Starting phenix.real_space_refine on Fri Jun 20 13:31:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uto_42544/06_2025/8uto_42544.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uto_42544/06_2025/8uto_42544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uto_42544/06_2025/8uto_42544.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uto_42544/06_2025/8uto_42544.map" model { file = "/net/cci-nas-00/data/ceres_data/8uto_42544/06_2025/8uto_42544.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uto_42544/06_2025/8uto_42544.cif" } resolution = 3.2 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 4 5.21 5 S 153 5.16 5 C 14863 2.51 5 N 4070 2.21 5 O 4683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23792 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 3038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3038 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 13, 'TRANS': 372} Chain: "N" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3055 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 13, 'TRANS': 375} Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Conformer: "B" Number of residues, atoms: 432, 3398 Classifications: {'peptide': 432} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} bond proxies already assigned to first conformer: 3444 Chain: "E" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "I" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} Conformer: "B" Number of residues, atoms: 433, 3407 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 412} bond proxies already assigned to first conformer: 3444 Chain: "S" Number of atoms: 3524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3524 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 20, 'TRANS': 430} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" N ATHR B 429 " occ=0.45 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.55 residue: pdb=" N AALA B 430 " occ=0.45 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.55 residue: pdb=" N AASP B 431 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.55 residue: pdb=" N AGLU B 432 " occ=0.45 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.55 residue: pdb=" N ATHR I 429 " occ=0.54 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.46 residue: pdb=" N AALA I 430 " occ=0.54 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.46 residue: pdb=" N AASP I 431 " occ=0.54 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.46 residue: pdb=" N AGLU I 432 " occ=0.54 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.46 residue: pdb=" N AGLN I 433 " occ=0.54 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.46 Time building chain proxies: 18.63, per 1000 atoms: 0.78 Number of scatterers: 23792 At special positions: 0 Unit cell: (81.024, 113.096, 241.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 153 16.00 P 19 15.00 Mg 4 11.99 O 4683 8.00 N 4070 7.00 C 14863 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: 6.56 Conformation dependent library (CDL) restraints added in 4.4 seconds 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5554 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 24 sheets defined 49.5% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 Creating SS restraints... Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 69 through 77 Processing helix chain 'K' and resid 77 through 87 Processing helix chain 'K' and resid 102 through 108 Processing helix chain 'K' and resid 117 through 133 Processing helix chain 'K' and resid 188 through 203 Processing helix chain 'K' and resid 254 through 259 Processing helix chain 'K' and resid 262 through 295 removed outlier: 3.761A pdb=" N LEU K 278 " --> pdb=" O SER K 274 " (cutoff:3.500A) Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.742A pdb=" N ASP K 308 " --> pdb=" O PRO K 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 309 through 315 Processing helix chain 'K' and resid 315 through 320 removed outlier: 3.598A pdb=" N GLY K 320 " --> pdb=" O ARG K 316 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 352 removed outlier: 4.310A pdb=" N SER K 343 " --> pdb=" O ASP K 339 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR K 344 " --> pdb=" O GLU K 340 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS K 352 " --> pdb=" O ALA K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 363 through 386 Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 69 through 77 Processing helix chain 'N' and resid 77 through 88 removed outlier: 3.602A pdb=" N GLY N 88 " --> pdb=" O HIS N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 109 removed outlier: 4.050A pdb=" N THR N 106 " --> pdb=" O GLY N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 117 through 132 removed outlier: 3.832A pdb=" N GLN N 121 " --> pdb=" O GLY N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 201 Processing helix chain 'N' and resid 262 through 296 Proline residue: N 292 - end of helix Processing helix chain 'N' and resid 305 through 308 removed outlier: 3.765A pdb=" N ASP N 308 " --> pdb=" O PRO N 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 309 through 315 Processing helix chain 'N' and resid 315 through 320 Processing helix chain 'N' and resid 337 through 349 removed outlier: 3.511A pdb=" N SER N 343 " --> pdb=" O ASP N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 386 Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 43 removed outlier: 4.286A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.811A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.117A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.569A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 223 through 240 removed outlier: 3.752A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 251 through 258 removed outlier: 3.568A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 4.256A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.088A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.671A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.578A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.063A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.960A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 4.254A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 44 removed outlier: 3.714A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 40 through 44' Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.603A pdb=" N MET B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 126 removed outlier: 3.865A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.589A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.703A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.835A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.323A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.153A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.845A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 426 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 4.101A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.578A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.578A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.236A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.593A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 206 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.794A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 243 No H-bonds generated for 'chain 'E' and resid 241 through 243' Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.808A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.065A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.857A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.608A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 4.067A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.172A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.955A pdb=" N ALA E 421 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG E 422 " --> pdb=" O PHE E 418 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 436 " --> pdb=" O TYR E 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 29 Processing helix