Starting phenix.real_space_refine on Fri May 23 03:26:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utn_42543/05_2025/8utn_42543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utn_42543/05_2025/8utn_42543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8utn_42543/05_2025/8utn_42543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utn_42543/05_2025/8utn_42543.map" model { file = "/net/cci-nas-00/data/ceres_data/8utn_42543/05_2025/8utn_42543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utn_42543/05_2025/8utn_42543.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 152 5.16 5 C 14858 2.51 5 N 4069 2.21 5 O 4682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23784 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: 3047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3047 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 13, 'TRANS': 374} 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=0.51 ... (12 atoms not shown) pdb=" CG2BTHR B 429 " occ=0.49 residue: pdb=" N AALA B 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA B 430 " occ=0.49 residue: pdb=" N AASP B 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP B 431 " occ=0.49 residue: pdb=" N AGLU B 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU B 432 " occ=0.49 residue: pdb=" N ATHR I 429 " occ=0.51 ... (12 atoms not shown) pdb=" CG2BTHR I 429 " occ=0.49 residue: pdb=" N AALA I 430 " occ=0.51 ... (8 atoms not shown) pdb=" CB BALA I 430 " occ=0.49 residue: pdb=" N AASP I 431 " occ=0.51 ... (14 atoms not shown) pdb=" OD2BASP I 431 " occ=0.49 residue: pdb=" N AGLU I 432 " occ=0.51 ... (16 atoms not shown) pdb=" OE2BGLU I 432 " occ=0.49 residue: pdb=" N AGLN I 433 " occ=0.51 ... (16 atoms not shown) pdb=" NE2BGLN I 433 " occ=0.49 Time building chain proxies: 18.11, per 1000 atoms: 0.76 Number of scatterers: 23784 At special positions: 0 Unit cell: (80.18, 116.472, 238.008, 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 152 16.00 P 19 15.00 Mg 4 11.99 O 4682 8.00 N 4069 7.00 C 14858 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: 6.37 Conformation dependent library (CDL) restraints added in 4.0 seconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5552 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 24 sheets defined 49.4% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.64 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 159 through 163 removed outlier: 3.904A pdb=" N ASN K 162 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS K 163 " --> pdb=" O PRO K 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 159 through 163' 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 294 Proline residue: K 292 - end of helix Processing helix chain 'K' and resid 305 through 308 removed outlier: 3.865A 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 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 354 removed outlier: 3.978A pdb=" N SER K 343 " --> pdb=" O ASP K 339 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN K 353 " --> pdb=" O ASP K 349 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE K 354 " --> pdb=" O ARG K 350 " (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 87 removed outlier: 4.604A pdb=" N GLU N 79 " --> pdb=" O ARG N 75 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLU N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 108 Processing helix chain 'N' and resid 117 through 133 removed outlier: 3.894A 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: 3.753A 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: 3.908A 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: 4.232A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.731A 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 113 through 129 removed outlier: 4.252A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.177A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.514A 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: 3.801A 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: 3.659A pdb=" N ASN A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.692A pdb=" N ILE A 265 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.919A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.781A 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: 3.525A pdb=" N VAL A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.820A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.133A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.044A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.520A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 69 through 78 removed outlier: 4.545A 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: 3.810A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.650A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.683A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 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: 4.081A 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: 4.258A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 400 removed outlier: 4.170A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.810A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 36 through 43 removed outlier: 3.904A pdb=" N LYS E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 removed outlier: 4.637A pdb=" N ILE E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E 80 " --> pdb=" O ASP E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 114 through 128 Processing helix chain 'E' and resid 143 through 161 removed outlier: 3.510A pdb=" N SER E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.703A pdb=" N ASN E 186 " --> pdb=" O VAL E 182 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER E 198 " --> pdb=" O THR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 223 through 240 removed outlier: 3.837A 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: 3.670A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.973A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.762A 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: 3.633A pdb=" N VAL E 328 " --> pdb=" O VAL E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.930A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 4.317A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 436 removed outlier: 4.398A pdb=" N PHE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 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: 3.701A 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: 3.738A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 Processing helix chain 'I' and resid 180 through 193 removed outlier: 3.522A pdb=" N ASN I 184 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 214 removed outlier: 3.505A pdb=" N LEU I 207 " --> pdb=" O ASP I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 3.649A pdb=" N LEU I 225 " --> pdb=" O THR I 221 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 242 removed outlier: 4.089A pdb=" N ARG I 241 " --> pdb=" O THR I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 275 through 282 removed outlier: 4.361A pdb=" N GLN I 280 " --> pdb=" O GLY I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 294 Processing helix chain 'I' and resid 295 through 