Starting phenix.real_space_refine on Sun Aug 24 23:26:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utn_42543/08_2025/8utn_42543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utn_42543/08_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_42543/08_2025/8utn_42543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utn_42543/08_2025/8utn_42543.map" model { file = "/net/cci-nas-00/data/ceres_data/8utn_42543/08_2025/8utn_42543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utn_42543/08_2025/8utn_42543.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 7.38, per 1000 atoms: 0.31 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: 2.27 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.98 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: 4.90 Time building geometry restraints manager: 2.99 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 through 502)) selection = (chain 'I' and (resid 1 through 428 or resid 501 through 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: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.710 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- 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 : 5.09 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.015 0.001 ARG K 75 TYR 0.015 0.002 TYR K 74 PHE 0.034 0.002 PHE S 255 TRP 0.015 0.002 TRP K 57 HIS 0.013 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00598 (24284) covalent geometry : angle 0.89206 (32964) hydrogen bonds : bond 0.15633 ( 1097) hydrogen bonds : angle 5.99429 ( 3351) *********************** 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 : 1.813 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 288 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7783 (ptm) 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: 0.8090 (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: 0.0346 (p90) outliers start: 37 outliers final: 12 residues processed: 513 average time/residue: 0.1763 time to fit residues: 141.3535 Evaluate side-chains 489 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 472 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 288 MET 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN K 293 ASN N 98 GLN N 318 ASN A 256 GLN B 165 ASN B 335 ASN B 424 GLN B 426 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.137352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.105743 restraints weight = 31202.331| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.14 r_work: 0.3361 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 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 = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1220 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= 0.126 Angle : 0.593 11.707 32964 Z= 0.294 Chirality : 0.044 0.322 3616 Planarity : 0.004 0.055 4287 Dihedral : 12.843 155.228 3646 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.40 % Favored : 96.36 % Rotamer: Outliers : 2.81 % Allowed : 14.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.15), residues: 2976 helix: 1.54 (0.15), residues: 1247 sheet: 0.17 (0.22), residues: 540 loop : -1.25 (0.17), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.015 0.001 TYR K 74 PHE 0.018 0.001 PHE E 255 TRP 0.015 0.001 TRP E 388 HIS 0.005 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00274 (24284) covalent geometry : angle 0.59260 (32964) hydrogen bonds : bond 0.04472 ( 1097) hydrogen bonds : angle 4.21215 ( 3351) *********************** 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 554 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 487 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: K 19 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7126 (mp0) REVERT: K 60 THR cc_start: 0.6455 (p) cc_final: 0.6130 (p) REVERT: K 98 GLN cc_start: 0.8595 (pt0) cc_final: 0.8330 (pt0) REVERT: K 340 GLU cc_start: 0.7821 (mp0) cc_final: 0.7317 (mp0) REVERT: N 82 LEU cc_start: 0.6001 (OUTLIER) cc_final: 0.5602 (mm) REVERT: N 107 MET cc_start: 0.7691 (mmm) cc_final: 0.6905 (tpp) REVERT: N 274 SER cc_start: 0.8754 (t) cc_final: 0.8247 (p) REVERT: A 119 LEU cc_start: 0.8313 (mp) cc_final: 0.7906 (mt) REVERT: A 254 GLU cc_start: 0.4468 (mm-30) cc_final: 0.3097 (pt0) REVERT: A 256 GLN cc_start: 0.8034 (mt0) cc_final: 0.7645 (mt0) REVERT: B 195 ASN cc_start: 0.8405 (m-40) cc_final: 0.8088 (m-40) REVERT: B 213 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8169 (mtm180) REVERT: B 226 ASN cc_start: 0.8078 (m-40) cc_final: 0.7836 (m-40) REVERT: B 426 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: E 449 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.4396 (pp20) REVERT: S 24 TYR cc_start: 0.8460 (m-80) cc_final: 0.7959 (m-80) REVERT: S 108 TYR cc_start: 0.8557 (m-80) cc_final: 0.7969 (m-10) REVERT: S 129 CYS cc_start: 0.8006 (m) cc_final: 0.7695 (m) REVERT: S 401 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8287 (mtmt) outliers start: 67 outliers final: 32 residues processed: 520 average time/residue: 0.1684 time to fit residues: 137.9758 Evaluate side-chains 490 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 455 