chain 'I' and resid 40 through 44 removed outlier: 3.651A pdb=" N GLN I 43 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 40 through 44' Processing helix chain 'I' and resid 46 through 49 Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.505A pdb=" N PHE I 85 " --> pdb=" O GLY I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 88 No H-bonds generated for 'chain 'I' and resid 86 through 88' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 108 through 126 removed outlier: 3.771A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 removed outlier: 3.501A pdb=" N GLY I 146 " --> pdb=" O GLY I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.549A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR I 196 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.536A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.590A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 241 Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 282 removed outlier: 4.142A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG I 282 " --> pdb=" O GLN I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.730A pdb=" N MET I 299 " --> pdb=" O SER I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 Processing helix chain 'I' and resid 322 through 337 Processing helix chain 'I' and resid 338 through 341 removed outlier: 3.751A pdb=" N PHE I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 338 through 341' Processing helix chain 'I' and resid 373 through 390 removed outlier: 4.263A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 400 Processing helix chain 'I' and resid 404 through 425 removed outlier: 4.073A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR I 409 " --> pdb=" O GLU I 405 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TYR I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 4.053A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.408A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 129 Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.051A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 197 removed outlier: 4.555A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 217 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.809A pdb=" N LEU S 227 " --> pdb=" O THR S 223 " (cutoff:3.500A) Processing helix chain 'S' and resid 241 through 243 No H-bonds generated for 'chain 'S' and resid 241 through 243' Processing helix chain 'S' and resid 251 through 260 removed outlier: 3.779A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.054A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.712A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU S 297 " --> pdb=" O ASN S 293 " (cutoff:3.500A) Processing helix chain 'S' and resid 298 through 301 Processing helix chain 'S' and resid 306 through 310 Processing helix chain 'S' and resid 324 through 337 removed outlier: 3.712A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 3.939A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 removed outlier: 4.113A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU S 411 " --> pdb=" O TRP S 407 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.362A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY S 436 " --> pdb=" O TYR S 432 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 Processing sheet with id=AA3, first strand: chain 'K' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.163A pdb=" N ARG K 167 " --> pdb=" O GLU K 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 205 through 206 Processing sheet with id=AA6, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.563A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 54 through 57 removed outlier: 8.563A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS N 92 " --> pdb=" O ALA N 326 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL N 328 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE N 94 " --> pdb=" O VAL N 328 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA N 330 " --> pdb=" O PHE N 94 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR N 96 " --> pdb=" O ALA N 330 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL N 91 " --> pdb=" O SER N 245 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VAL N 247 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE N 93 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N THR N 238 " --> pdb=" O ARG N 229 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG N 229 " --> pdb=" O THR N 238 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS N 240 " --> pdb=" O GLN N 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 28 through 31 Processing sheet with id=AA9, first strand: chain 'N' and resid 168 through 171 Processing sheet with id=AB1, first strand: chain 'N' and resid 205 through 206 Processing sheet with id=AB2, first strand: chain 'A' and resid 65 through 68 removed outlier: 7.597A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.172A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.722A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N SER E 140 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 8.861A pdb=" N VAL E 9 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 272 Processing sheet with id=AC1, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.150A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.150A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER I 168 " --> pdb=" O ILE I 202 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC4, first strand: chain 'S' and resid 65 through 68 removed outlier: 8.562A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLU S 3 " --> pdb=" O GLY S 134 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N LEU S 136 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE S 5 " --> pdb=" O LEU S 136 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE S 138 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE S 7 " --> pdb=" O PHE S 138 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'S' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'S' and resid 269 through 272 1173 hydrogen bonds defined for protein. 3357 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: 9.84 Time building geometry restraints manager: 7.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4214 1.32 - 1.45: 6333 1.45 - 1.57: 13458 1.57 - 1.69: 43 1.69 - 1.82: 244 Bond restraints: 24292 Sorted by residual: bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" O5' ANP K 502 " pdb=" PA ANP K 502 " ideal model delta sigma weight residual 1.655 1.578 0.077 2.00e-02 2.50e+03 1.50e+01 ... (remaining 24287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 32610 3.45 - 6.91: 346 6.91 - 10.36: 13 10.36 - 13.82: 3 13.82 - 17.27: 2 Bond angle restraints: 32974 Sorted by residual: angle pdb=" N GLU E 417 " pdb=" CA GLU E 417 " pdb=" C GLU E 417 " ideal model delta sigma weight residual 113.20 104.86 8.34 1.21e+00 6.83e-01 4.76e+01 angle pdb=" PB ANP N 501 " pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 126.95 109.68 17.27 3.00e+00 1.11e-01 3.32e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 111.09 15.86 3.00e+00 1.11e-01 2.79e+01 angle pdb=" N TYR A 432 " pdb=" CA TYR A 432 " pdb=" C TYR A 432 " ideal model delta sigma weight residual 112.97 108.19 4.78 1.06e+00 8.90e-01 2.04e+01 angle pdb=" N ILE S 114 " pdb=" CA ILE S 114 " pdb=" C ILE S 114 " ideal model delta sigma weight residual 113.71 109.62 4.09 9.50e-01 1.11e+00 1.86e+01 ... (remaining 32969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.96: 14109 31.96 - 63.93: 533 63.93 - 95.89: 86 95.89 - 127.85: 15 127.85 - 159.82: 21 Dihedral angle restraints: 14764 sinusoidal: 6106 harmonic: 8658 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -130.91 -159.82 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C4' GTP A 501 " pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 260.87 111.93 148.94 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -39.31 143.90 1 2.00e+01 2.50e-03 4.34e+01 ... (remaining 14761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 3474 0.109 - 0.217: 139 0.217 - 0.326: 3 0.326 - 0.435: 