299 removed outlier: 3.609A 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: 3.623A 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: 4.278A pdb=" N LEU I 377 " --> pdb=" O ALA I 373 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE I 378 " --> pdb=" O ILE I 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 400 removed outlier: 4.152A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 4.337A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR I 409 " --> pdb=" O GLU I 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR I 422 " --> pdb=" O LEU I 418 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 29 Processing helix chain 'S' and resid 36 through 43 removed outlier: 3.970A pdb=" N LYS S 40 " --> pdb=" O MET S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 80 removed outlier: 4.407A pdb=" N ILE S 75 " --> pdb=" O GLU S 71 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL S 78 " --> pdb=" O VAL S 74 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR S 80 " --> pdb=" O ASP S 76 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 108 Processing helix chain 'S' and resid 114 through 128 Processing helix chain 'S' and resid 143 through 161 removed outlier: 4.105A pdb=" N THR S 150 " --> pdb=" O GLY S 146 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 198 removed outlier: 3.606A pdb=" N ASN S 186 " --> pdb=" O VAL S 182 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS S 192 " --> pdb=" O ILE S 188 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR S 193 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU S 196 " --> pdb=" O HIS S 192 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER S 198 " --> pdb=" O THR S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 205 through 216 Processing helix chain 'S' and resid 223 through 240 removed outlier: 3.812A 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: 3.717A pdb=" N GLN S 256 " --> pdb=" O LEU S 252 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 282 removed outlier: 4.020A pdb=" N TYR S 282 " --> pdb=" O ALA S 278 " (cutoff:3.500A) Processing helix chain 'S' and resid 287 through 297 removed outlier: 3.684A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.707A pdb=" N VAL S 328 " --> pdb=" O VAL S 324 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR S 337 " --> pdb=" O ALA S 333 " (cutoff:3.500A) Processing helix chain 'S' and resid 383 through 400 removed outlier: 4.019A pdb=" N ALA S 387 " --> pdb=" O ALA S 383 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU S 391 " --> pdb=" O ALA S 387 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 410 removed outlier: 4.296A pdb=" N TYR S 408 " --> pdb=" O PHE S 404 " (cutoff:3.500A) Processing helix chain 'S' and resid 414 through 436 removed outlier: 4.313A pdb=" N PHE S 418 " --> pdb=" O GLU S 414 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER S 419 " --> pdb=" O GLU S 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.576A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.576A pdb=" N LYS K 7 " --> pdb=" O MET K 327 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ALA K 329 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA K 9 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU K 331 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG K 11 " --> pdb=" O LEU K 331 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL K 91 " --> pdb=" O SER K 245 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL K 247 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE K 93 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL K 142 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL K 186 " --> pdb=" O VAL K 142 " (cutoff:3.500A) 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 168 through 171 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 56 removed outlier: 8.901A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 3.866A 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 56 removed outlier: 8.901A pdb=" N TYR N 54 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL N 8 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N TYR N 56 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL N 10 " --> pdb=" O TYR N 56 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA N 326 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 3.866A 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: 8.766A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU A 3 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 135 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 5 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL A 137 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 7 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A 139 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 9 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 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 removed outlier: 6.722A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 90 through 91 removed outlier: 8.098A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA B 9 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N ILE B 163 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.942A 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 54 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 7.634A pdb=" N GLU E 3 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE E 135 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE E 5 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 137 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 7 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N HIS E 139 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL E 9 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.521A 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: 8.110A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.559A 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: 8.110A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA I 9 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL I 169 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS I 137 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 4.938A 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: 8.390A pdb=" N VAL S 66 " --> pdb=" O CYS S 4 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N SER S 6 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL S 68 " --> pdb=" O SER S 6 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N HIS S 8 " --> pdb=" O VAL S 68 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU S 3 " --> pdb=" O LEU S 132 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY S 134 " --> pdb=" O GLU S 3 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N SER S 140 " --> pdb=" O VAL S 9 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLN S 133 " --> pdb=" O SER S 165 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU S 167 " --> pdb=" O GLN S 133 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE S 135 " --> pdb=" O LEU S 167 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE S 169 " --> pdb=" O PHE S 135 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N VAL S 137 " --> pdb=" O PHE S 169 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE S 171 " --> pdb=" O VAL S 137 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS S 139 " --> pdb=" O ILE S 171 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS S 166 " --> pdb=" O CYS S 200 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE S 202 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU S 168 " --> pdb=" O PHE S 202 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N VAL S 204 " --> pdb=" O GLU S 168 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER S 170 " --> pdb=" O VAL S 204 " (cutoff:3.500A) 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 1165 hydrogen bonds defined for protein. 