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 261 LYS Chi-restraints excluded: chain N residue 283 SER Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain A residue 305 CYS 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 66 VAL Chi-restraints excluded: chain E residue 417 GLU Chi-restraints excluded: chain E residue 449 GLU 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 240 optimal weight: 0.0870 chunk 282 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 142 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 200 optimal weight: 0.3980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 A 128 GLN B 204 ASN B 279 GLN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 GLN S 15 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.138761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106778 restraints weight = 34652.679| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.26 r_work: 0.3367 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24284 Z= 0.118 Angle : 0.545 7.683 32964 Z= 0.272 Chirality : 0.044 0.460 3616 Planarity : 0.004 0.059 4287 Dihedral : 9.844 153.558 3616 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.10 % Favored : 96.66 % Rotamer: Outliers : 2.77 % Allowed : 15.31 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.16), residues: 2976 helix: 1.80 (0.15), residues: 1243 sheet: 0.34 (0.22), residues: 543 loop : -1.14 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 390 TYR 0.017 0.001 TYR K 74 PHE 0.017 0.001 PHE S 296 TRP 0.015 0.001 TRP S 388 HIS 0.004 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00260 (24284) covalent geometry : angle 0.54479 (32964) hydrogen bonds : bond 0.04000 ( 1097) hydrogen bonds : angle 3.94825 ( 3351) *********************** 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 538 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 473 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: K 60 THR cc_start: 0.6537 (p) cc_final: 0.6209 (p) REVERT: K 340 GLU cc_start: 0.7856 (mp0) cc_final: 0.7129 (mp0) REVERT: N 13 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7436 (ppt170) REVERT: N 82 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5603 (mm) REVERT: N 98 GLN cc_start: 0.7318 (mp10) cc_final: 0.6960 (mp10) REVERT: N 107 MET cc_start: 0.7679 (mmm) cc_final: 0.6898 (tpp) REVERT: N 274 SER cc_start: 0.8737 (t) cc_final: 0.8192 (p) REVERT: A 254 GLU cc_start: 0.4519 (mm-30) cc_final: 0.2942 (pt0) REVERT: A 256 GLN cc_start: 0.7947 (mt0) cc_final: 0.7641 (mt0) REVERT: B 195 ASN cc_start: 0.8396 (m-40) cc_final: 0.8097 (m-40) REVERT: B 213 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8211 (mtm180) REVERT: B 226 ASN cc_start: 0.8126 (m-40) cc_final: 0.7784 (m110) REVERT: B 335 ASN cc_start: 0.8365 (m110) cc_final: 0.8139 (m-40) REVERT: E 203 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8105 (mtt) REVERT: I 1 MET cc_start: 0.6955 (mmp) cc_final: 0.6564 (mmp) REVERT: I 26 ASP cc_start: 0.8181 (t70) cc_final: 0.7812 (t0) REVERT: I 213 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7969 (mtp180) REVERT: I 297 LYS cc_start: 0.8783 (pttm) cc_final: 0.8458 (mmtm) REVERT: S 108 TYR cc_start: 0.8529 (m-80) cc_final: 0.7926 (m-10) REVERT: S 129 CYS cc_start: 0.7906 (m) cc_final: 0.7613 (m) REVERT: S 275 VAL cc_start: 0.8236 (t) cc_final: 0.8021 (p) REVERT: S 401 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8285 (mtmt) outliers start: 65 outliers final: 48 residues processed: 506 average time/residue: 0.1712 time to fit residues: 135.7954 Evaluate side-chains 500 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 449 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 270 ASN 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 283 SER Chi-restraints excluded: chain N residue 297 LYS Chi-restraints excluded: chain A residue 92 LEU 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 161 ASP 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 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 72 THR Chi-restraints excluded: chain I residue 176 SER 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 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 287 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 213 optimal weight: 0.0970 chunk 279 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 136 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 E 15 GLN S 197 HIS S 301 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 = 0.136234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.104052 restraints weight = 35360.874| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.28 r_work: 0.3320 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24284 Z= 0.177 Angle : 0.564 8.948 32964 Z= 0.284 Chirality : 0.045 0.341 3616 Planarity : 0.004 0.063 4287 Dihedral : 9.547 154.153 3613 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.57 % Favored : 96.26 % Rotamer: Outliers : 3.20 % Allowed : 15.23 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.16), residues: 2976 helix: 1.86 (0.15), residues: 1234 sheet: 0.43 (0.22), residues: 539 loop : -1.23 