0 0.435 - 0.543: 1 Chirality restraints: 3617 Sorted by residual: chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.62 -0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" C3' ANP N 501 " pdb=" C2' ANP N 501 " pdb=" C4' ANP N 501 " pdb=" O3' ANP N 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' ANP K 502 " pdb=" C2' ANP K 502 " pdb=" C4' ANP K 502 " pdb=" O3' ANP K 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 3614 not shown) Planarity restraints: 4288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 291 " 0.066 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO N 292 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO N 292 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO N 292 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 291 " 0.059 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO K 292 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 46 " -0.055 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO N 47 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO N 47 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO N 47 " -0.046 5.00e-02 4.00e+02 ... (remaining 4285 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 139 2.53 - 3.12: 17880 3.12 - 3.72: 35601 3.72 - 4.31: 49378 4.31 - 4.90: 85619 Nonbonded interactions: 188617 Sorted by model distance: nonbonded pdb="MG MG K 501 " pdb=" O1G ANP K 502 " model vdw 1.940 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.946 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.952 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.954 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 1.955 2.170 ... (remaining 188612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 1 through 440 or resid 501 through 502)) selection = (chain 'S' and (resid 1 through 440 or resid 501 through 502)) } ncs_group { reference = (chain 'B' and (resid 1 through 428 or resid 501 or resid 502)) selection = (chain 'I' and (resid 1 through 428 or resid 501 or resid 502)) } ncs_group { reference = (chain 'K' and resid 4 through 389) selection = (chain 'N' and resid 4 through 389) } 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=0.45 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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.940 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 63.750 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.005 0.147 24292 Z= 0.231 Angle : 0.812 17.275 32974 Z= 0.419 Chirality : 0.047 0.543 3617 Planarity : 0.006 0.100 4288 Dihedral : 18.597 159.819 9210 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.84 % Favored : 95.86 % Rotamer: Outliers : 0.59 % Allowed : 13.78 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.15), residues: 2977 helix: 0.97 (0.15), residues: 1217 sheet: -0.06 (0.22), residues: 538 loop : -1.11 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 21 HIS 0.015 0.001 HIS I 37 PHE 0.022 0.002 PHE E 255 TYR 0.039 0.002 TYR S 24 ARG 0.015 0.001 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.15362 ( 1101) hydrogen bonds : angle 6.08227 ( 3357) covalent geometry : bond 0.00491 (24292) covalent geometry : angle 0.81211 (32974) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 528 time to evaluate : 2.807 Fit side-chains REVERT: K 81 MET cc_start: 0.8227 (mmt) cc_final: 0.7768 (mmt) REVERT: K 189 TYR cc_start: 0.8442 (t80) cc_final: 0.8119 (t80) REVERT: N 66 ASN cc_start: 0.7761 (m-40) cc_final: 0.7376 (m110) REVERT: N 107 MET cc_start: 0.8013 (tmm) cc_final: 0.7364 (tmm) REVERT: N 346 ARG cc_start: 0.9045 (mtt90) cc_final: 0.8840 (mmm-85) REVERT: N 347 TYR cc_start: 0.8232 (t80) cc_final: 0.7841 (t80) REVERT: A 9 VAL cc_start: 0.8996 (t) cc_final: 0.8695 (m) REVERT: A 347 CYS cc_start: 0.9105 (t) cc_final: 0.8863 (t) REVERT: A 423 GLU cc_start: 0.7961 (mp0) cc_final: 0.7344 (mp0) REVERT: E 214 ARG cc_start: 0.8767 (tmm160) cc_final: 0.8465 (tmm-80) REVERT: I 31 ASP cc_start: 0.8546 (t70) cc_final: 0.8131 (t70) REVERT: I 67 ASP cc_start: 0.8314 (t0) cc_final: 0.7978 (t0) REVERT: I 100 ASN cc_start: 0.8788 (t0) cc_final: 0.8522 (t0) REVERT: S 36 MET cc_start: 0.8093 (ttp) cc_final: 0.7763 (ttt) REVERT: S 413 MET cc_start: 0.8108 (mtp) cc_final: 0.7684 (ttp) outliers start: 9 outliers final: 5 residues processed: 533 average time/residue: 0.3658 time to fit residues: 303.5516 Evaluate side-chains 508 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 503 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 217 SER Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain S residue 101 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.9980 chunk 224 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 268 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN N 98 GLN N 270 ASN N 295 ASN A 309 HIS B 99 ASN B 137 HIS B 165 ASN B 195 ASN B 423 GLN E 358 GLN I 37 HIS I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 107 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.126230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.094929 restraints weight = 51752.026| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.96 r_work: 0.3249 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24292 Z= 0.138 Angle : 0.578 11.137 32974 Z= 0.289 Chirality : 0.045 0.362 3617 Planarity : 0.005 0.091 4288 Dihedral : 12.755 153.646 3610 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.00 % Favored : 96.73 % Rotamer: Outliers : 2.19 % Allowed : 13.27 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 2977 helix: 1.57 (0.15), residues: 1226 sheet: 0.19 (0.22), residues: 540 loop : -0.99 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 388 HIS 0.006 0.001 HIS I 37 PHE 0.017 0.001 PHE K 94 TYR 0.023 0.001 TYR N 177 ARG 0.007 0.001 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 1101) hydrogen bonds : angle 4.32529 ( 3357) covalent geometry : bond 0.00313 (24292) covalent geometry : angle 0.57795 (32974) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 526 time to evaluate : 2.558 Fit side-chains REVERT: K 115 GLN cc_start: 0.8325 (pm20) cc_final: 0.7939 (pm20) REVERT: K 189 TYR cc_start: 0.8124 (t80) cc_final: 0.7886 (t80) REVERT: K 318 ASN cc_start: 0.8629 (m-40) cc_final: 0.8329 (m110) REVERT: N 66 ASN cc_start: 0.7767 (m-40) cc_final: 0.7346 (m110) REVERT: N 107 MET cc_start: 0.8075 (tmm) cc_final: 0.7698 (tpp) REVERT: N 116 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6149 (mp10) REVERT: A 9 VAL cc_start: 0.8975 (t) cc_final: 0.8658 (m) REVERT: A 24 TYR cc_start: 0.8591 (m-80) cc_final: 0.8230 (m-80) REVERT: A 423 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7516 (mp0) REVERT: A 430 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7969 (ttpp) REVERT: A 434 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 170 MET cc_start: 0.8317 (ptp) cc_final: 0.7859 (mtt) REVERT: B 347 ASN cc_start: 0.7489 (t0) cc_final: 0.7225 (t0) REVERT: E 154 MET cc_start: 0.8648 (mmt) cc_final: 0.8247 (mmt) REVERT: E 214 ARG cc_start: 0.8783 (tmm160) cc_final: 0.8469 (tmm-80) REVERT: I 31 ASP cc_start: 0.8488 (t70) cc_final: 0.8135 (t70) REVERT: I 67 ASP cc_start: 0.8298 (t0) cc_final: 0.7947 (t0) REVERT: I 318 ARG cc_start: 0.8390 (mtp85) cc_final: 0.8055 (mtp180) REVERT: S 36 MET cc_start: 0.8346 (ttp) cc_final: 0.7852 (ttt) REVERT: S 80 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7912 (p) REVERT: S 112 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8732 (mmtm) REVERT: S 392 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7772 (t0) REVERT: S 397 LEU cc_start: 0.8874 (mt) cc_final: 0.8505 (tt) REVERT: S 413 MET cc_start: 0.8146 (mtp) cc_final: 0.7375 (ttp) REVERT: S 414 GLU cc_start: 0.7017 (pm20) cc_final: 0.6752 (pt0) outliers start: 50 outliers final: 27 residues processed: 546 average time/residue: 0.3490 time to fit residues: 298.8648 Evaluate side-chains 525 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 495 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 270 ASN Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 199 ASP Chi-restraints excluded: chain S residue 265 ILE Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 