3351 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: 7.73 Time building geometry restraints manager: 7.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4082 1.32 - 1.44: 6432 1.44 - 1.57: 13488 1.57 - 1.69: 40 1.69 - 1.82: 242 Bond restraints: 24284 Sorted by residual: bond pdb=" N3B ANP N 501 " pdb=" PG ANP N 501 " ideal model delta sigma weight residual 1.795 1.613 0.182 2.00e-02 2.50e+03 8.32e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C ASN K 293 " pdb=" O ASN K 293 " ideal model delta sigma weight residual 1.235 1.303 -0.068 1.10e-02 8.26e+03 3.79e+01 bond pdb=" O3A ANP N 501 " pdb=" PB ANP N 501 " ideal model delta sigma weight residual 1.700 1.588 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N ASP I 427 " pdb=" CA ASP I 427 " ideal model delta sigma weight residual 1.457 1.529 -0.071 1.29e-02 6.01e+03 3.06e+01 ... (remaining 24279 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 32568 3.53 - 7.06: 371 7.06 - 10.58: 16 10.58 - 14.11: 8 14.11 - 17.64: 1 Bond angle restraints: 32964 Sorted by residual: angle pdb=" N GLU I 27 " pdb=" CA GLU I 27 " pdb=" C GLU I 27 " ideal model delta sigma weight residual 113.88 101.64 12.24 1.23e+00 6.61e-01 9.90e+01 angle pdb=" C ASN K 293 " pdb=" N LYS K 294 " pdb=" CA LYS K 294 " ideal model delta sigma weight residual 121.81 109.46 12.35 1.83e+00 2.99e-01 4.56e+01 angle pdb=" C PRO N 333 " pdb=" CA PRO N 333 " pdb=" CB PRO N 333 " ideal model delta sigma weight residual 111.56 101.39 10.17 1.65e+00 3.67e-01 3.80e+01 angle pdb=" PB ANP K 502 " pdb=" N3B ANP K 502 " pdb=" PG ANP K 502 " ideal model delta sigma weight residual 126.95 109.31 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" N ASP K 114 " pdb=" CA ASP K 114 " pdb=" C ASP K 114 " ideal model delta sigma weight residual 113.02 106.38 6.64 1.20e+00 6.94e-01 3.06e+01 ... (remaining 32959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.39: 13975 30.39 - 60.77: 651 60.77 - 91.16: 95 91.16 - 121.55: 11 121.55 - 151.93: 26 Dihedral angle restraints: 14758 sinusoidal: 6103 harmonic: 8655 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 -138.80 -151.93 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" C5' GTP S 501 " pdb=" O5' GTP S 501 " pdb=" PA GTP S 501 " pdb=" O3A GTP S 501 " ideal model delta sinusoidal sigma weight residual 69.27 -141.99 -148.74 1 2.00e+01 2.50e-03 4.45e+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 260.87 113.35 147.52 1 2.00e+01 2.50e-03 4.42e+01 ... (remaining 14755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 3490 0.115 - 0.231: 120 0.231 - 0.346: 5 0.346 - 0.461: 0 0.461 - 0.577: 1 Chirality restraints: 3616 Sorted by residual: chirality pdb=" C18 TA1 I 502 " pdb=" C10 TA1 I 502 " pdb=" C17 TA1 I 502 " pdb=" C20 TA1 I 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.59 -0.58 2.00e-01 2.50e+01 8.32e+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 -2.67 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ILE N 27 " pdb=" N ILE N 27 " pdb=" C ILE N 27 " pdb=" CB ILE N 27 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3613 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS K 296 " 0.022 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C LYS K 296 " -0.080 2.00e-02 2.50e+03 pdb=" O LYS K 296 " 0.029 2.00e-02 2.50e+03 pdb=" N LYS K 297 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG N 11 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG N 11 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG N 11 " -0.030 2.00e-02 2.50e+03 pdb=" N VAL N 12 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP I 21 " -0.023 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C TRP I 21 " 0.077 2.00e-02 2.50e+03 pdb=" O TRP I 21 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU I 22 " -0.026 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 141 2.52 - 3.11: 17365 3.11 - 3.71: 35131 3.71 - 4.30: 50377 4.30 - 4.90: 86969 Nonbonded interactions: 189983 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.920 2.170 nonbonded pdb=" O1B GTP S 501 " pdb="MG MG S 502 " model vdw 1.944 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.950 2.170 nonbonded pdb=" OE1 GLU S 71 " pdb="MG MG S 502 " model vdw 1.959 2.170 nonbonded pdb=" O1G GTP S 501 " pdb="MG MG S 502 " model vdw 1.967 2.170 ... (remaining 189978 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=0.49 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: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 57.470 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.006 0.182 24284 Z= 0.309 Angle : 0.892 17.641 32964 Z= 0.484 Chirality : 0.050 0.577 3616 Planarity : 0.006 0.086 4287 Dihedral : 18.882 151.934 9206 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.84 % Allowed : 3.67 % Favored : 95.48 % Rotamer: Outliers : 1.64 % Allowed : 16.48 % Favored : 81.88 % Cbeta Deviations : 0.07 % 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: -0.26 (0.15), residues: 2976 helix: 0.97 (0.15), residues: 1216 sheet: -0.09 (0.22), residues: 527 loop : -1.35 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 57 HIS 0.013 0.001 HIS I 28 PHE 0.034 0.002 PHE S 255 TYR 0.015 0.002 TYR K 74 ARG 0.015 0.001 ARG K 75 Details of bonding type rmsd hydrogen bonds : bond 0.15633 ( 1097) hydrogen bonds : angle 5.99429 ( 3351) covalent geometry : bond 0.00598 (24284) covalent geometry : angle 0.89206 (32964) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 485 time to evaluate : 2.627 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7114 (mp0) REVERT: K 56 TYR cc_start: 0.7932 (m-80) cc_final: 0.7509 (m-10) REVERT: K 116 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7193 (mt0) REVERT: N 107 MET cc_start: 0.7588 (mmm) cc_final: 0.6927 (tpp) REVERT: N 274 SER cc_start: 0.8769 (t) cc_final: 0.8263 (p) REVERT: N 333 PRO cc_start: 0.8570 (OUTLIER) cc_final: 0.8349 (Cg_endo) REVERT: N 352 LYS cc_start: 0.6008 (OUTLIER) cc_final: 0.5619 (pttp) REVERT: A 254 GLU cc_start: 0.4542 (mm-30) cc_final: 0.3057 (pt0) REVERT: B 195 ASN cc_start: 0.8235 (m-40) cc_final: 0.7850 (m110) REVERT: B 239 CYS cc_start: 0.8586 (m) cc_final: 0.8371 (m) REVERT: E 195 LEU cc_start: 0.7892 (tt) cc_final: 0.7691 (tt) REVERT: I 1 MET cc_start: 0.6078 (mmp) cc_final: 0.5760 (mmp) REVERT: I 417 ASP cc_start: 0.7533 (m-30) cc_final: 0.7038 (m-30) REVERT: S 108 TYR cc_start: 0.8565 (m-80) cc_final: 0.8073 (m-10) REVERT: S 401 LYS cc_start: 0.8972 (mtpp) cc_final: 0.8341 (mtmt) REVERT: S 451 TYR cc_start: 0.0947 (OUTLIER) cc_final: 0.0345 (p90) outliers start: 37 outliers final: 12 