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.034 0.001 TYR S 24 PHE 0.015 0.002 PHE E 67 TRP 0.013 0.002 TRP I 344 HIS 0.007 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00425 (24284) covalent geometry : angle 0.56357 (32964) hydrogen bonds : bond 0.04489 ( 1097) hydrogen bonds : angle 3.96029 ( 3351) *********************** 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 551 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 475 time to evaluate : 0.950 Fit side-chains REVERT: K 30 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7495 (mtt) REVERT: K 60 THR cc_start: 0.6627 (p) cc_final: 0.6309 (p) REVERT: K 98 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: K 197 ASP cc_start: 0.7490 (m-30) cc_final: 0.7290 (m-30) REVERT: K 340 GLU cc_start: 0.7813 (mp0) cc_final: 0.7415 (mp0) REVERT: N 13 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.6959 (ppt170) REVERT: N 82 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5788 (mt) REVERT: N 107 MET cc_start: 0.7716 (mmm) cc_final: 0.6888 (tpp) REVERT: N 274 SER cc_start: 0.8772 (t) cc_final: 0.8244 (p) REVERT: A 191 THR cc_start: 0.8368 (m) cc_final: 0.8028 (p) REVERT: A 254 GLU cc_start: 0.4552 (mm-30) cc_final: 0.3561 (tp30) REVERT: A 256 GLN cc_start: 0.8005 (mt0) cc_final: 0.7723 (mt0) REVERT: A 275 VAL cc_start: 0.8759 (t) cc_final: 0.8546 (p) REVERT: B 75 SER cc_start: 0.8722 (t) cc_final: 0.8449 (t) REVERT: B 213 ARG cc_start: 0.8568 (ttp80) cc_final: 0.8261 (mtm180) REVERT: B 226 ASN cc_start: 0.8206 (m-40) cc_final: 0.7891 (m110) REVERT: B 426 GLN cc_start: 0.8509 (tm-30) cc_final: 0.7987 (tm-30) REVERT: E 203 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: E 449 GLU cc_start: 0.4744 (OUTLIER) cc_final: 0.4444 (pp20) REVERT: I 1 MET cc_start: 0.7001 (mmp) cc_final: 0.6645 (mmp) REVERT: I 26 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7886 (t0) REVERT: S 108 TYR cc_start: 0.8554 (m-80) cc_final: 0.7854 (m-10) REVERT: S 129 CYS cc_start: 0.7912 (m) cc_final: 0.7652 (m) REVERT: S 302 MET cc_start: 0.8251 (mmm) cc_final: 0.7858 (mmm) REVERT: S 401 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8255 (mtmt) outliers start: 76 outliers final: 58 residues processed: 509 average time/residue: 0.1718 time to fit residues: 138.8398 Evaluate side-chains 512 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 447 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 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 342 LEU 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 337 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 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 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 271 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 45 optimal weight: 8.9990 chunk 259 optimal weight: 0.2980 chunk 260 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 240 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 200 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 265 optimal weight: 0.3980 chunk 195 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 165 ASN B 195 ASN I 57 ASN I 131 GLN I 416 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.136973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.105337 restraints weight = 35412.677| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.18 r_work: 0.3368 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24284 Z= 0.109 Angle : 0.516 7.879 32964 Z= 0.260 Chirality : 0.043 0.288 3616 Planarity : 0.004 0.060 4287 Dihedral : 9.206 155.791 3609 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.07 % Favored : 96.80 % Rotamer: Outliers : 2.81 % Allowed : 16.20 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.16), residues: 2976 helix: 1.99 (0.15), residues: 1239 sheet: 0.50 (0.22), residues: 540 loop : -1.15 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 129 TYR 0.042 0.001 TYR S 24 PHE 0.013 0.001 PHE K 221 TRP 0.011 0.001 TRP I 344 HIS 0.004 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00242 (24284) covalent geometry : angle 0.51630 (32964) hydrogen bonds : bond 0.03706 ( 1097) hydrogen bonds : angle 3.82171 ( 3351) *********************** 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 538 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 472 time to evaluate : 0.919 Fit side-chains REVERT: K 60 THR cc_start: 0.6641 (p) cc_final: 0.6309 (p) REVERT: K 98 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: K 197 ASP cc_start: 0.7456 (m-30) cc_final: 0.7241 (m-30) REVERT: K 277 THR cc_start: 0.8419 (m) cc_final: 0.8189 (m) REVERT: K 301 THR cc_start: 0.3524 (OUTLIER) cc_final: 0.3188 (p) REVERT: K 340 GLU cc_start: 0.7838 (mp0) cc_final: 0.7363 (mp0) REVERT: N 13 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7343 (ppt170) REVERT: N 82 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5605 (mm) REVERT: N 107 MET cc_start: 0.7678 (mmm) cc_final: 0.6906 (tpp) REVERT: N 226 THR cc_start: 0.6751 (m) cc_final: 0.6503 (p) REVERT: N 274 SER cc_start: 0.8755 (t) cc_final: 0.8209 (p) REVERT: A 191 THR cc_start: 0.8319 (m) cc_final: 0.7987 (p) REVERT: A 245 ASP cc_start: 