193 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 231 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 98 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 322 ASN A 285 GLN A 356 ASN B 99 ASN B 204 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN E 128 GLN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.125332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.095375 restraints weight = 36605.879| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.41 r_work: 0.3275 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24292 Z= 0.137 Angle : 0.542 9.015 32974 Z= 0.273 Chirality : 0.044 0.438 3617 Planarity : 0.004 0.086 4288 Dihedral : 10.368 157.504 3607 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.07 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 14.40 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 2977 helix: 1.67 (0.15), residues: 1249 sheet: 0.34 (0.22), residues: 534 loop : -1.04 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 388 HIS 0.004 0.001 HIS E 139 PHE 0.020 0.001 PHE E 255 TYR 0.023 0.001 TYR N 177 ARG 0.004 0.000 ARG E 123 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 1101) hydrogen bonds : angle 4.08836 ( 3357) covalent geometry : bond 0.00317 (24292) covalent geometry : angle 0.54195 (32974) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 534 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 75 ARG cc_start: 0.8849 (mtt180) cc_final: 0.8454 (tpt170) REVERT: K 115 GLN cc_start: 0.8305 (pm20) cc_final: 0.7899 (pm20) REVERT: K 180 ASP cc_start: 0.7495 (t0) cc_final: 0.7227 (t0) REVERT: K 240 LYS cc_start: 0.7756 (mttm) cc_final: 0.7521 (ttmm) REVERT: K 288 MET cc_start: 0.5920 (tpt) cc_final: 0.5648 (tpt) REVERT: K 318 ASN cc_start: 0.8707 (m-40) cc_final: 0.8468 (m110) REVERT: N 66 ASN cc_start: 0.7735 (m-40) cc_final: 0.7304 (m110) REVERT: N 107 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7405 (tmm) REVERT: N 201 LYS cc_start: 0.9048 (tttm) cc_final: 0.8461 (mtmm) REVERT: N 253 GLU cc_start: 0.7852 (pt0) cc_final: 0.7619 (pp20) REVERT: N 270 ASN cc_start: 0.8597 (m-40) cc_final: 0.8345 (m110) REVERT: A 9 VAL cc_start: 0.9051 (t) cc_final: 0.8751 (m) REVERT: A 24 TYR cc_start: 0.8669 (m-80) cc_final: 0.8339 (m-80) REVERT: A 322 ASP cc_start: 0.8909 (t0) cc_final: 0.8693 (t0) REVERT: A 423 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7858 (mt-10) REVERT: A 430 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8163 (ttpp) REVERT: A 434 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8349 (mt-10) REVERT: B 170 MET cc_start: 0.8569 (ptp) cc_final: 0.8144 (mtt) REVERT: B 217 LEU cc_start: 0.8787 (mt) cc_final: 0.8559 (mp) REVERT: B 347 ASN cc_start: 0.7676 (t0) cc_final: 0.7410 (t0) REVERT: E 69 ASP cc_start: 0.8655 (t0) cc_final: 0.8422 (t70) REVERT: I 31 ASP cc_start: 0.8637 (t70) cc_final: 0.8300 (t70) REVERT: I 168 SER cc_start: 0.9171 (p) cc_final: 0.8687 (m) REVERT: I 398 TYR cc_start: 0.8903 (m-80) cc_final: 0.8598 (m-80) REVERT: I 404 ASP cc_start: 0.8455 (p0) cc_final: 0.8199 (p0) REVERT: I 417 ASP cc_start: 0.8426 (m-30) cc_final: 0.8137 (m-30) REVERT: S 36 MET cc_start: 0.8514 (ttp) cc_final: 0.7991 (ttt) REVERT: S 80 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7912 (p) REVERT: S 112 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8698 (mmtm) REVERT: S 392 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7939 (t0) REVERT: S 397 LEU cc_start: 0.8892 (mt) cc_final: 0.8551 (tt) outliers start: 50 outliers final: 33 residues processed: 553 average time/residue: 0.3739 time to fit residues: 320.4922 Evaluate side-chains 532 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 496 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 258 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 251 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 ASN A 192 HIS A 285 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 204 ASN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 301 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.121698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092112 restraints weight = 38819.539| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.40 r_work: 0.3236 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24292 Z= 0.254 Angle : 0.616 8.473 32974 Z= 0.313 Chirality : 0.047 0.354 3617 Planarity : 0.005 0.082 4288 Dihedral : 10.189 157.764 3606 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.71 % Favored : 96.06 % Rotamer: Outliers : 3.20 % Allowed : 15.03 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2977 helix: 1.54 (0.15), residues: 1242 sheet: 0.34 (0.23), residues: 534 loop : -1.19 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP S 388 HIS 0.009 0.001 HIS A 88 PHE 0.023 0.002 PHE E 255 TYR 0.030 0.002 TYR K 189 ARG 0.008 0.001 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 1101) hydrogen bonds : angle 4.22630 ( 3357) covalent geometry : bond 0.00607 (24292) covalent geometry : angle 0.61570 (32974) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 519 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7609 (ttt-90) REVERT: K 75 ARG cc_start: 0.8872 (mtt180) cc_final: 0.8488 (tpt170) REVERT: K 98 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: K 115 GLN cc_start: 0.8330 (pm20) cc_final: 0.7851 (pm20) REVERT: K 180 ASP cc_start: 0.7751 (t0) cc_final: 0.7494 (t0) REVERT: K 240 LYS cc_start: 0.7822 (mttm) cc_final: 0.7569 (ttmm) REVERT: N 66 ASN cc_start: 0.7780 (m-40) cc_final: 0.7385 (m110) REVERT: N 107 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7409 (tmm) REVERT: N 201 LYS cc_start: 0.9101 (tttm) cc_final: 0.8518 (mtmm) REVERT: N 249 LEU cc_start: 0.8728 (mm) cc_final: 0.8474 (mp) REVERT: N 289 ASP cc_start: 0.4419 (OUTLIER) cc_final: 0.3979 (t0) REVERT: A 9 VAL cc_start: 0.9105 (t) cc_final: 0.8837 (m) REVERT: A 24 TYR cc_start: 0.8707 (m-80) cc_final: 0.8398 (m-80) REVERT: A 120 ASP cc_start: 0.8711 (t70) cc_final: 0.8379 (t70) REVERT: A 322 ASP cc_start: 0.8960 (t0) cc_final: 0.8686 (t0) REVERT: A 423 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7864 (mt-10) REVERT: A 430 LYS cc_start: 0.8657 (ttpp) cc_final: 0.8437 (ttpp) REVERT: A 432 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7956 (t80) REVERT: A 434 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8423 (mt-10) REVERT: B 170 MET cc_start: 0.8586 (ptp) cc_final: 0.8131 (mtt) REVERT: B 213 ARG cc_start: 0.8817 (mmm-85) cc_final: 0.8497 (mtm-85) REVERT: B 257 MET cc_start: 0.8447 (mmm) cc_final: 0.8207 (mmm) REVERT: B 347 ASN cc_start: 0.7840 (t0) cc_final: 0.7588 (t0) REVERT: B 401 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8326 (mm-30) REVERT: E 3 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7679 (mt-10) REVERT: E 69 ASP cc_start: 0.8753 (t0) cc_final: 0.8529 (t70) REVERT: E 129 CYS cc_start: 0.8633 (m) cc_final: 0.8322 (m) REVERT: E 242 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9157 (pp) REVERT: I 31 ASP cc_start: 0.8623 (t70) cc_final: 0.8332 (t70) REVERT: I 67 ASP cc_start: 0.8537 (t0) cc_final: 0.8196 (t0) REVERT: I 168 SER cc_start: 0.9156 (p) cc_final: 0.8731 (m) REVERT: I 318 ARG cc_start: 0.8618 (mtp85) cc_final: 0.8244 (mtp180) REVERT: I 398 TYR cc_start: 0.8928 (m-80) cc_final: 0.8727 (m-80) REVERT: I 417 ASP cc_start: 0.8394 (m-30) cc_final: 0.8087 (m-30) REVERT: S 36 MET cc_start: 0.8542 (ttp) cc_final: 0.8004 (ttt) REVERT: S 69 ASP cc_start: 0.8794 (t70) cc_final: 0.7846 (t70) REVERT: S 80 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7908 (p) REVERT: S 112 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8766 (mmtm) REVERT: S 160 ASP cc_start: 0.7783 (m-30) cc_final: 0.7502 (m-30) REVERT: S 199 ASP cc_start: 0.8535 (t0) cc_final: 0.7852 (t0) REVERT: S 242 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8885 (pp) REVERT: S 306 ASP cc_start: 0.8552 (t0) cc_final: 0.8118 (t0) REVERT: S 322 ASP cc_start: 0.8873 (t0) cc_final: 0.8504 (t70) REVERT: S 392 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7979 (t0) REVERT: S 394 LYS cc_start: 0.8210 (mttt) cc_final: 0.7769 (mmtt) REVERT: S 397 LEU cc_start: 0.8983 (mt) cc_final: 0.8659 (tt) REVERT: S 434 GLU cc_start: 0.8602 (tt0) cc_final: 0.8389 (tt0) outliers start: 76 outliers final: 50 residues processed: 555 average time/residue: 0.3622 time to fit residues: 311.2522 Evaluate side-chains 540 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 481 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 210 MET Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 379 SER Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 140 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 318 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 HIS A 285 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 99 ASN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.122653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092993 restraints weight = 37349.148| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.37 r_work: 0.3249 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24292 Z= 0.179 Angle : 0.565 8.705 32974 Z= 0.286 Chirality : 0.045 0.291 3617 Planarity : 0.004 0.080 4288 Dihedral : 9.900 159.654 3606 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 3.08 % Allowed : 16.08 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 2977 helix: 1.56 (0.15), residues: 1246 sheet: 0.35 (0.23), residues: 540 loop : -1.22 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 388 HIS 0.007 0.001 HIS I 37 PHE 0.018 0.002 PHE S 255 TYR 0.036 0.001 TYR N 74 ARG 0.008 0.000 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 1101) hydrogen bonds : angle 4.08634 ( 3357) covalent geometry : bond 0.00424 (24292) covalent geometry : angle 0.56506 (32974) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 506 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7597 (ttt-90) REVERT: K 75 ARG cc_start: 0.8858 (mtt180) cc_final: 0.8455 (tpt170) REVERT: K 81 MET cc_start: 0.8213 (mmm) cc_final: 0.7877 (mmt) REVERT: K 98 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: K 138 MET cc_start: 0.7141 (tpp) cc_final: 0.6691 (mmm) REVERT: K 143 GLU cc_start: 0.8112 (tt0) cc_final: 0.7864 (tt0) REVERT: K 180 ASP cc_start: 0.7695 (t0) cc_final: 0.7446 (t0) REVERT: K 240 LYS cc_start: 0.7797 (mttm) cc_final: 0.7560 (ttmm) REVERT: K 318 ASN cc_start: 0.8678 (m-40) cc_final: 0.8350 (m110) REVERT: N 54 TYR cc_start: 0.8373 (m-80) cc_final: 0.8138 (m-10) REVERT: N 66 ASN cc_start: 0.7761 (m-40) cc_final: 0.7370 (m110) REVERT: N 80 GLU cc_start: 0.7833 (tp30) cc_final: 0.7597 (tp30) REVERT: N 107 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7362 (tmm) REVERT: N 201 LYS cc_start: 0.9089 (tttm) cc_final: 0.8495 (mtmm) REVERT: N 249 LEU cc_start: 0.8754 (mm) cc_final: 0.8530 (mp) REVERT: N 289 ASP cc_start: 0.4485 (OUTLIER) cc_final: 0.4072 (t0) REVERT: A 9 VAL cc_start: 0.9081 (t) cc_final: 0.8815 (m) REVERT: A 24 TYR cc_start: 0.8696 (m-10) cc_final: 0.8404 (m-80) REVERT: A 322 ASP cc_start: 0.8931 (t0) cc_final: 0.8584 (t0) REVERT: A 423 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 432 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8043 (t80) REVERT: A 434 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 170 MET cc_start: 0.8567 (ptp) cc_final: 0.8119 (mtt) REVERT: B 213 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8469 (mtm-85) REVERT: B 347 ASN cc_start: 0.7815 (t0) cc_final: 0.7521 (t0) REVERT: E 1 MET cc_start: 0.7711 (mpp) cc_final: 0.7290 (pmm) REVERT: E 3 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 129 CYS cc_start: 0.8636 (m) cc_final: 0.8318 (m) REVERT: E 242 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9144 (pp) REVERT: I 31 ASP cc_start: 0.8622 (t70) cc_final: 0.8329 (t70) REVERT: I 67 ASP cc_start: 0.8521 (t0) cc_final: 0.8195 (t0) REVERT: I 168 SER cc_start: 0.9156 (p) cc_final: 0.8698 (m) REVERT: I 417 ASP cc_start: 0.8407 (m-30) cc_final: 0.8128 (m-30) REVERT: S 36 MET cc_start: 0.8508 (ttp) cc_final: 0.7995 (ttt) REVERT: S 80 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7839 (p) REVERT: S 112 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8752 (mmtm) REVERT: S 160 ASP cc_start: 0.7769 (m-30) cc_final: 0.7488 (m-30) REVERT: S 242 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8907 (pp) REVERT: S 392 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7986 (t0) REVERT: S 394 LYS cc_start: 0.8233 (mttt) cc_final: 0.7795 (mmtt) REVERT: S 397 LEU cc_start: 0.8966 (mt) cc_final: 0.8673 (tt) REVERT: S 401 LYS cc_start: 0.5715 (mtmt) cc_final: 0.5463 (mtmt) REVERT: S 433 GLU cc_start: 0.8721 (tp30) cc_final: 0.8205 (tt0) REVERT: S 434 GLU cc_start: 0.8584 (tt0) cc_final: 0.8232 (tt0) outliers start: 73 outliers final: 48 residues processed: 544 average time/residue: 0.3585 time to fit residues: 302.3774 Evaluate side-chains 539 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 482 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 292 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 192 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 121 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.121539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092380 restraints weight = 34494.300| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.24 r_work: 0.3240 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24292 Z= 0.224 Angle : 0.600 8.893 32974 Z= 0.303 Chirality : 0.046 0.269 3617 Planarity : 0.005 0.078 4288 Dihedral : 9.872 159.644 3606 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.98 % Favored : 95.82 % Rotamer: Outliers : 3.36 % Allowed : 15.96 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 2977 helix: 1.53 (0.15), residues: 1237 sheet: 0.28 (0.22), residues: 546 loop : -1.27 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 388 HIS 0.008 0.001 HIS A 88 PHE 0.020 0.002 PHE K 94 TYR 0.027 0.002 TYR K 189 ARG 0.009 0.001 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.04578 ( 1101) hydrogen bonds : angle 4.14598 ( 3357) covalent geometry : bond 0.00536 (24292) covalent geometry : angle 0.59953 (32974) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 507 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7607 (ttt-90) REVERT: K 75 ARG cc_start: 0.8881 (mtt180) cc_final: 0.8463 (tpt170) REVERT: K 98 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7502 (tt0) REVERT: K 138 MET cc_start: 0.7174 (tpp) cc_final: 0.6722 (mmm) REVERT: K 143 GLU cc_start: 0.8075 (tt0) cc_final: 0.7746 (tt0) REVERT: K 180 ASP cc_start: 0.7820 (t0) cc_final: 0.7588 (t0) REVERT: K 240 LYS cc_start: 0.7816 (mttm) cc_final: 0.7434 (ttmm) REVERT: K 327 MET cc_start: 0.8161 (ttt) cc_final: 0.7861 (ttt) REVERT: N 66 ASN cc_start: 0.7755 (m-40) cc_final: 0.7372 (m110) REVERT: N 107 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7355 (tmm) REVERT: N 201 LYS cc_start: 0.9099 (tttm) cc_final: 0.8480 (mtmm) REVERT: N 210 MET cc_start: 0.5565 (ttt) cc_final: 0.5278 (ttm) REVERT: N 249 LEU cc_start: 0.8751 (mm) cc_final: 0.8547 (mp) REVERT: N 289 ASP cc_start: 0.4648 (OUTLIER) cc_final: 0.4262 (t0) REVERT: N 340 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7936 (mp0) REVERT: A 9 VAL cc_start: 0.9108 (t) cc_final: 0.8847 (m) REVERT: A 120 ASP cc_start: 0.8716 (t70) cc_final: 0.8403 (t70) REVERT: A 345 ASP cc_start: 0.8868 (t0) cc_final: 0.8349 (m-30) REVERT: A 423 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7811 (mt-10) REVERT: A 432 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 434 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 170 MET cc_start: 0.8514 (ptp) cc_final: 0.8059 (mtt) REVERT: B 213 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8496 (mtm-85) REVERT: B 347 ASN cc_start: 0.7851 (t0) cc_final: 0.7554 (t0) REVERT: B 401 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8328 (mm-30) REVERT: E 1 MET cc_start: 0.7774 (mpp) cc_final: 0.7412 (pmm) REVERT: E 15 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: E 242 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9171 (pp) REVERT: E 392 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8621 (t0) REVERT: I 31 ASP cc_start: 0.8625 (t70) cc_final: 0.8342 (t70) REVERT: I 67 ASP