start: 0.7516 (mm110) cc_final: 0.7263 (mm110) REVERT: I 127 GLN cc_start: 0.7984 (tp40) cc_final: 0.7708 (tp40) REVERT: I 156 ASN cc_start: 0.7996 (m-40) cc_final: 0.7763 (m-40) REVERT: I 191 PRO cc_start: 0.8267 (Cg_endo) cc_final: 0.8047 (Cg_exo) REVERT: I 213 LEU cc_start: 0.7980 (tt) cc_final: 0.7690 (mt) REVERT: I 215 GLU cc_start: 0.8316 (tp30) cc_final: 0.7786 (tm-30) REVERT: I 219 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7406 (mtm-85) REVERT: I 229 SER cc_start: 0.8392 (t) cc_final: 0.8058 (m) REVERT: I 235 GLU cc_start: 0.8449 (tp30) cc_final: 0.8158 (mm-30) REVERT: I 297 MET cc_start: 0.7723 (tmm) cc_final: 0.7285 (tmm) REVERT: I 344 TYR cc_start: 0.8453 (m-10) cc_final: 0.7858 (m-10) REVERT: I 359 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7140 (tm-30) REVERT: J 81 LEU cc_start: 0.8498 (tp) cc_final: 0.8224 (tp) REVERT: J 82 PHE cc_start: 0.8251 (t80) cc_final: 0.7706 (t80) REVERT: J 84 TRP cc_start: 0.6330 (t60) cc_final: 0.6031 (t60) REVERT: J 131 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.6779 (t80) REVERT: J 146 THR cc_start: 0.8274 (t) cc_final: 0.7968 (p) REVERT: J 184 MET cc_start: 0.8050 (mtm) cc_final: 0.7690 (mtm) REVERT: J 186 LEU cc_start: 0.8342 (mt) cc_final: 0.8102 (pp) REVERT: J 248 LEU cc_start: 0.8532 (tp) cc_final: 0.8329 (tp) REVERT: J 366 TRP cc_start: 0.7155 (m100) cc_final: 0.6692 (m100) REVERT: J 386 THR cc_start: 0.8693 (m) cc_final: 0.8444 (m) REVERT: J 425 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7662 (tm-30) REVERT: J 434 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7632 (mt-10) REVERT: J 466 GLN cc_start: 0.8375 (tp40) cc_final: 0.8141 (tp40) REVERT: J 487 ILE cc_start: 0.8196 (mt) cc_final: 0.7979 (mm) outliers start: 129 outliers final: 108 residues processed: 1116 average time/residue: 0.4507 time to fit residues: 764.8159 Evaluate side-chains 1167 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 1048 time to evaluate : 3.202 ------------------------------------------------------------------------------- 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 286 THR 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 62 ILE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 255 ASP 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 321 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 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 276 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 332 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 167 VAL Chi-restraints excluded: chain F residue 192 LYS 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 F residue 372 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 100 THR 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 222 SER 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 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 217 GLU Chi-restraints excluded: chain H residue 224 LEU 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 248 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 306 GLN 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 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 39 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 131 TYR 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 403 ASN 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 283 optimal weight: 0.8980 chunk 342 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 329 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 230 optimal weight: 0.0570 chunk 312 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN G 397 GLN H 41 GLN H 210 ASN I 320 HIS I 346 GLN J 129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114312 restraints weight = 46021.087| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.94 r_work: 0.3289 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29983 Z= 0.173 Angle : 0.589 12.973 40800 Z= 0.308 Chirality : 0.041 0.159 4829 Planarity : 0.005 0.061 5352 Dihedral : 4.156 77.901 4145 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.66 % Allowed : 20.