0.7844 (m-30) cc_final: 0.7643 (m-30) REVERT: A 254 GLU cc_start: 0.4563 (mm-30) cc_final: 0.3653 (tp30) REVERT: A 256 GLN cc_start: 0.7947 (mt0) cc_final: 0.7576 (mt0) REVERT: A 275 VAL cc_start: 0.8707 (t) cc_final: 0.8485 (p) REVERT: B 75 SER cc_start: 0.8656 (t) cc_final: 0.8376 (t) REVERT: B 195 ASN cc_start: 0.8356 (m-40) cc_final: 0.8073 (m-40) REVERT: B 213 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8153 (mtm180) REVERT: B 226 ASN cc_start: 0.8152 (m-40) cc_final: 0.7818 (m110) REVERT: B 426 GLN cc_start: 0.8474 (tm-30) cc_final: 0.7994 (tm-30) REVERT: E 449 GLU cc_start: 0.4707 (OUTLIER) cc_final: 0.4432 (pp20) REVERT: I 1 MET cc_start: 0.6828 (mmp) cc_final: 0.6478 (mmp) REVERT: S 24 TYR cc_start: 0.8307 (m-80) cc_final: 0.8041 (m-80) REVERT: S 108 TYR cc_start: 0.8524 (m-80) cc_final: 0.7737 (m-10) REVERT: S 129 CYS cc_start: 0.7859 (m) cc_final: 0.7532 (m) REVERT: S 302 MET cc_start: 0.8179 (mmm) cc_final: 0.7814 (mmm) REVERT: S 401 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8171 (mtmt) outliers start: 66 outliers final: 48 residues processed: 506 average time/residue: 0.1700 time to fit residues: 136.4825 Evaluate side-chains 504 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 451 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 301 THR 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 196 MET 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 A residue 92 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU 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 66 VAL Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 191 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 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 68 VAL Chi-restraints excluded: chain S residue 80 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 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 167 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 62 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN N 200 ASN I 204 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 = 0.3976 r_free = 0.3976 target = 0.133747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.101374 restraints weight = 41889.683| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.48 r_work: 0.3285 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3113 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3113 r_free = 0.3113 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24284 Z= 0.195 Angle : 0.572 9.126 32964 Z= 0.289 Chirality : 0.045 0.266 3616 Planarity : 0.005 0.059 4287 Dihedral : 9.309 154.756 3609 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 3.24 % Allowed : 16.01 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.16), residues: 2976 helix: 1.94 (0.15), residues: 1235 sheet: 0.51 (0.22), residues: 535 loop : -1.25 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.031 0.002 TYR S 24 PHE 0.018 0.002 PHE E 67 TRP 0.013 0.002 TRP I 344 HIS 0.008 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00473 (24284) covalent geometry : angle 0.57231 (32964) hydrogen bonds : bond 0.04616 ( 1097) hydrogen bonds : angle 3.90308 ( 3351) *********************** 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 540 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 463 time to evaluate : 0.972 Fit side-chains REVERT: K 60 THR cc_start: 0.6716 (p) cc_final: 0.6403 (p) REVERT: K 98 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: K 146 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.6944 (t80) REVERT: K 197 ASP cc_start: 0.7551 (m-30) cc_final: 0.7341 (m-30) REVERT: K 301 THR cc_start: 0.3515 (OUTLIER) cc_final: 0.3176 (p) REVERT: K 340 GLU cc_start: 0.7875 (mp0) cc_final: 0.7320 (mp0) REVERT: N 71 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7310 (mmtp) REVERT: N 82 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5822 (mt) REVERT: N 107 MET cc_start: 0.7703 (mmm) cc_final: 0.6914 (tpp) REVERT: N 270 ASN cc_start: 0.8413 (m-40) cc_final: 0.8209 (m-40) REVERT: N 274 SER cc_start: 0.8842 (t) cc_final: 0.8320 (p) REVERT: N 276 THR cc_start: 0.8314 (m) cc_final: 0.7380 (p) REVERT: A 3 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: A 191 THR cc_start: 0.8352 (m) cc_final: 0.8073 (p) REVERT: A 254 GLU cc_start: 0.4744 (mm-30) cc_final: 0.3813 (tp30) REVERT: A 334 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8178 (t) REVERT: B 75 SER cc_start: 0.8646 (t) cc_final: 0.8394 (t) REVERT: B 226 ASN cc_start: 0.8255 (m-40) cc_final: 0.7948 (m110) REVERT: B 426 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8013 (tm-30) REVERT: E 147 SER cc_start: 0.8151 (p) cc_final: 0.7934 (p) REVERT: E 203 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8362 (mtt) REVERT: E 449 GLU cc_start: 0.4723 (OUTLIER) cc_final: 0.4439 (pp20) REVERT: I 1 MET cc_start: 0.7022 (mmp) cc_final: 0.6661 (mmp) REVERT: I 26 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8123 (t0) REVERT: I 73 MET cc_start: 0.8721 (mmp) cc_final: 0.8461 (mmm) REVERT: S 24 TYR cc_start: 0.8354 (m-80) cc_final: 0.8140 (m-80) REVERT: S 108 TYR cc_start: 0.8550 (m-80) cc_final: 0.7691 (m-10) REVERT: S 302 MET cc_start: 0.8392 (mmm) cc_final: 0.8046 (mmm) REVERT: S 401 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8226 (mtmt) REVERT: S 434 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8063 (mt-10) outliers start: 77 outliers final: 57 residues processed: 500 average time/residue: 0.1695 time to fit residues: 134.7143 Evaluate side-chains 522 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 456 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 92 CYS 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 204 THR 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 38 VAL 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 A residue 3 GLU Chi-restraints excluded: chain A residue 92 LEU 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 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 161 ASP 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 130 THR Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 MET 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 170 MET 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 68 VAL Chi-restraints excluded: chain S residue 80 THR 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 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 413 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 32 optimal weight: 9.9990 chunk 231 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 260 optimal weight: 0.1980 chunk 175 optimal weight: 0.6980 chunk 233 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 242 optimal weight: 0.1980 chunk 67 optimal weight: 20.0000 chunk 163 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN K 322 ASN B 195 ASN I 396 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.137308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.104751 restraints weight = 41546.489| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.51 r_work: 0.3338 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24284 Z= 0.104 Angle : 0.509 7.437 32964 Z= 0.257 Chirality : 0.043 0.260 3616 Planarity : 0.004 0.056 4287 Dihedral : 9.012 156.896 3609 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.03 % Favored : 96.87 % Rotamer: Outliers : 2.89 % Allowed : 16.79 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2976 helix: 2.10 (0.15), residues: 1237 sheet: 0.54 (0.22), residues: 539 loop : -1.14 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 129 TYR 0.030 0.001 TYR S 24 PHE 0.012 0.001 PHE E 255 TRP 0.011 0.001 TRP E 21 HIS 0.003 0.001 HIS I 137 Details of bonding type rmsd covalent geometry : bond 0.00226 (24284) covalent geometry : angle 0.50917 (32964) hydrogen bonds : bond 0.03556 ( 1097) hydrogen bonds : angle 3.74795 ( 3351) *********************** 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 530 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 462 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 22 ARG cc_start: 0.6564 (ttm170) cc_final: 0.6297 (ttm-80) REVERT: K 60 THR cc_start: 0.6702 (p) cc_final: 0.6434 (p) REVERT: K 98 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: K 146 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.6975 (t80) REVERT: K 301 THR cc_start: 0.3507 (OUTLIER) cc_final: 0.3150 (p) REVERT: K 340 GLU cc_start: 0.7854 (mp0) cc_final: 0.7361 (mp0) REVERT: N 71 LYS cc_start: 0.7508 (mmtt) cc_final: 0.7296 (mmtm) REVERT: N 82 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5677 (mm) REVERT: N 107 MET cc_start: 0.7681 (mmm) cc_final: 0.7416 (mmm) REVERT: N 270 ASN cc_start: 0.8360 (m-40) cc_final: 0.8150 (m-40) REVERT: N 274 SER cc_start: 0.8791 (t) cc_final: 0.8250 (p) REVERT: A 191 THR cc_start: 0.8336 (m) cc_final: 0.8063 (p) REVERT: A 254 GLU cc_start: 0.4757 (mm-30) cc_final: 0.3933 (tp30) REVERT: A 256 GLN cc_start: 0.7891 (mt0) cc_final: 0.7661 (mt0) REVERT: B 75 SER cc_start: 0.8622 (t) cc_final: 0.8351 (t) REVERT: B 195 ASN cc_start: 0.8387 (m-40) cc_final: 0.8116 (m-40) REVERT: B 213 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8175 (mtm180) REVERT: B 219 THR cc_start: 0.8953 (m) cc_final: 0.8668 (p) REVERT: B 226 ASN cc_start: 0.8202 (m-40) cc_final: 0.7875 (m110) REVERT: B 426 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8055 (tm-30) REVERT: E 203 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8135 (mtt) REVERT: E 449 GLU cc_start: 0.4656 (OUTLIER) cc_final: 0.4385 (pp20) REVERT: I 1 MET cc_start: 0.6969 (mmp) cc_final: 0.6620 (mmp) REVERT: S 108 TYR cc_start: 0.8540 (m-80) cc_final: 0.7733 (m-10) REVERT: S 302 MET cc_start: 0.8245 (mmm) cc_final: 0.7913 (mmm) REVERT: S 401 LYS cc_start: 0.8861 (mtpp) cc_final: 0.8168 (mtmt) outliers start: 68 outliers final: 48 residues processed: 500 average time/residue: 0.1723 time to fit residues: 136.5839 Evaluate side-chains 504 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 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 301 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 134 THR 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 A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 147 MET 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 