residues processed: 513 average time/residue: 0.3482 time to fit residues: 277.7403 Evaluate side-chains 488 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 472 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 116 GLN Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 283 SER Chi-restraints excluded: chain K residue 288 MET Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 289 ASP Chi-restraints excluded: chain N residue 295 ASN Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 333 PRO Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 359 ARG Chi-restraints excluded: chain S residue 451 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 0.6980 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 232 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 268 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 116 GLN K 293 ASN N 98 GLN N 318 ASN A 256 GLN B 165 ASN B 204 ASN B 335 ASN B 424 GLN B 426 GLN E 15 GLN E 107 HIS E 128 GLN E 197 HIS E 358 GLN I 195 ASN I 416 ASN I 426 GLN I 433 GLN A S 285 GLN S 358 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.136840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104898 restraints weight = 35257.755| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.29 r_work: 0.3353 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24284 Z= 0.133 Angle : 0.597 11.888 32964 Z= 0.296 Chirality : 0.044 0.342 3616 Planarity : 0.004 0.055 4287 Dihedral : 12.700 155.282 3643 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.40 % Favored : 96.36 % Rotamer: Outliers : 3.01 % Allowed : 14.76 % Favored : 82.23 % 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: 0.28 (0.15), residues: 2976 helix: 1.53 (0.15), residues: 1247 sheet: 0.20 (0.22), residues: 539 loop : -1.27 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 388 HIS 0.005 0.001 HIS I 137 PHE 0.015 0.001 PHE E 255 TYR 0.016 0.001 TYR K 74 ARG 0.005 0.000 ARG I 241 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 1097) hydrogen bonds : angle 4.19544 ( 3351) covalent geometry : bond 0.00296 (24284) covalent geometry : angle 0.59679 (32964) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 492 time to evaluate : 2.407 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7141 (mp0) REVERT: K 60 THR cc_start: 0.6434 (p) cc_final: 0.6116 (p) REVERT: K 340 GLU cc_start: 0.7844 (mp0) cc_final: 0.7217 (mp0) REVERT: N 82 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5616 (mm) REVERT: N 107 MET cc_start: 0.7676 (mmm) cc_final: 0.6906 (tpp) REVERT: N 274 SER cc_start: 0.8740 (t) cc_final: 0.8222 (p) REVERT: A 119 LEU cc_start: 0.8381 (mp) cc_final: 0.7980 (mt) REVERT: A 254 GLU cc_start: 0.4509 (mm-30) cc_final: 0.3112 (pt0) REVERT: A 256 GLN cc_start: 0.8045 (mt0) cc_final: 0.7649 (mt0) REVERT: B 195 ASN cc_start: 0.8429 (m-40) cc_final: 0.8108 (m-40) REVERT: B 213 ARG cc_start: 0.8555 (ttp80) cc_final: 0.8235 (mtm180) REVERT: B 226 ASN cc_start: 0.8134 (m-40) cc_final: 0.7898 (m-40) REVERT: B 237 THR cc_start: 0.8831 (p) cc_final: 0.8612 (t) REVERT: B 426 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: E 449 GLU cc_start: 0.4849 (OUTLIER) cc_final: 0.4413 (pp20) REVERT: S 24 TYR cc_start: 0.8457 (m-80) cc_final: 0.7960 (m-80) REVERT: S 69 ASP cc_start: 0.8578 (t70) cc_final: 0.8325 (t70) REVERT: S 108 TYR cc_start: 0.8579 (m-80) cc_final: 0.7994 (m-10) REVERT: S 129 CYS cc_start: 0.8025 (m) cc_final: 0.7718 (m) REVERT: S 275 VAL cc_start: 0.8223 (t) cc_final: 0.7982 (p) REVERT: S 401 LYS cc_start: 0.8975 (mtpp) cc_final: 0.8289 (mtmt) outliers start: 72 outliers final: 40 residues processed: 530 average time/residue: 0.3441 time to fit residues: 286.9743 Evaluate side-chains 497 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 454 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 283 SER Chi-restraints excluded: chain K residue 319 LEU Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 265 ILE Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 367 ASP Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 200 ASN N 227 GLN B 165 ASN B 279 GLN S 15 GLN S 197 HIS S 301 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.137057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104991 restraints weight = 36901.672| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.33 r_work: 0.3332 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24284 Z= 0.143 Angle : 0.562 8.368 32964 Z= 0.282 Chirality : 0.045 0.457 3616 Planarity : 0.004 0.060 4287 Dihedral : 10.086 153.706 3622 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.27 % Favored : 96.49 % Rotamer: Outliers : 3.05 % Allowed : 15.23 % Favored : 81.73 % 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 (0.15), residues: 2976 helix: 1.75 (0.15), residues: 1239 sheet: 0.35 (0.22), residues: 542 loop : -1.19 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 21 HIS 0.005 0.001 HIS E 88 PHE 0.017 0.001 PHE S 296 TYR 0.015 0.001 TYR K 74 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 1097) hydrogen bonds : angle 4.01325 ( 3351) covalent geometry : bond 0.00331 (24284) covalent geometry : angle 0.56220 (32964) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 471 time to evaluate : 2.517 Fit side-chains REVERT: K 60 THR cc_start: 0.6528 (p) cc_final: 0.6212 (p) REVERT: K 98 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: N 13 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7445 (ppt170) REVERT: N 82 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5773 (mt) REVERT: N 98 GLN cc_start: 0.7388 (mp10) cc_final: 0.6950 (mp10) REVERT: N 107 MET cc_start: 0.7679 (mmm) cc_final: 0.6886 (tpp) REVERT: N 274 SER cc_start: 0.8756 (t) cc_final: 0.8233 (p) REVERT: A 3 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: A 254 GLU cc_start: 0.4626 (mm-30) cc_final: 0.3116 (pt0) REVERT: A 256 GLN cc_start: 0.7994 (mt0) cc_final: 0.7708 (mt0) REVERT: B 147 MET cc_start: 0.8172 (mtp) cc_final: 0.7963 (mtm) REVERT: B 213 ARG cc_start: 0.8554 (ttp80) cc_final: 0.8236 (mtm180) REVERT: B 226 ASN cc_start: 0.8160 (m-40) cc_final: 0.7839 (m110) REVERT: B 237 THR cc_start: 0.8871 (p) cc_final: 0.8570 (t) REVERT: B 335 ASN cc_start: 0.8360 (m110) cc_final: 0.8121 (m-40) REVERT: E 203 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8208 (mtt) REVERT: E 449 GLU cc_start: 0.4850 (OUTLIER) cc_final: 0.4465 (pp20) REVERT: I 1 MET cc_start: 0.6989 (mmp) cc_final: 0.6623 (mmp) REVERT: I 321 MET cc_start: 0.9169 (ptp) cc_final: 0.8935 (ptp) REVERT: S 108 TYR cc_start: 0.8560 (m-80) cc_final: 0.7928 (m-10) REVERT: S 129 CYS cc_start: 0.7952 (m) cc_final: 0.7676 (m) REVERT: S 275 VAL cc_start: 0.8271 (t) cc_final: 0.8071 (p) REVERT: S 401 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8295 (mtmt) outliers start: 72 outliers final: 55 residues processed: 507 average time/residue: 0.3309 time to fit residues: 263.1221 Evaluate side-chains 518 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 457 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 265 ILE Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Chi-restraints excluded: chain S residue 451 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 14 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 286 