cc_start: 0.8497 (t0) cc_final: 0.8177 (t0) REVERT: I 168 SER cc_start: 0.9144 (p) cc_final: 0.8703 (m) REVERT: I 304 ASP cc_start: 0.8218 (t0) cc_final: 0.7903 (t0) REVERT: I 306 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8488 (mtm180) REVERT: I 318 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8249 (mtp180) REVERT: I 417 ASP cc_start: 0.8365 (m-30) cc_final: 0.8051 (m-30) REVERT: S 36 MET cc_start: 0.8482 (ttp) cc_final: 0.7998 (ttt) REVERT: S 55 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: S 80 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7794 (p) REVERT: S 112 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8757 (mmtm) REVERT: S 160 ASP cc_start: 0.7768 (m-30) cc_final: 0.7459 (m-30) REVERT: S 242 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8908 (pp) REVERT: S 392 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7980 (t0) REVERT: S 394 LYS cc_start: 0.8246 (mttt) cc_final: 0.7860 (mmtt) REVERT: S 397 LEU cc_start: 0.8974 (mt) cc_final: 0.8678 (tt) REVERT: S 401 LYS cc_start: 0.5765 (mtmt) cc_final: 0.5498 (mtmt) REVERT: S 434 GLU cc_start: 0.8600 (tt0) cc_final: 0.8237 (tt0) outliers start: 80 outliers final: 62 residues processed: 549 average time/residue: 0.3834 time to fit residues: 328.7819 Evaluate side-chains 565 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 491 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 ASP Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 190 ASN Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 334 THR Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 379 SER Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 232 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 171 optimal weight: 0.0050 chunk 46 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 318 ASN N 98 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 37 HIS I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 HIS S 15 GLN S 186 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.125798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095134 restraints weight = 44129.188| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.75 r_work: 0.3280 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24292 Z= 0.111 Angle : 0.530 9.427 32974 Z= 0.266 Chirality : 0.043 0.265 3617 Planarity : 0.004 0.077 4288 Dihedral : 9.377 162.321 3603 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.44 % Favored : 96.36 % Rotamer: Outliers : 2.54 % Allowed : 17.10 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2977 helix: 1.68 (0.15), residues: 1254 sheet: 0.35 (0.22), residues: 549 loop : -1.18 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP S 388 HIS 0.006 0.001 HIS I 37 PHE 0.015 0.001 PHE K 94 TYR 0.042 0.001 TYR N 74 ARG 0.008 0.000 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 1101) hydrogen bonds : angle 3.94839 ( 3357) covalent geometry : bond 0.00245 (24292) covalent geometry : angle 0.53025 (32974) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 507 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 98 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: K 138 MET cc_start: 0.7030 (tpp) cc_final: 0.6582 (mmm) REVERT: K 240 LYS cc_start: 0.7737 (mttm) cc_final: 0.7408 (ttmm) REVERT: K 318 ASN cc_start: 0.8596 (m-40) cc_final: 0.8360 (m-40) REVERT: K 327 MET cc_start: 0.7903 (ttt) cc_final: 0.7540 (ttt) REVERT: N 66 ASN cc_start: 0.7751 (m-40) cc_final: 0.7367 (m110) REVERT: N 107 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: N 129 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7630 (ttm110) REVERT: N 201 LYS cc_start: 0.8994 (tttm) cc_final: 0.8389 (mtmm) REVERT: N 249 LEU cc_start: 0.8656 (mm) cc_final: 0.8380 (mp) REVERT: N 289 ASP cc_start: 0.4452 (OUTLIER) cc_final: 0.4087 (t0) REVERT: A 9 VAL cc_start: 0.9000 (t) cc_final: 0.8695 (m) REVERT: A 24 TYR cc_start: 0.8618 (m-10) cc_final: 0.8263 (m-80) REVERT: A 322 ASP cc_start: 0.8749 (t0) cc_final: 0.8406 (t0) REVERT: A 423 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7559 (mt-10) REVERT: A 432 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.8156 (t80) REVERT: A 434 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8269 (mt-10) REVERT: B 125 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: B 170 MET cc_start: 0.8310 (ptp) cc_final: 0.7870 (mtt) REVERT: B 213 ARG cc_start: 0.8694 (mtm-85) cc_final: 0.8338 (mtm-85) REVERT: B 288 GLU cc_start: 0.8401 (mm-30) cc_final: 0.7946 (mm-30) REVERT: B 347 ASN cc_start: 0.7645 (t0) cc_final: 0.7333 (t0) REVERT: E 1 MET cc_start: 0.7541 (mpp) cc_final: 0.7202 (pmm) REVERT: E 15 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: E 176 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8577 (mt0) REVERT: E 242 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9076 (pp) REVERT: I 31 ASP cc_start: 0.8494 (t70) cc_final: 0.8170 (t70) REVERT: I 67 ASP cc_start: 0.8359 (t0) cc_final: 0.7769 (t0) REVERT: I 72 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8490 (p) REVERT: I 168 SER cc_start: 0.9079 (p) cc_final: 0.8571 (m) REVERT: I 306 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8370 (mtm180) REVERT: I 318 ARG cc_start: 0.8523 (mtp85) cc_final: 0.8081 (mtp180) REVERT: I 417 ASP cc_start: 0.8221 (m-30) cc_final: 0.7929 (m-30) REVERT: I 426 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8234 (tt0) REVERT: S 36 MET cc_start: 0.8398 (ttp) cc_final: 0.7892 (ttt) REVERT: S 55 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7596 (tm-30) REVERT: S 109 THR cc_start: 0.8548 (t) cc_final: 0.8160 (p) REVERT: S 112 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8739 (mmtm) REVERT: S 160 ASP cc_start: 0.7552 (m-30) cc_final: 0.7254 (m-30) REVERT: S 242 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8811 (pp) REVERT: S 392 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7879 (t0) REVERT: S 394 LYS cc_start: 0.8158 (mttt) cc_final: 0.7747 (mmtt) REVERT: S 396 ASP cc_start: 0.8128 (m-30) cc_final: 0.7920 (m-30) REVERT: S 397 LEU cc_start: 0.8894 (mt) cc_final: 0.8581 (tt) REVERT: S 401 LYS cc_start: 0.5377 (mtmt) cc_final: 0.5164 (mtmt) REVERT: S 433 GLU cc_start: 0.8569 (tp30) cc_final: 0.8065 (tt0) outliers start: 59 outliers final: 41 residues processed: 540 average time/residue: 0.3488 time to fit residues: 292.8065 Evaluate side-chains 545 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 494 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 27 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 449 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 241 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 295 optimal weight: 30.0000 chunk 202 optimal weight: 2.9990 chunk 284 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 212 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.123048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.093821 restraints weight = 34720.258| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.27 r_work: 0.3269 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24292 Z= 0.193 Angle : 0.581 11.754 32974 Z= 0.292 Chirality : 0.045 0.244 3617 Planarity : 0.004 0.076 4288 Dihedral : 9.454 162.104 3603 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.04 % Favored : 95.79 % Rotamer: Outliers : 2.89 % Allowed : 17.25 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.15), residues: 2977 helix: 1.65 (0.15), residues: 1246 sheet: 0.35 (0.22), residues: 546 loop : -1.22 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 388 HIS 0.007 0.001 HIS I 137 PHE 0.020 0.002 PHE K 94 TYR 0.033 0.001 TYR N 74 ARG 0.009 0.000 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 1101) hydrogen bonds : angle 4.03053 ( 3357) covalent geometry : bond 0.00462 (24292) covalent geometry : angle 0.58133 (32974) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 502 time to evaluate : 2.