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 271 THR Chi-restraints excluded: chain E residue 286 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 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 242 LEU Chi-restraints excluded: chain S residue 303 VAL Chi-restraints excluded: chain S residue 362 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 4.9990 chunk 170 optimal weight: 0.0060 chunk 200 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 288 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN A 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.135105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.102025 restraints weight = 53000.992| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.02 r_work: 0.3265 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24284 Z= 0.154 Angle : 0.544 8.037 32964 Z= 0.275 Chirality : 0.044 0.241 3616 Planarity : 0.004 0.053 4287 Dihedral : 9.032 156.888 3609 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 2.89 % Allowed : 17.22 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.16), residues: 2976 helix: 2.08 (0.15), residues: 1236 sheet: 0.53 (0.22), residues: 538 loop : -1.16 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 320 TYR 0.045 0.001 TYR S 24 PHE 0.014 0.002 PHE E 67 TRP 0.012 0.001 TRP I 344 HIS 0.006 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00367 (24284) covalent geometry : angle 0.54354 (32964) hydrogen bonds : bond 0.04116 ( 1097) hydrogen bonds : angle 3.80698 ( 3351) *********************** 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 544 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 476 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: K 22 ARG cc_start: 0.6629 (ttm170) cc_final: 0.6360 (ttm-80) REVERT: K 60 THR cc_start: 0.6817 (p) cc_final: 0.6540 (p) REVERT: K 146 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.6881 (t80) REVERT: K 301 THR cc_start: 0.3335 (OUTLIER) cc_final: 0.2971 (p) REVERT: K 340 GLU cc_start: 0.7799 (mp0) cc_final: 0.7257 (mp0) REVERT: N 107 MET cc_start: 0.7616 (mmm) cc_final: 0.7341 (mmm) REVERT: N 274 SER cc_start: 0.8711 (t) cc_final: 0.8156 (p) REVERT: N 276 THR cc_start: 0.8152 (m) cc_final: 0.7235 (p) REVERT: A 191 THR cc_start: 0.8290 (m) cc_final: 0.8044 (p) REVERT: A 254 GLU cc_start: 0.4676 (mm-30) cc_final: 0.3815 (tp30) REVERT: A 256 GLN cc_start: 0.7864 (mt0) cc_final: 0.7651 (mt0) REVERT: A 433 GLU cc_start: 0.7962 (tt0) cc_final: 0.7546 (tt0) REVERT: B 75 SER cc_start: 0.8547 (t) cc_final: 0.8268 (t) REVERT: B 195 ASN cc_start: 0.8339 (m-40) cc_final: 0.8043 (m-40) REVERT: B 218 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8369 (m) REVERT: B 219 THR cc_start: 0.8928 (m) cc_final: 0.8626 (p) REVERT: B 226 ASN cc_start: 0.8097 (m-40) cc_final: 0.7778 (m110) REVERT: B 426 GLN cc_start: 0.8439 (tm-30) cc_final: 0.7975 (tm-30) REVERT: E 1 MET cc_start: 0.7319 (mpp) cc_final: 0.6919 (mpp) REVERT: E 147 SER cc_start: 0.7980 (p) cc_final: 0.7745 (p) REVERT: E 203 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8102 (mtt) REVERT: E 449 GLU cc_start: 0.4715 (OUTLIER) cc_final: 0.4370 (pp20) REVERT: I 1 MET cc_start: 0.6612 (mmp) cc_final: 0.6271 (mmp) REVERT: I 26 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (t0) REVERT: S 24 TYR cc_start: 0.8134 (m-80) cc_final: 0.7884 (m-80) REVERT: S 97 GLU cc_start: 0.8484 (mp0) cc_final: 0.7544 (mt-10) REVERT: S 302 MET cc_start: 0.8236 (mmm) cc_final: 0.7874 (mmm) REVERT: S 340 SER cc_start: 0.8815 (p) cc_final: 0.8402 (t) REVERT: S 401 LYS cc_start: 0.8863 (mtpp) cc_final: 0.8162 (mtmt) REVERT: S 414 GLU cc_start: 0.6713 (pt0) cc_final: 0.6461 (mt-10) REVERT: S 434 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7810 (mt-10) outliers start: 68 outliers final: 56 residues processed: 513 average time/residue: 0.1692 time to fit residues: 137.6681 Evaluate side-chains 526 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 464 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 234 THR Chi-restraints excluded: chain K residue 236 ILE Chi-restraints excluded: chain K residue 253 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 134 THR 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 A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 305 CYS 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 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 93 ILE 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 271 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 335 ILE 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 170 MET Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain I residue 197 ASP 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 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 219 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 240 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 223 optimal weight: 0.2980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN A 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.136200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104153 restraints weight = 