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN B 165 ASN B 195 ASN S 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.134050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101789 restraints weight = 41754.411| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.47 r_work: 0.3268 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3095 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3095 r_free = 0.3095 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24284 Z= 0.232 Angle : 0.603 8.398 32964 Z= 0.305 Chirality : 0.047 0.351 3616 Planarity : 0.005 0.067 4287 Dihedral : 9.751 153.868 3615 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 3.63 % Allowed : 15.31 % Favored : 81.06 % 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: 2976 helix: 1.74 (0.15), residues: 1232 sheet: 0.41 (0.22), residues: 535 loop : -1.34 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 21 HIS 0.009 0.001 HIS A 88 PHE 0.022 0.002 PHE E 255 TYR 0.023 0.002 TYR S 24 ARG 0.006 0.001 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 1097) hydrogen bonds : angle 4.08629 ( 3351) covalent geometry : bond 0.00567 (24284) covalent geometry : angle 0.60310 (32964) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 491 time to evaluate : 2.631 Fit side-chains REVERT: K 30 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7480 (mtt) REVERT: K 60 THR cc_start: 0.6760 (p) cc_final: 0.6448 (p) REVERT: K 98 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8260 (pt0) REVERT: K 116 GLN cc_start: 0.7360 (mt0) cc_final: 0.6572 (mt0) REVERT: K 146 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7027 (t80) REVERT: N 13 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7389 (ppt170) REVERT: N 74 TYR cc_start: 0.7434 (t80) cc_final: 0.7190 (t80) REVERT: N 82 LEU cc_start: 0.6096 (OUTLIER) cc_final: 0.5826 (mt) REVERT: N 107 MET cc_start: 0.7690 (mmm) cc_final: 0.6880 (tpp) REVERT: N 274 SER cc_start: 0.8821 (t) cc_final: 0.8308 (p) REVERT: A 3 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7549 (pt0) REVERT: A 191 THR cc_start: 0.8383 (m) cc_final: 0.8056 (p) REVERT: A 254 GLU cc_start: 0.4751 (mm-30) cc_final: 0.3776 (tp30) REVERT: B 75 SER cc_start: 0.8725 (t) cc_final: 0.8441 (t) REVERT: B 195 ASN cc_start: 0.8477 (m-40) cc_final: 0.8175 (m-40) REVERT: B 226 ASN cc_start: 0.8273 (m-40) cc_final: 0.7963 (m110) REVERT: B 276 ARG cc_start: 0.8380 (ttp-170) cc_final: 0.8078 (ttp-170) REVERT: E 147 SER cc_start: 0.8210 (p) cc_final: 0.7975 (p) REVERT: E 168 GLU cc_start: 0.8270 (tt0) cc_final: 0.8070 (mt-10) REVERT: E 203 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8364 (mtt) REVERT: E 449 GLU cc_start: 0.4777 (OUTLIER) cc_final: 0.4476 (pp20) REVERT: I 1 MET cc_start: 0.7114 (mmp) cc_final: 0.6760 (mmp) REVERT: S 108 TYR cc_start: 0.8623 (m-80) cc_final: 0.7920 (m-10) REVERT: S 121 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7538 (mmm160) REVERT: S 129 CYS cc_start: 0.7972 (m) cc_final: 0.7713 (m) REVERT: S 177 VAL cc_start: 0.8614 (m) cc_final: 0.8413 (m) REVERT: S 401 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8280 (mtmt) REVERT: S 434 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8121 (mt-10) outliers start: 87 outliers final: 66 residues processed: 532 average time/residue: 0.3364 time to fit residues: 282.0782 Evaluate side-chains 549 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 475 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 204 THR Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 3 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 57 ASN Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 265 ILE Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 183 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 292 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 144 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 294 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 121 GLN A 128 GLN B 165 ASN E 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.135168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.103818 restraints weight = 35266.495| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.18 r_work: 0.3338 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24284 Z= 0.131 Angle : 0.533 7.767 32964 Z= 0.270 Chirality : 0.044 0.299 3616 Planarity : 0.004 0.064 4287 Dihedral : 9.423 156.373 3615 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer: Outliers : 3.48 % Allowed : 16.28 % Favored : 80.24 % 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: 0.57 (0.16), residues: 2976 helix: 1.85 (0.15), residues: 1240 sheet: 0.44 (0.22), residues: 541 loop : -1.26 (0.17), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 21 HIS 0.004 0.001 HIS E 88 PHE 0.013 0.001 PHE K 221 TYR 0.038 0.001 TYR S 24 ARG 0.005 0.000 ARG N 129 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 1097) hydrogen bonds : angle 3.90833 ( 3351) covalent geometry : bond 0.00301 (24284) covalent geometry : angle 0.53332 (32964) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 481 time to evaluate : 2.627 Fit side-chains REVERT: K 60 THR cc_start: 0.6701 (p) cc_final: 0.6378 (p) REVERT: K 98 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8450 (pt0) REVERT: K 301 THR cc_start: 0.3526 (OUTLIER) cc_final: 0.3223 (p) REVERT: N 13 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7416 (ppt170) REVERT: N 82 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5818 (mt) REVERT: N 107 MET cc_start: 0.7702 (mmm) cc_final: 0.6904 (tpp) REVERT: N 274 SER cc_start: 0.8777 (t) cc_final: 0.8242 (p) REVERT: N 352 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5760 (pttm) REVERT: A 191 THR cc_start: 0.8338 (m) cc_final: 0.8015 (p) REVERT: A 254 GLU cc_start: 0.4705 (mm-30) cc_final: 0.3810 (tp30) REVERT: A 256 GLN cc_start: 0.7989 (mt0) cc_final: 0.7704 (mt0) REVERT: B 75 SER cc_start: 0.8661 (t) cc_final: 0.8389 (t) REVERT: B 147 MET cc_start: 0.8169 (mtp) cc_final: 0.7935 (mtp) REVERT: B 195 ASN cc_start: 0.8412 (m-40) cc_final: 0.8114 (m-40) REVERT: B 213 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8189 (mtm180) REVERT: B 219 THR cc_start: 0.8944 (m) cc_final: 0.8626 (p) REVERT: B 226 ASN cc_start: 0.8180 (m-40) cc_final: 0.7851 (m110) REVERT: B 237 THR cc_start: 0.8865 (p) cc_final: 0.8561 (t) REVERT: B 276 ARG cc_start: 0.8309 (ttp-170) cc_final: 0.8047 (ttp-170) REVERT: B 282 ARG cc_start: 0.8465 (mtp85) cc_final: 0.8191 (ptm-80) REVERT: E 147 SER cc_start: 0.8138 (p) cc_final: 0.7899 (p) REVERT: E 203 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8208 (mtt) REVERT: I 1 MET cc_start: 0.6833 (mmp) cc_final: 0.6523 (mmp) REVERT: I 26 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7960 (t0) REVERT: S 108 TYR cc_start: 0.8546 (m-80) cc_final: 0.7753 (m-10) REVERT: S 129 CYS cc_start: 0.7907 (m) cc_final: 0.7599 (m) REVERT: S 401 LYS cc_start: 0.8893 (mtpp) cc_final: 0.8180 (mtmt) outliers start: 83 outliers final: 57 residues processed: 517 average time/residue: 0.3358 time to fit residues: 273.5517 Evaluate side-chains 521 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 457 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 26 ASP Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 74 