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.14), residues: 3821 helix: 3.26 (0.11), residues: 1998 sheet: -0.21 (0.24), residues: 486 loop : -1.12 (0.16), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 143 HIS 0.030 0.001 HIS I 320 PHE 0.033 0.001 PHE I 288 TYR 0.023 0.001 TYR H 125 ARG 0.014 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08195 ( 1864) hydrogen bonds : angle 4.30408 ( 5454) covalent geometry : bond 0.00360 (29983) covalent geometry : angle 0.58889 (40800) ********************** 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 1172 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1055 time to evaluate : 3.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 GLN cc_start: 0.8275 (tp40) cc_final: 0.7747 (tm-30) REVERT: A 143 TYR cc_start: 0.8626 (t80) cc_final: 0.8307 (t80) REVERT: A 144 ASN cc_start: 0.8381 (m-40) cc_final: 0.7985 (m110) REVERT: A 171 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7468 (tp-100) REVERT: A 188 ILE cc_start: 0.8500 (mm) cc_final: 0.8249 (mt) REVERT: A 242 PRO cc_start: 0.8358 (Cg_endo) cc_final: 0.8115 (Cg_exo) REVERT: A 259 LYS cc_start: 0.8266 (mtmm) cc_final: 0.8046 (mtmm) REVERT: A 260 GLU cc_start: 0.7478 (pt0) cc_final: 0.6951 (pt0) REVERT: A 349 ASN cc_start: 0.8602 (t0) cc_final: 0.8337 (t0) REVERT: A 355 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6470 (mp) REVERT: A 385 VAL cc_start: 0.8486 (p) cc_final: 0.8219 (m) REVERT: A 386 LYS cc_start: 0.8547 (tttt) cc_final: 0.8220 (tttt) REVERT: B 50 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7119 (mm-30) REVERT: B 133 LYS cc_start: 0.8401 (mtpp) cc_final: 0.8159 (mtpp) REVERT: B 140 GLN cc_start: 0.8407 (tp40) cc_final: 0.7811 (tp40) REVERT: B 277 ASP cc_start: 0.7401 (p0) cc_final: 0.7077 (p0) REVERT: B 350 ARG cc_start: 0.8906 (ptp-170) cc_final: 0.8657 (ptp-170) REVERT: C 51 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6716 (mt-10) REVERT: C 54 ASP cc_start: 0.8022 (t0) cc_final: 0.7750 (t0) REVERT: C 81 ASP cc_start: 0.8263 (m-30) cc_final: 0.7304 (m-30) REVERT: C 140 GLN cc_start: 0.8292 (tp-100) cc_final: 0.7725 (tp-100) REVERT: C 146 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.8072 (mtt-85) REVERT: C 180 GLN cc_start: 0.8439 (mt0) cc_final: 0.8224 (mt0) REVERT: C 205 GLU cc_start: 0.8024 (tp30) cc_final: 0.7487 (tp30) REVERT: C 229 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8393 (tmm-80) REVERT: C 284 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7956 (mmmt) REVERT: C 371 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7542 (mt-10) REVERT: D 103 LYS cc_start: 0.7523 (tttm) cc_final: 0.7276 (tttm) REVERT: D 110 SER cc_start: 0.8625 (t) cc_final: 0.8170 (p) REVERT: D 288 LYS cc_start: 0.8366 (ptpt) cc_final: 0.7955 (ptpt) REVERT: D 324 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7731 (tm-30) REVERT: D 328 LYS cc_start: 0.8340 (tttp) cc_final: 0.8136 (tttp) REVERT: D 331 GLU cc_start: 0.7724 (mp0) cc_final: 0.7139 (mp0) REVERT: D 349 ASN cc_start: 0.8310 (t0) cc_final: 0.8087 (t0) REVERT: D 368 THR cc_start: 0.8373 (m) cc_final: 0.7846 (t) REVERT: D 371 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7583 (mt-10) REVERT: E 84 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8058 (mmmm) REVERT: E 102 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7099 (mm-30) REVERT: E 143 TYR cc_start: 0.8716 (t80) cc_final: 0.8467 (t80) REVERT: E 194 GLU cc_start: 0.7576 (mp0) cc_final: 0.7276 (mp0) REVERT: E 217 ARG cc_start: 0.7955 (mtm-85) cc_final: 0.7615 (mtm-85) REVERT: E 266 MET cc_start: 0.8605 (mtt) cc_final: 0.8292 (mtp) REVERT: E 341 THR cc_start: 0.8177 (p) cc_final: 0.7860 (p) REVERT: E 379 LYS cc_start: 0.8135 (tttt) cc_final: 0.7877 (tttt) REVERT: E 382 ASP cc_start: 0.8302 (t0) cc_final: 0.8086 (t0) REVERT: F 87 ASP cc_start: 0.7646 (t0) cc_final: 0.7411 (t0) REVERT: F 140 GLN cc_start: 0.8351 (tp-100) cc_final: 0.8108 (tp-100) REVERT: F 171 GLN cc_start: 0.8651 (tp40) cc_final: 0.8342 (tp40) REVERT: F 194 GLU cc_start: 0.8155 (mp0) cc_final: 0.7771 (mp0) REVERT: F 327 GLN cc_start: 0.7680 (mm-40) cc_final: 0.7407 (mm110) REVERT: F 328 LYS cc_start: 0.8803 (tttt) cc_final: 0.8502 (tttt) REVERT: G 5 GLN cc_start: 0.8020 (mt0) cc_final: 0.7670 (mt0) REVERT: G 30 LYS cc_start: 0.8308 (tttt) cc_final: 0.7890 (tttt) REVERT: G 82 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7498 (mmt-90) REVERT: G 156 ASN cc_start: 0.7823 (t0) cc_final: 0.7490 (t0) REVERT: G 160 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7271 (mp-120) REVERT: G 183 ARG cc_start: 0.7296 (tmt170) cc_final: 0.6938 (tmt-80) REVERT: G 188 ASN cc_start: 0.8001 (m110) cc_final: 0.7503 (m-40) REVERT: G 217 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7370 (tm-30) REVERT: G 229 SER cc_start: 0.8221 (t) cc_final: 0.7955 (m) REVERT: G 237 ILE cc_start: 0.7729 (mt) cc_final: 0.7454 (mt) REVERT: G 248 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7201 (pt) REVERT: G 288 PHE cc_start: 0.7636 (t80) cc_final: 0.7052 (t80) REVERT: G 344 TYR cc_start: 0.8608 (m-10) cc_final: 0.8216 (m-80) REVERT: G 385 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7524 (mm-30) REVERT: G 390 ARG cc_start: 0.8628 (mtt90) cc_final: 0.8407 (mtt-85) REVERT: H 5 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7265 (mt0) REVERT: H 11 ARG cc_start: 0.7634 (tpt-90) cc_final: 0.7346 (tpt-90) REVERT: H 29 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7912 (tm-30) REVERT: H 30 LYS cc_start: 0.8833 (tppp) cc_final: 0.8359 (tptm) REVERT: H 42 LEU cc_start: 0.8230 (mt) cc_final: 0.7829 (mt) REVERT: H 70 GLN cc_start: 0.7873 (mp10) cc_final: 0.7574 (mp10) REVERT: H 130 LYS cc_start: 0.8433 (tmmt) cc_final: 0.8010 (ttmt) REVERT: H 131 GLU cc_start: 0.8035 (tp30) cc_final: 0.7559 (tp30) REVERT: H 135 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7427 (ttm-80) REVERT: H 158 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7380 (tpp-160) REVERT: H 164 VAL cc_start: 0.8640 (p) cc_final: 0.8423 (t) REVERT: H 175 LEU cc_start: 0.8468 (tp) cc_final: 0.8267 (tt) REVERT: H 225 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7400 (tp40) REVERT: H 227 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7409 (ttm-80) REVERT: H 229 SER cc_start: 0.8459 (m) cc_final: 0.8179 (t) REVERT: H 242 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7400 (t0) REVERT: H 254 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7206 (m) REVERT: H 328 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7832 (mmt90) REVERT: H 350 SER cc_start: 0.8466 (t) cc_final: 0.8135 (m) REVERT: H 359 GLU cc_start: 0.8119 (tp30) cc_final: 0.7687 (tp30) REVERT: H 390 ARG cc_start: 0.8582 (mtt180) cc_final: 0.8329 (mtt180) REVERT: H 391 TYR cc_start: 0.8436 (m-10) cc_final: 0.8174 (m-10) REVERT: H 393 TYR cc_start: 0.8707 (t80) cc_final: 0.8475 (t80) REVERT: I 7 TYR cc_start: 0.8125 (t80) cc_final: 0.7814 (t80) REVERT: I 19 LYS cc_start: 0.7623 (ttmm) cc_final: 0.7311 (ttmm) REVERT: I 44 LEU cc_start: 0.7293 (tt) cc_final: 0.6520 (mp) REVERT: I 70 GLN cc_start: 0.7506 (mm110) cc_final: 0.7252 (mm110) REVERT: I 127 GLN cc_start: 0.7987 (tp40) cc_final: 0.7714 (tp40) REVERT: I 156 ASN cc_start: 0.7975 (m-40) cc_final: 0.7736 (m-40) REVERT: I 204 ASP cc_start: 0.6606 (t70) cc_final: 0.6278 (t0) REVERT: I 213 LEU cc_start: 0.7982 (tt) cc_final: 0.7677 (mt) REVERT: I 215 GLU cc_start: 0.8285 (tp30) cc_final: 0.7765 (tm-30) REVERT: I 219 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7415 (mtm-85) REVERT: I 229 SER cc_start: 0.8382 (t) cc_final: 0.8056 (m) REVERT: I 235 GLU cc_start: 0.8426 (tp30) cc_final: 0.8134 (mm-30) REVERT: I 297 MET cc_start: 0.7712 (tmm) cc_final: 0.7227 (tmm) REVERT: I 344 TYR cc_start: 0.8456 (m-10) cc_final: 0.7850 (m-10) REVERT: I 359 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7174 (tm-30) REVERT: J 81 LEU cc_start: 0.8480 (tp) cc_final: 0.8200 (tp) REVERT: J 82 PHE cc_start: 0.8251 (t80) cc_final: 0.7741 (t80) REVERT: J 84 TRP cc_start: 0.6328 (t60) cc_final: 0.6028 (t60) REVERT: J 131 