39608.047| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.34 r_work: 0.3335 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2435 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= 0.127 Angle : 0.529 7.631 32964 Z= 0.267 Chirality : 0.043 0.233 3616 Planarity : 0.004 0.052 4287 Dihedral : 8.934 157.454 3609 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 3.01 % Allowed : 17.26 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.16), residues: 2976 helix: 2.09 (0.15), residues: 1238 sheet: 0.56 (0.22), residues: 536 loop : -1.14 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 129 TYR 0.033 0.001 TYR S 24 PHE 0.012 0.001 PHE K 221 TRP 0.015 0.001 TRP S 388 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00295 (24284) covalent geometry : angle 0.52927 (32964) hydrogen bonds : bond 0.03851 ( 1097) hydrogen bonds : angle 3.76825 ( 3351) *********************** 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 549 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 478 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 22 ARG cc_start: 0.6570 (ttm170) cc_final: 0.6303 (ttm-80) REVERT: K 60 THR cc_start: 0.6811 (p) cc_final: 0.6531 (p) REVERT: K 146 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6891 (t80) REVERT: K 301 THR cc_start: 0.3138 (OUTLIER) cc_final: 0.2791 (p) REVERT: N 107 MET cc_start: 0.7671 (mmm) cc_final: 0.6866 (tpp) REVERT: N 146 TYR cc_start: 0.7780 (t80) cc_final: 0.7373 (t80) REVERT: N 274 SER cc_start: 0.8799 (t) cc_final: 0.8265 (p) REVERT: N 276 THR cc_start: 0.8283 (m) cc_final: 0.7242 (p) REVERT: N 345 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8150 (mp) REVERT: A 191 THR cc_start: 0.8340 (m) cc_final: 0.8110 (p) REVERT: A 254 GLU cc_start: 0.4724 (mm-30) cc_final: 0.3893 (tp30) REVERT: A 256 GLN cc_start: 0.7884 (mt0) cc_final: 0.7641 (mt0) REVERT: A 433 GLU cc_start: 0.8068 (tt0) cc_final: 0.7649 (tt0) REVERT: B 75 SER cc_start: 0.8571 (t) cc_final: 0.8307 (t) REVERT: B 195 ASN cc_start: 0.8400 (m-40) cc_final: 0.8123 (m-40) REVERT: B 213 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8159 (mtm180) REVERT: B 218 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8390 (m) REVERT: B 219 THR cc_start: 0.8964 (m) cc_final: 0.8715 (p) REVERT: B 226 ASN cc_start: 0.8193 (m-40) cc_final: 0.7880 (m110) REVERT: B 426 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8027 (tm-30) REVERT: E 1 MET cc_start: 0.7534 (mpp) cc_final: 0.7145 (mpp) REVERT: E 147 SER cc_start: 0.8048 (p) cc_final: 0.7818 (p) REVERT: E 203 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8178 (mtt) REVERT: E 449 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.4395 (pp20) REVERT: I 1 MET cc_start: 0.6897 (mmp) cc_final: 0.6570 (mmp) REVERT: I 26 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8211 (t0) REVERT: I 95 SER cc_start: 0.8223 (m) cc_final: 0.7981 (p) REVERT: S 24 TYR cc_start: 0.8080 (m-80) cc_final: 0.7880 (m-80) REVERT: S 52 PHE cc_start: 0.7769 (m-80) cc_final: 0.7394 (m-10) REVERT: S 97 GLU cc_start: 0.8506 (mp0) cc_final: 0.7581 (mt-10) REVERT: S 121 ARG cc_start: 0.7662 (mmm-85) cc_final: 0.7459 (mmm160) REVERT: S 302 MET cc_start: 0.8274 (mmm) cc_final: 0.7935 (mmm) REVERT: S 340 SER cc_start: 0.8830 (p) cc_final: 0.8441 (t) REVERT: S 401 LYS cc_start: 0.8864 (mtpp) cc_final: 0.8167 (mtmt) REVERT: S 414 GLU cc_start: 0.6758 (pt0) cc_final: 0.6462 (mt-10) REVERT: S 434 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7920 (mt-10) outliers start: 71 outliers final: 57 residues processed: 515 average time/residue: 0.1636 time to fit residues: 133.8354 Evaluate side-chains 536 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 472 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 204 THR 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 301 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 134 THR 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 A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE 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 147 MET 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 93 ILE 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 271 THR Chi-restraints excluded: chain E residue 286 LEU 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 26 ASP 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 236 VAL 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 303 VAL Chi-restraints excluded: chain S residue 362 VAL Chi-restraints excluded: chain S residue 371 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 155 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 241 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.135940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103699 restraints weight = 43733.824| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.55 r_work: 0.3311 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24284 Z= 0.129 Angle : 0.541 9.896 32964 Z= 0.271 Chirality : 0.043 0.230 3616 Planarity : 0.004 0.051 4287 Dihedral : 8.888 158.229 3609 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 2.85 % Allowed : 18.00 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.16), residues: 