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 236 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN B 165 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.135515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.104016 restraints weight = 35425.533| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.20 r_work: 0.3337 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24284 Z= 0.132 Angle : 0.532 7.799 32964 Z= 0.268 Chirality : 0.043 0.262 3616 Planarity : 0.004 0.060 4287 Dihedral : 9.262 158.033 3615 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.43 % Rotamer: Outliers : 3.51 % Allowed : 16.32 % Favored : 80.16 % 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: 0.65 (0.16), residues: 2976 helix: 1.92 (0.15), residues: 1240 sheet: 0.50 (0.22), residues: 535 loop : -1.23 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS E 88 PHE 0.014 0.001 PHE E 255 TYR 0.036 0.001 TYR S 24 ARG 0.005 0.000 ARG S 215 Details of bonding type rmsd hydrogen bonds : bond 0.04043 ( 1097) hydrogen bonds : angle 3.86011 ( 3351) covalent geometry : bond 0.00307 (24284) covalent geometry : angle 0.53232 (32964) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 481 time to evaluate : 2.708 Fit side-chains REVERT: K 60 THR cc_start: 0.6714 (p) cc_final: 0.6390 (p) REVERT: K 146 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.6901 (t80) REVERT: K 301 THR cc_start: 0.3475 (OUTLIER) cc_final: 0.3142 (p) REVERT: N 13 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7536 (ppt170) REVERT: N 82 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5765 (mt) REVERT: N 107 MET cc_start: 0.7661 (mmm) cc_final: 0.6917 (tpp) REVERT: N 274 SER cc_start: 0.8773 (t) cc_final: 0.8236 (p) REVERT: N 276 THR cc_start: 0.8259 (m) cc_final: 0.7190 (p) REVERT: N 352 LYS cc_start: 0.6077 (OUTLIER) cc_final: 0.5744 (pttm) REVERT: A 191 THR cc_start: 0.8305 (m) cc_final: 0.8016 (p) REVERT: A 254 GLU cc_start: 0.4742 (mm-30) cc_final: 0.3881 (tp30) REVERT: A 256 GLN cc_start: 0.7939 (mt0) cc_final: 0.7676 (mt0) REVERT: B 75 SER cc_start: 0.8642 (t) cc_final: 0.8370 (t) REVERT: B 213 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8201 (mtm180) REVERT: B 219 THR cc_start: 0.8952 (m) cc_final: 0.8664 (p) REVERT: B 226 ASN cc_start: 0.8187 (m-40) cc_final: 0.7868 (m110) REVERT: B 237 THR cc_start: 0.8860 (p) cc_final: 0.8573 (t) REVERT: B 276 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.8051 (ttp-170) REVERT: B 282 ARG cc_start: 0.8450 (mtp85) cc_final: 0.8226 (ptm-80) REVERT: E 147 SER cc_start: 0.8089 (p) cc_final: 0.7854 (p) REVERT: E 203 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8189 (mtt) REVERT: E 242 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8752 (pp) REVERT: E 449 GLU cc_start: 0.4696 (OUTLIER) cc_final: 0.4430 (pp20) REVERT: I 1 MET cc_start: 0.6896 (mmp) cc_final: 0.6541 (mmp) REVERT: I 26 ASP cc_start: 0.8357 (t70) cc_final: 0.8019 (t0) REVERT: S 24 TYR cc_start: 0.8299 (m-80) cc_final: 0.8029 (m-80) REVERT: S 97 GLU cc_start: 0.8501 (mp0) cc_final: 0.8088 (mp0) REVERT: S 108 TYR cc_start: 0.8546 (m-80) cc_final: 0.7796 (m-10) REVERT: S 302 MET cc_start: 0.8173 (mmm) cc_final: 0.7537 (mmm) REVERT: S 401 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8169 (mtmt) REVERT: S 434 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7954 (mt-10) outliers start: 84 outliers final: 67 residues processed: 521 average time/residue: 0.3311 time to fit residues: 270.9533 Evaluate side-chains 541 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 466 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 222 ASN Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 242 LEU Chi-restraints excluded: chain S residue 245 ASP Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 224 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 257 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN I 204 ASN S 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.131819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099839 restraints weight = 42139.495| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.45 r_work: 0.3262 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 24284 Z= 0.248 Angle : 0.605 9.010 32964 Z= 0.307 Chirality : 0.047 0.262 3616 Planarity : 0.005 0.058 4287 Dihedral : 9.456 155.038 3613 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.91 % Favored : 95.99 % Rotamer: Outliers : 3.90 % Allowed : 16.17 % Favored : 79.93 % 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: 0.42 (0.15), residues: 2976 helix: 1.76 (0.15), residues: 1232 sheet: 0.42 (0.22), residues: 535 loop : -1.39 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 21 HIS 0.010 0.002 HIS A 88 PHE 0.018 0.002 PHE E 141 TYR 0.031 0.002 TYR S 24 ARG 0.005 0.001 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 1097) hydrogen bonds : angle 4.05223 ( 3351) covalent geometry : bond 0.00609 (24284) covalent geometry : angle 0.60510 (32964) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 491 time to evaluate : 2.437 Fit side-chains revert: symmetry clash REVERT: K 60 THR cc_start: 0.6859 (p) cc_final: 0.6542 (p) REVERT: K 146 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7054 (t80) REVERT: K 301 THR cc_start: 0.3444 (OUTLIER) cc_final: 0.3072 (p) REVERT: K 340 GLU cc_start: 0.7904 (mp0) cc_final: 0.7225 (mt-10) REVERT: N 13 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7458 (ppt170) REVERT: N 107 MET cc_start: 0.7636 (mmm) cc_final: 0.6922 (tpp) REVERT: N 169 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8128 (mtt-85) REVERT: N 274 SER cc_start: 0.8833 (t) cc_final: 0.8315 (p) REVERT: N 345 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8257 (mp) REVERT: N 352 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5711 (pttm) REVERT: A 191 THR cc_start: 0.8361 (m) cc_final: 0.8103 (p) REVERT: A 254 GLU cc_start: 0.4689 (mm-30) cc_final: 0.3884 (tp30) REVERT: A 334 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8156 (t) REVERT: A 433 GLU cc_start: 0.8283 (tt0) cc_final: 0.7882 (tt0) REVERT: B 75 SER cc_start: 0.8653 (t) cc_final: 0.8372 (t) REVERT: B 195 ASN cc_start: 0.8510 (m-40) cc_final: 0.8215 (m-40) REVERT: B 219 THR cc_start: 0.8971 (m) cc_final: 0.8692 (p) REVERT: B 226 ASN cc_start: 0.8271 (m-40) cc_final: 0.7966 (m110) REVERT: B 276 ARG cc_start: 0.8393 (ttp-170) cc_final: 0.8116 (ttp-170) REVERT: B 299 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: E 1 MET cc_start: 0.7527 (mpp) cc_final: 0.7114 (mpp) REVERT: E 147 SER cc_start: 0.8207 (p) cc_final: 0.7990 (p) REVERT: E 203 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8430 (mtt) REVERT: E 449 GLU cc_start: 0.4664 (OUTLIER) cc_final: 0.4385 (pp20) REVERT: S 24 TYR cc_start: 0.8348 (m-80) cc_final: 0.8121 (m-80) REVERT: S 75 ILE cc_start: 0.8785 (mm) cc_final: 0.8421 (mt) REVERT: S 97 GLU cc_start: 0.8501 (mp0) cc_final: 0.8099 (mp0) REVERT: S 401 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8223 (mtmt) REVERT: S 434 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8110 (mt-10) outliers start: 94 outliers final: 70 residues processed: 537 average time/residue: 0.3295 time to fit residues: 279.1775 Evaluate side-chains 558 