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6900 (mt0) REVERT: K 98 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: K 138 MET cc_start: 0.7117 (tpp) cc_final: 0.6658 (mmm) REVERT: K 240 LYS cc_start: 0.7800 (mttm) cc_final: 0.7460 (ttmm) REVERT: K 327 MET cc_start: 0.8167 (ttt) cc_final: 0.7845 (ttt) REVERT: N 66 ASN cc_start: 0.7765 (m-40) cc_final: 0.7379 (m110) REVERT: N 79 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7777 (mp0) REVERT: N 107 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7340 (tmm) REVERT: N 129 ARG cc_start: 0.7893 (ttt90) cc_final: 0.7622 (ttm110) REVERT: N 201 LYS cc_start: 0.9057 (tttm) cc_final: 0.8436 (mtmm) REVERT: N 289 ASP cc_start: 0.4623 (OUTLIER) cc_final: 0.4193 (t0) REVERT: A 9 VAL cc_start: 0.9089 (t) cc_final: 0.8823 (m) REVERT: A 24 TYR cc_start: 0.8715 (m-10) cc_final: 0.8355 (m-80) REVERT: A 120 ASP cc_start: 0.8710 (t70) cc_final: 0.8389 (t70) REVERT: A 322 ASP cc_start: 0.8866 (t0) cc_final: 0.8590 (t0) REVERT: A 345 ASP cc_start: 0.8893 (t0) cc_final: 0.8354 (m-30) REVERT: A 423 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7793 (mt-10) REVERT: A 432 TYR cc_start: 0.8906 (OUTLIER) cc_final: 0.8119 (t80) REVERT: A 434 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8457 (mt-10) REVERT: B 170 MET cc_start: 0.8554 (ptp) cc_final: 0.8139 (mtt) REVERT: B 213 ARG cc_start: 0.8796 (mtm-85) cc_final: 0.8494 (mtm-85) REVERT: B 288 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8203 (mm-30) REVERT: B 347 ASN cc_start: 0.7810 (t0) cc_final: 0.7518 (t0) REVERT: B 401 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8285 (mm-30) REVERT: E 1 MET cc_start: 0.7716 (mpp) cc_final: 0.7303 (pmm) REVERT: E 3 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7633 (mt-10) REVERT: E 15 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8009 (mt0) REVERT: E 176 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8667 (mt0) REVERT: E 242 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9141 (pp) REVERT: I 31 ASP cc_start: 0.8620 (t70) cc_final: 0.8310 (t70) REVERT: I 67 ASP cc_start: 0.8511 (t0) cc_final: 0.7996 (t0) REVERT: I 72 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8557 (p) REVERT: I 168 SER cc_start: 0.9120 (p) cc_final: 0.8665 (m) REVERT: I 318 ARG cc_start: 0.8655 (mtp85) cc_final: 0.8253 (mtp180) REVERT: I 417 ASP cc_start: 0.8398 (m-30) cc_final: 0.8119 (m-30) REVERT: I 426 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8433 (tt0) REVERT: S 36 MET cc_start: 0.8523 (ttp) cc_final: 0.8003 (ttt) REVERT: S 55 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: S 109 THR cc_start: 0.8562 (t) cc_final: 0.8287 (p) REVERT: S 112 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8800 (mmtm) REVERT: S 113 GLU cc_start: 0.8550 (pm20) cc_final: 0.8180 (pt0) REVERT: S 160 ASP cc_start: 0.7729 (m-30) cc_final: 0.7431 (m-30) REVERT: S 242 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8914 (pp) REVERT: S 392 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7991 (t0) REVERT: S 394 LYS cc_start: 0.8225 (mttt) cc_final: 0.7807 (mmtt) REVERT: S 397 LEU cc_start: 0.8933 (mt) cc_final: 0.8633 (tt) REVERT: S 401 LYS cc_start: 0.5603 (mtmt) cc_final: 0.5356 (mtmt) REVERT: S 433 GLU cc_start: 0.8714 (tp30) cc_final: 0.8206 (tt0) outliers start: 68 outliers final: 49 residues processed: 539 average time/residue: 0.3670 time to fit residues: 310.0444 Evaluate side-chains 556 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 497 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 284 LEU Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 424 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 23 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 chunk 44 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 318 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN I 279 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.125428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.095884 restraints weight = 34251.139| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.28 r_work: 0.3288 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24292 Z= 0.158 Angle : 0.560 10.016 32974 Z= 0.281 Chirality : 0.044 0.221 3617 Planarity : 0.004 0.075 4288 Dihedral : 9.385 162.462 3603 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.67 % Favored : 96.16 % Rotamer: Outliers : 2.62 % Allowed : 17.45 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.16), residues: 2977 helix: 1.67 (0.15), residues: 1247 sheet: 0.36 (0.22), residues: 544 loop : -1.24 (0.17), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP S 388 HIS 0.007 0.001 HIS I 137 PHE 0.018 0.001 PHE K 94 TYR 0.033 0.001 TYR N 74 ARG 0.009 0.000 ARG K 129 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 1101) hydrogen bonds : angle 3.99902 ( 3357) covalent geometry : bond 0.00375 (24292) covalent geometry : angle 0.56007 (32974) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 493 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 42 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6920 (mt0) REVERT: K 81 MET cc_start: 0.8218 (mmm) cc_final: 0.7589 (mmt) REVERT: K 98 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: K 138 MET cc_start: 0.7099 (tpp) cc_final: 0.6660 (mmm) REVERT: K 180 ASP cc_start: 0.7469 (t0) cc_final: 0.7248 (t0) REVERT: K 240 LYS cc_start: 0.7797 (mttm) cc_final: 0.7460 (ttmm) REVERT: K 327 MET cc_start: 0.8114 (ttt) cc_final: 0.7821 (ttt) REVERT: N 66 ASN cc_start: 0.7760 (m-40) cc_final: 0.7381 (m110) REVERT: N 107 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7785 (tpp) REVERT: N 129 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7638 (ttm110) REVERT: N 143 GLU cc_start: 0.7160 (pt0) cc_final: 0.6956 (pt0) REVERT: N 201 LYS cc_start: 0.9051 (tttm) cc_final: 0.8368 (mtmm) REVERT: N 289 ASP cc_start: 0.4679 (OUTLIER) cc_final: 0.4243 (t0) REVERT: A 9 VAL cc_start: 0.9081 (t) cc_final: 0.8806 (m) REVERT: A 24 TYR cc_start: 0.8701 (m-10) cc_final: 0.8334 (m-80) REVERT: A 322 ASP cc_start: 0.8853 (t0) cc_final: 0.8546 (t0) REVERT: A 345 ASP cc_start: 0.8887 (t0) cc_final: 0.8338 (m-30) REVERT: A 423 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7785 (mt-10) REVERT: A 432 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8207 (t80) REVERT: A 434 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8421 (mt-10) REVERT: B 170 MET cc_start: 0.8553 (ptp) cc_final: 0.8108 (mtt) REVERT: B 213 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.8505 (mtm-85) REVERT: B 288 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8156 (mm-30) REVERT: B 347 ASN cc_start: 0.7783 (t0) cc_final: 0.7501 (t0) REVERT: B 401 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8261 (mm-30) REVERT: E 1 MET cc_start: 0.7676 (mpp) cc_final: 0.7300 (pmm) REVERT: E 3 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7646 (mt-10) REVERT: E 15 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: E 176 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8665 (mt0) REVERT: E 242 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9146 (pp) REVERT: I 31 ASP cc_start: 0.8631 (t70) cc_final: 0.8322 (t70) REVERT: I 72 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8544 (p) REVERT: I 168 SER cc_start: 0.9118 (p) cc_final: 0.8650 (m) REVERT: I 306 ARG cc_start: 0.8805 (mtm180) cc_final: 0.8523 (mtm180) REVERT: I 318 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8223 (mtp180) REVERT: I 417 ASP cc_start: 0.8397 (m-30) cc_final: 0.8123 (m-30) REVERT: I 426 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8410 (tt0) REVERT: S 36 MET cc_start: 0.8525 (ttp) cc_final: 0.8065 (ttt) REVERT: S 55 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7703 (tm-30) REVERT: S 109 THR cc_start: 0.8562 (t) cc_final: 0.8319 (p) REVERT: S 112 LYS cc_start: 0.9023 (mmmt) cc_final: 0.8805 (mmtm) REVERT: S 113 GLU cc_start: 0.8515 (pm20) cc_final: 0.8131 (pt0) REVERT: S 160 ASP cc_start: 0.7694 (m-30) cc_final: 0.7393 (m-30) REVERT: S 242 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8915 (pp) REVERT: S 392 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8015 (t0) REVERT: S 394 LYS cc_start: 0.8225 (mttt) cc_final: 0.7813 (mmtt) REVERT: S 397 LEU cc_start: 0.8917 (mt) cc_final: 0.8622 (tt) REVERT: S 401 LYS cc_start: 0.5578 (mtmt) cc_final: 0.5338 (mtmt) REVERT: S 413 MET cc_start: 0.7740 (mtp) cc_final: 