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.6781 (t80) REVERT: J 146 THR cc_start: 0.8129 (t) cc_final: 0.7876 (p) REVERT: J 184 MET cc_start: 0.7990 (mtm) cc_final: 0.7617 (mtm) REVERT: J 186 LEU cc_start: 0.8334 (mt) cc_final: 0.8085 (pp) REVERT: J 242 VAL cc_start: 0.8491 (m) cc_final: 0.8175 (p) REVERT: J 366 TRP cc_start: 0.7126 (m100) cc_final: 0.6666 (m100) REVERT: J 382 LEU cc_start: 0.8557 (tp) cc_final: 0.8278 (mt) REVERT: J 383 THR cc_start: 0.8064 (m) cc_final: 0.7604 (p) REVERT: J 386 THR cc_start: 0.8690 (m) cc_final: 0.8461 (m) REVERT: J 425 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7721 (tm-30) REVERT: J 434 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7609 (mt-10) REVERT: J 466 GLN cc_start: 0.8342 (tp40) cc_final: 0.8119 (tp40) REVERT: J 487 ILE cc_start: 0.8196 (mt) cc_final: 0.7979 (mm) outliers start: 117 outliers final: 99 residues processed: 1111 average time/residue: 0.4456 time to fit residues: 754.1888 Evaluate side-chains 1156 residues out of total 3197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1047 time to evaluate : 2.977 ------------------------------------------------------------------------------- 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 286 THR 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 123 LYS Chi-restraints excluded: chain B residue 138 LYS Chi-restraints excluded: chain B residue 147 VAL 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 321 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 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 276 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 192 LYS 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 F residue 372 ILE Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 100 THR 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 222 SER 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 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 217 GLU Chi-restraints excluded: chain H residue 224 LEU 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 248 LEU Chi-restraints excluded: chain H residue 254 THR Chi-restraints excluded: chain H residue 306 GLN 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 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 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 39 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 131 TYR 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 359 MET Chi-restraints excluded: chain J residue 393 GLU Chi-restraints excluded: chain J residue 403 ASN 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 277 optimal weight: 0.9990 chunk 284 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 272 optimal weight: 0.0970 chunk 368 optimal weight: 0.8980 chunk 275 optimal weight: 2.9990 chunk 3 optimal weight: 0.4980 chunk 349 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN H 41 GLN ** I 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 HIS I 346 GLN J 129 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.113454 restraints weight = 46168.756| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.91 r_work: 0.3294 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 29983 Z= 0.171 Angle : 0.591 12.894 40800 Z= 0.308 Chirality : 0.041 0.164 4829 Planarity : 0.005 0.059 5352 Dihedral : 4.127 78.256 4145 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.57 % Allowed : 20.99 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.14), residues: 3821 helix: 3.28 (0.11), residues: 1996 sheet: -0.19 (0.24), residues: 486 loop : -1.11 (0.16), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 210 HIS 0.016 0.001 HIS I 320 PHE 0.033 0.001 PHE I 288 TYR 0.025 0.001 TYR H 125 ARG 0.013 0.001 ARG H 227 Details of bonding type rmsd hydrogen bonds : bond 0.08086 ( 1864) hydrogen bonds : angle 4.27821 ( 5454) covalent geometry : bond 0.00357 (29983) covalent geometry : angle 0.59112 (40800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19293.34 seconds wall clock time: 332 minutes 54.84 seconds (19974.84 seconds total)