2976 helix: 2.08 (0.15), residues: 1239 sheet: 0.59 (0.22), residues: 534 loop : -1.11 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 320 TYR 0.030 0.001 TYR S 24 PHE 0.012 0.001 PHE K 221 TRP 0.016 0.001 TRP I 344 HIS 0.004 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00299 (24284) covalent geometry : angle 0.54070 (32964) hydrogen bonds : bond 0.03894 ( 1097) hydrogen bonds : angle 3.76312 ( 3351) ********************** 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 532 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 465 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: K 22 ARG cc_start: 0.6608 (ttm170) cc_final: 0.6350 (ttm-80) REVERT: K 146 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.6994 (t80) REVERT: N 107 MET cc_start: 0.7599 (mmm) cc_final: 0.6858 (tpp) REVERT: N 138 MET cc_start: 0.7271 (tpp) cc_final: 0.6939 (mmm) REVERT: N 270 ASN cc_start: 0.8240 (m-40) cc_final: 0.8015 (m-40) REVERT: N 274 SER cc_start: 0.8686 (t) cc_final: 0.8132 (p) REVERT: N 276 THR cc_start: 0.8133 (m) cc_final: 0.7209 (p) REVERT: N 345 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8101 (mp) REVERT: A 191 THR cc_start: 0.8274 (m) cc_final: 0.8070 (p) REVERT: A 254 GLU cc_start: 0.4637 (mm-30) cc_final: 0.3857 (tp30) REVERT: A 433 GLU cc_start: 0.7927 (tt0) cc_final: 0.7498 (tt0) REVERT: B 75 SER cc_start: 0.8509 (t) cc_final: 0.8242 (t) REVERT: B 195 ASN cc_start: 0.8264 (m-40) cc_final: 0.7985 (m-40) REVERT: B 213 ARG cc_start: 0.8412 (ttp80) cc_final: 0.8088 (mtm180) REVERT: B 218 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8401 (m) REVERT: B 219 THR cc_start: 0.8927 (m) cc_final: 0.8695 (p) REVERT: B 226 ASN cc_start: 0.8048 (m-40) cc_final: 0.7722 (m110) REVERT: B 426 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7940 (tm-30) REVERT: E 1 MET cc_start: 0.7224 (mpp) cc_final: 0.6875 (mpp) REVERT: E 147 SER cc_start: 0.7930 (p) cc_final: 0.7684 (p) REVERT: E 203 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: E 449 GLU cc_start: 0.4547 (OUTLIER) cc_final: 0.4331 (pp20) REVERT: I 95 SER cc_start: 0.8120 (m) cc_final: 0.7865 (p) REVERT: I 213 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7764 (mtp180) REVERT: S 24 TYR cc_start: 0.8033 (m-80) cc_final: 0.7816 (m-80) REVERT: S 52 PHE cc_start: 0.7543 (m-80) cc_final: 0.7071 (m-10) REVERT: S 97 GLU cc_start: 0.8440 (mp0) cc_final: 0.7570 (mt-10) REVERT: S 302 MET cc_start: 0.8197 (mmm) cc_final: 0.7831 (mmm) REVERT: S 340 SER cc_start: 0.8802 (p) cc_final: 0.8425 (t) REVERT: S 371 VAL cc_start: 0.8976 (t) cc_final: 0.8772 (m) REVERT: S 401 LYS cc_start: 0.8847 (mtpp) cc_final: 0.8146 (mtmt) REVERT: S 414 GLU cc_start: 0.6669 (pt0) cc_final: 0.6364 (mt-10) REVERT: S 434 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7808 (mt-10) outliers start: 67 outliers final: 57 residues processed: 502 average time/residue: 0.1689 time to fit residues: 134.2578 Evaluate side-chains 523 residues out of total 2547 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 461 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 118 ILE 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 253 GLU Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 38 VAL Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 134 THR 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 A residue 56 THR Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain B residue 147 MET 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 56 THR Chi-restraints excluded: chain E residue 93 ILE 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 271 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 335 ILE 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 236 VAL 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 303 VAL Chi-restraints excluded: chain S residue 362 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 164 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 0.0000 chunk 158 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.135496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.104390 restraints weight = 33384.882| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.18 r_work: 0.3343 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24284 Z= 0.138 Angle : 0.548 9.265 32964 Z= 0.274 Chirality : 0.044 0.232 3616 Planarity : 0.004 0.050 4287 Dihedral : 8.881 158.038 3609 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.33 % Rotamer: Outliers : 3.08 % Allowed : 17.61 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.16), residues: 2976 helix: 2.10 (0.15), residues: 1236 sheet: 0.59 (0.22), residues: 534 loop : -1.12 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 320 TYR 0.030 0.001 TYR S 24 PHE 0.012 0.001 PHE E 255 TRP 0.016 0.001 TRP S 388 HIS 0.005 0.001 HIS E 88 Details of bonding type rmsd covalent geometry : bond 0.00327 (24284) covalent geometry : angle 0.54848 (32964) hydrogen bonds : bond 0.03946 ( 1097) hydrogen bonds : angle 3.75931 ( 3351) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7849.55 seconds wall clock time: 134 minutes 51.05 seconds (8091.05 seconds total)