0.7414 (ttt) REVERT: S 433 GLU cc_start: 0.8680 (tp30) cc_final: 0.8171 (tt0) outliers start: 61 outliers final: 47 residues processed: 528 average time/residue: 0.3710 time to fit residues: 309.8529 Evaluate side-chains 545 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 489 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 224 ILE Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 279 GLN Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 424 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 13 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 115 GLN K 318 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.124773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094411 restraints weight = 44142.007| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.63 r_work: 0.3266 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24292 Z= 0.135 Angle : 0.555 9.743 32974 Z= 0.278 Chirality : 0.044 0.317 3617 Planarity : 0.004 0.075 4288 Dihedral : 9.278 163.489 3603 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.02 % Rotamer: Outliers : 2.65 % Allowed : 17.53 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.16), residues: 2977 helix: 1.74 (0.15), residues: 1245 sheet: 0.38 (0.22), residues: 547 loop : -1.21 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP S 388 HIS 0.006 0.001 HIS I 137 PHE 0.016 0.001 PHE K 94 TYR 0.029 0.001 TYR N 74 ARG 0.006 0.000 ARG S 215 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 1101) hydrogen bonds : angle 3.96900 ( 3357) covalent geometry : bond 0.00315 (24292) covalent geometry : angle 0.55512 (32974) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5954 Ramachandran restraints generated. 2977 Oldfield, 0 Emsley, 2977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 498 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 11 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7450 (ttt-90) REVERT: K 42 GLN cc_start: 0.7170 (mm-40) cc_final: 0.6932 (mt0) REVERT: K 81 MET cc_start: 0.8208 (mmm) cc_final: 0.7577 (mmt) REVERT: K 98 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: K 138 MET cc_start: 0.7009 (tpp) cc_final: 0.6512 (mmm) REVERT: K 180 ASP cc_start: 0.7321 (t0) cc_final: 0.7112 (t0) REVERT: K 240 LYS cc_start: 0.7787 (mttm) cc_final: 0.7494 (ttmm) REVERT: N 66 ASN cc_start: 0.7740 (m-40) cc_final: 0.7361 (m110) REVERT: N 107 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7716 (tpp) REVERT: N 129 ARG cc_start: 0.7878 (ttt90) cc_final: 0.7595 (ttm110) REVERT: N 143 GLU cc_start: 0.7024 (pt0) cc_final: 0.6823 (pt0) REVERT: N 201 LYS cc_start: 0.8967 (tttm) cc_final: 0.8294 (mtmm) REVERT: N 289 ASP cc_start: 0.4614 (OUTLIER) cc_final: 0.4223 (t0) REVERT: A 9 VAL cc_start: 0.9020 (t) cc_final: 0.8732 (m) REVERT: A 24 TYR cc_start: 0.8613 (m-10) cc_final: 0.8255 (m-80) REVERT: A 163 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8677 (mmtp) REVERT: A 322 ASP cc_start: 0.8730 (t0) cc_final: 0.8451 (t0) REVERT: A 345 ASP cc_start: 0.8739 (t0) cc_final: 0.8290 (m-30) REVERT: A 423 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7570 (mt-10) REVERT: A 432 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8150 (t80) REVERT: A 434 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 125 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: B 170 MET cc_start: 0.8273 (ptp) cc_final: 0.7862 (mtt) REVERT: B 213 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8369 (mtm-85) REVERT: B 288 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 347 ASN cc_start: 0.7654 (t0) cc_final: 0.7360 (t0) REVERT: B 401 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8041 (mm-30) REVERT: E 1 MET cc_start: 0.7522 (mpp) cc_final: 0.7163 (pmm) REVERT: E 3 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7471 (mt-10) REVERT: E 15 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: E 176 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8587 (mt0) REVERT: E 242 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9101 (pp) REVERT: I 31 ASP cc_start: 0.8472 (t70) cc_final: 0.8198 (t70) REVERT: I 67 ASP cc_start: 0.8321 (t0) cc_final: 0.7777 (t0) REVERT: I 72 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8513 (p) REVERT: I 168 SER cc_start: 0.9086 (p) cc_final: 0.8599 (m) REVERT: I 306 ARG cc_start: 0.8698 (mtm180) cc_final: 0.8404 (mtm180) REVERT: I 318 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8117 (mtp180) REVERT: I 388 MET cc_start: 0.8638 (mtp) cc_final: 0.8362 (ttm) REVERT: I 417 ASP cc_start: 0.8195 (m-30) cc_final: 0.7910 (m-30) REVERT: I 426 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8269 (tt0) REVERT: S 36 MET cc_start: 0.8428 (ttp) cc_final: 0.7984 (ttt) REVERT: S 55 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: S 109 THR cc_start: 0.8454 (t) cc_final: 0.8220 (p) REVERT: S 112 LYS cc_start: 0.9037 (mmmt) cc_final: 0.8796 (mmtm) REVERT: S 113 GLU cc_start: 0.8438 (pm20) cc_final: 0.8023 (pm20) REVERT: S 160 ASP cc_start: 0.7594 (m-30) cc_final: 0.7285 (m-30) REVERT: S 242 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8853 (pp) REVERT: S 392 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7870 (t0) REVERT: S 394 LYS cc_start: 0.8211 (mttt) cc_final: 0.7807 (mmtt) REVERT: S 396 ASP cc_start: 0.8116 (m-30) cc_final: 0.7859 (m-30) REVERT: S 397 LEU cc_start: 0.8889 (mt) cc_final: 0.8575 (tt) REVERT: S 401 LYS cc_start: 0.5203 (mtmt) cc_final: 0.4988 (mtmt) REVERT: S 413 MET cc_start: 0.7636 (mtp) cc_final: 0.7299 (ttt) REVERT: S 433 GLU cc_start: 0.8548 (tp30) cc_final: 0.8068 (tt0) outliers start: 62 outliers final: 47 residues processed: 535 average time/residue: 0.3670 time to fit residues: 307.0942 Evaluate side-chains 546 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 487 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 5 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 226 THR Chi-restraints excluded: chain K residue 318 ASN Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 107 MET Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain A residue 2 ARG Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 432 TYR Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 403 MET Chi-restraints excluded: chain I residue 415 MET Chi-restraints excluded: chain S residue 55 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 239 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 324 VAL Chi-restraints excluded: chain S residue 337 THR Chi-restraints excluded: chain S residue 363 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 392 ASP Chi-restraints excluded: chain S residue 429 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 4 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 284 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 288 optimal weight: 0.2980 chunk 257 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 279 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 318 ASN ** N 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 18 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.123605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.093896 restraints weight = 36828.846| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.35 r_work: 0.3273 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24292 Z= 0.174 Angle : 0.569 9.119 32974 Z= 0.285 Chirality : 0.045 0.315 3617 Planarity : 0.004 0.075 4288 Dihedral : 9.318 163.213 3603 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.96 % Rotamer: Outliers : 2.81 % Allowed : 17.72 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2977 helix: 1.71 (0.15), residues: 1242 sheet: 0.35 (0.22), residues: 548 loop : -1.24 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP S 388 HIS 0.007 0.001 HIS I 37 PHE 0.018 0.001 PHE K 94 TYR 0.029 0.001 TYR N 74 ARG 0.006 0.000 ARG S 215 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 1101) hydrogen bonds : angle 4.00321 ( 3357) covalent geometry : bond 0.00416 (24292) covalent geometry : angle 0.56888 (32974) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16402.64 seconds wall clock time: 283 minutes 36.56 seconds (17016.56 seconds total)