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 479 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 31 SER Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 93 ILE Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 165 ASN Chi-restraints excluded: chain K residue 186 VAL Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 147 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 125 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 259 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 182 optimal weight: 0.7980 chunk 225 optimal weight: 0.8980 chunk 167 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 259 optimal weight: 0.0770 chunk 6 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 152 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 A 128 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 GLN E 301 GLN I 131 GLN I 396 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.135579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103810 restraints weight = 39629.137| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.35 r_work: 0.3331 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24284 Z= 0.117 Angle : 0.530 7.998 32964 Z= 0.267 Chirality : 0.043 0.238 3616 Planarity : 0.004 0.055 4287 Dihedral : 9.127 157.388 3613 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 3.01 % Allowed : 17.57 % Favored : 79.42 % 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: 0.63 (0.16), residues: 2976 helix: 1.94 (0.15), residues: 1233 sheet: 0.50 (0.22), residues: 534 loop : -1.28 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 388 HIS 0.003 0.001 HIS B 137 PHE 0.014 0.001 PHE E 255 TYR 0.030 0.001 TYR S 24 ARG 0.005 0.000 ARG S 215 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 1097) hydrogen bonds : angle 3.85659 ( 3351) covalent geometry : bond 0.00263 (24284) covalent geometry : angle 0.52983 (32964) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 484 time to evaluate : 2.565 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7062 (mp0) REVERT: K 60 THR cc_start: 0.6800 (p) cc_final: 0.6487 (p) REVERT: K 146 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.6924 (t80) REVERT: K 301 THR cc_start: 0.3413 (OUTLIER) cc_final: 0.3060 (p) REVERT: N 13 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7541 (ppt170) REVERT: N 82 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5795 (mt) REVERT: N 107 MET cc_start: 0.7695 (mmm) cc_final: 0.6956 (tpp) REVERT: N 274 SER cc_start: 0.8778 (t) cc_final: 0.8259 (p) REVERT: N 276 THR cc_start: 0.8277 (m) cc_final: 0.7321 (p) REVERT: N 352 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5574 (pttm) REVERT: A 191 THR cc_start: 0.8308 (m) cc_final: 0.8051 (p) REVERT: A 254 GLU cc_start: 0.4717 (mm-30) cc_final: 0.3914 (tp30) REVERT: A 256 GLN cc_start: 0.7909 (mt0) cc_final: 0.7668 (mt0) REVERT: B 75 SER cc_start: 0.8618 (t) cc_final: 0.8351 (t) REVERT: B 195 ASN cc_start: 0.8405 (m-40) cc_final: 0.8112 (m-40) REVERT: B 213 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8192 (mtm180) REVERT: B 218 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 219 THR cc_start: 0.8977 (m) cc_final: 0.8705 (p) REVERT: B 226 ASN cc_start: 0.8189 (m-40) cc_final: 0.7862 (m110) REVERT: B 237 THR cc_start: 0.8839 (p) cc_final: 0.8553 (t) REVERT: B 276 ARG cc_start: 0.8271 (ttp-170) cc_final: 0.8026 (ttp-170) REVERT: B 282 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8233 (ptm-80) REVERT: E 1 MET cc_start: 0.7427 (mpp) cc_final: 0.7047 (mpp) REVERT: E 147 SER cc_start: 0.8123 (p) cc_final: 0.7904 (p) REVERT: E 203 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8235 (mtt) REVERT: E 242 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (pp) REVERT: I 95 SER cc_start: 0.8257 (m) cc_final: 0.8021 (p) REVERT: I 416 ASN cc_start: 0.8455 (m-40) cc_final: 0.8241 (m-40) REVERT: S 69 ASP cc_start: 0.8532 (t70) cc_final: 0.8233 (t70) REVERT: S 97 GLU cc_start: 0.8458 (mp0) cc_final: 0.8061 (mp0) REVERT: S 238 ILE cc_start: 0.8126 (mt) cc_final: 0.7665 (tt) REVERT: S 302 MET cc_start: 0.8227 (mmm) cc_final: 0.7586 (mmm) REVERT: S 306 ASP cc_start: 0.8238 (t0) cc_final: 0.7972 (t0) REVERT: S 401 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8159 (mtmt) REVERT: S 414 GLU cc_start: 0.6825 (pt0) cc_final: 0.6567 (mt-10) REVERT: S 434 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7961 (mt-10) outliers start: 71 outliers final: 54 residues processed: 523 average time/residue: 0.3401 time to fit residues: 280.8308 Evaluate side-chains 536 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 474 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 122 ILE Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU 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 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 91 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 285 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.133602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.101495 restraints weight = 48795.953| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.72 r_work: 0.3270 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24284 Z= 0.183 Angle : 0.576 11.322 32964 Z= 0.290 Chirality : 0.045 0.277 3616 Planarity : 0.004 0.054 4287 Dihedral : 9.174 157.214 3613 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 3.20 % Allowed : 17.73 % Favored : 79.07 % 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: 0.56 (0.16), residues: 2976 helix: 1.86 (0.15), residues: 1234 sheet: 0.49 (0.22), residues: 532 loop : -1.30 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 21 HIS 0.007 0.001 HIS E 88 PHE 0.021 0.002 PHE S 296 TYR 0.037 0.001 TYR S 24 ARG 0.008 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 1097) hydrogen bonds : angle 3.93098 ( 3351) covalent geometry : bond 0.00441 (24284) covalent geometry : angle 0.57593 (32964) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 482 time to evaluate : 2.593 Fit side-chains revert: symmetry clash REVERT: K 60 THR cc_start: 0.6892 (p) cc_final: 0.6574 (p) REVERT: K 146 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7023 (t80) REVERT: K 301 THR cc_start: 0.3208 (OUTLIER) cc_final: 0.2840 (p) REVERT: N 13 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7415 (ppt170) REVERT: N 107 MET cc_start: 0.7581 (mmm) cc_final: 0.6856 (tpp) REVERT: N 146 TYR cc_start: 0.7956 (t80) cc_final: 0.7635 (t80) REVERT: N 169 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7957 (mtt-85) REVERT: N 270 ASN cc_start: 0.8266 (m-40) cc_final: 0.8042 (m-40) REVERT: N 274 SER cc_start: 0.8719 (t) cc_final: 0.8193 (p) REVERT: N 276 THR cc_start: 0.8192 (m) cc_final: 0.7274 (p) REVERT: N 352 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.5619 (pttp) REVERT: A 191 THR cc_start: 0.8278 (m) cc_final: 0.8037 (p) REVERT: A 254 GLU cc_start: 0.4700 (mm-30) cc_final: 0.3851 (tp30) REVERT: A 256 GLN cc_start: 0.7916 (mt0) cc_final: 0.7684 (mt0) REVERT: B 75 SER cc_start: 0.8578 (t) cc_final: 0.8300 (t) REVERT: B 213 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8129 (mtm180) REVERT: B 218 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8446 (m) REVERT: B 219 THR cc_start: 0.8944 (m) cc_final: 0.8699 (p) REVERT: B 226 ASN cc_start: 0.8094 (m-40) cc_final: 0.7779 (m110) REVERT: B 237 THR cc_start: 0.8841 (p) cc_final: 0.8518 (t) REVERT: B 276 ARG cc_start: 0.8279 (ttp-170) cc_final: 0.8010 (ttp-170) REVERT: E 1 MET cc_start: 0.7198 (mpp) cc_final: 0.6902 (mpp) REVERT: E 147 SER cc_start: 0.8055 (p) cc_final: 0.7839 (p) REVERT: E 203 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: I 95 SER cc_start: 0.8164 (m) cc_final: 0.7932 (p) REVERT: S 97 GLU cc_start: 0.8423 (mp0) cc_final: 0.8033 (mp0) REVERT: S 401 LYS cc_start: 0.8885 (mtpp) cc_final: 0.8165 (mtmt) REVERT: S 414 GLU cc_start: 0.6794 (pt0) cc_final: 0.6559 (mt-10) REVERT: S 434 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7844 (mt-10) outliers start: 76 outliers final: 63 residues processed: 525 average time/residue: 0.3434 time to fit residues: 283.9109 Evaluate side-chains 542 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 473 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 55 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 98 GLN Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 336 ILE Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 26 LEU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 295 CYS Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 198 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 213 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN B 195 ASN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.136076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104393 restraints weight = 42175.953| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.41 r_work: 0.3327 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24284 Z= 0.116 Angle : 0.544 10.723 32964 Z= 0.273 Chirality : 0.043 0.280 3616 Planarity : 0.004 0.053 4287 Dihedral : 9.012 159.014 3613 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Rotamer: Outliers : 2.69 % Allowed : 18.31 % Favored : 78.99 % 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: 0.66 (0.16), residues: 2976 helix: 1.92 (0.15), residues: 1243 sheet: 0.50 (0.22), residues: 534 loop : -1.22 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP S 388 HIS 0.003 0.001 HIS I 137 PHE 0.019 0.001 PHE S 296 TYR 0.035 0.001 TYR N 74 ARG 0.007 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 1097) hydrogen bonds : angle 3.85925 ( 3351) covalent geometry : bond 0.00262 (24284) covalent geometry : angle 0.54414 (32964) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 482 time to evaluate : 2.755 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7094 (mp0) REVERT: K 60 THR cc_start: 0.6855 (p) cc_final: 0.6534 (p) REVERT: K 146 TYR cc_start: 0.8180 (OUTLIER) cc_final: 0.7026 (t80) REVERT: K 301 THR cc_start: 0.3092 (OUTLIER) cc_final: 0.2725 (p) REVERT: N 13 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7494 (ppt170) REVERT: N 107 MET cc_start: 0.7617 (mmm) cc_final: 0.6949 (tpp) REVERT: N 270 ASN cc_start: 0.8366 (m-40) cc_final: 0.8157 (m-40) REVERT: N 274 SER cc_start: 0.8790 (t) cc_final: 0.8274 (p) REVERT: N 276 THR cc_start: 0.8299 (m) cc_final: 0.7335 (p) REVERT: A 191 THR cc_start: 0.8322 (m) cc_final: 0.8068 (p) REVERT: A 254 GLU cc_start: 0.4710 (mm-30) cc_final: 0.3563 (tp30) REVERT: A 256 GLN cc_start: 0.7889 (mt0) cc_final: 0.7641 (mt0) REVERT: A 258 ASN cc_start: 0.8866 (m110) cc_final: 0.8464 (m110) REVERT: B 73 MET cc_start: 0.8312 (mmm) cc_final: 0.8112 (mmt) REVERT: B 75 SER cc_start: 0.8569 (t) cc_final: 0.8299 (t) REVERT: B 195 ASN cc_start: 0.8409 (m-40) cc_final: 0.8144 (m-40) REVERT: B 213 ARG cc_start: 0.8486 (ttp80) cc_final: 0.8185 (mtm180) REVERT: B 218 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8428 (m) REVERT: B 219 THR cc_start: 0.8989 (m) cc_final: 0.8777 (p) REVERT: B 226 ASN cc_start: 0.8198 (m-40) cc_final: 0.7880 (m110) REVERT: B 237 THR cc_start: 0.8836 (p) cc_final: 0.8557 (t) REVERT: B 276 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7985 (ttp-170) REVERT: B 282 ARG cc_start: 0.8445 (mtm180) cc_final: 0.8117 (ptm-80) REVERT: E 1 MET cc_start: 0.7441 (mpp) cc_final: 0.7216 (mpp) REVERT: E 147 SER cc_start: 0.8120 (p) cc_final: 0.7900 (p) REVERT: E 203 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8244 (mtt) REVERT: I 95 SER cc_start: 0.8218 (m) cc_final: 0.7944 (p) REVERT: S 97 GLU cc_start: 0.8444 (mp0) cc_final: 0.8053 (mp0) REVERT: S 238 ILE cc_start: 0.8073 (mt) cc_final: 0.7582 (tt) REVERT: S 302 MET cc_start: 0.8190 (mmm) cc_final: 0.7563 (mmm) REVERT: S 340 SER cc_start: 0.8854 (p) cc_final: 0.8463 (t) REVERT: S 401 LYS cc_start: 0.8867 (mtpp) cc_final: 0.8155 (mtmt) REVERT: S 434 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7934 (mt-10) outliers start: 63 outliers final: 54 residues processed: 518 average time/residue: 0.3408 time to fit residues: 278.1816 Evaluate side-chains 537 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 478 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 146 TYR Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain K residue 210 MET Chi-restraints excluded: chain K residue 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 28 ILE Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 182 SER Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 342 LEU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 352 LYS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 239 THR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 414 GLU Chi-restraints excluded: chain E residue 449 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 197 ASP Chi-restraints excluded: chain I residue 407 GLU Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain S residue 191 THR Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 271 THR Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Chi-restraints excluded: chain S residue 377 MET Chi-restraints excluded: chain S residue 381 THR Chi-restraints excluded: chain S residue 413 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 253 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 263 optimal weight: 2.9990 chunk 49 optimal weight: 0.0570 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.135322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.104145 restraints weight = 37788.967| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.25 r_work: 0.3332 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24284 Z= 0.135 Angle : 0.549 10.335 32964 Z= 0.275 Chirality : 0.044 0.284 3616 Planarity : 0.004 0.052 4287 Dihedral : 8.970 160.129 3613 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Rotamer: Outliers : 3.20 % Allowed : 17.96 % Favored : 78.84 % 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: 0.66 (0.16), residues: 2976 helix: 1.93 (0.15), residues: 1244 sheet: 0.47 (0.22), residues: 536 loop : -1.23 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 388 HIS 0.004 0.001 HIS E 88 PHE 0.017 0.001 PHE S 296 TYR 0.040 0.001 TYR S 24 ARG 0.007 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.03975 ( 1097) hydrogen bonds : angle 3.84961 ( 3351) covalent geometry : bond 0.00317 (24284) covalent geometry : angle 0.54948 (32964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15240.03 seconds wall clock time: 263 minutes 34.44 seconds (15814.44 seconds total)